Mercurial > repos > eschen42 > mqppep_preproc
annotate mqppep_anova_script.Rmd @ 27:29775869faba draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
| author | eschen42 |
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| date | Wed, 26 Oct 2022 23:48:07 +0000 |
| parents | bac8e9515863 |
| children | 87794cf65bc0 |
| rev | line source |
|---|---|
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1 --- |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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2 title: "MaxQuant Phosphoproteomic Enrichment Pipeline ANOVA/KSEA" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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3 author: |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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4 - "Nick Graham^[ORCiD 0000-0002-6811-1941, University of Southern California: Los Angeles, CA, US]" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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5 - "Larry Cheng^[ORCiD 0000-0002-6922-6433, Rutgers School of Graduate Studies: New Brunswick, NJ, US]" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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6 - "Art Eschenlauer^[ORCiD 0000-0002-2882-0508, University of Minnesota: Minneapolis, Minnesota, US]" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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7 date: |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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8 - "May 28, 2018" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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9 - "; revised June 23, 2022" |
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27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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10 lot: true |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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11 output: |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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12 pdf_document: |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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13 toc: true |
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27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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14 toc_depth: 2 |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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15 keep_tex: true |
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27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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16 dev: pdf |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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17 includes: |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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18 in_header: mqppep_anova_preamble.tex |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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19 latex_macros: false |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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20 raw_tex: true |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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21 urlcolor: blue |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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22 params: |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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23 alphaFile: "test-data/alpha_levels.tabular" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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24 inputFile: "test-data/test_input_for_anova.tabular" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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25 preprocDb: "test-data/test_input_for_anova.sqlite" |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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26 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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27 regexSampleNames: "\\.\\d+[A-Z]$" |
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a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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28 regexSampleGrouping: "\\d+" |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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29 groupFilterPatterns: ".+" |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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30 groupFilter: !r c("none", "exclude", "include")[1] |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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31 imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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32 kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5] |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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33 #imputationMethod: !r c("group-median", "median", "mean", "random")[1] |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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34 |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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35 # how should sample groups be interpreted? |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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36 # - "f": fixed patterns (like `grep -F`) |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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37 # - "p": PERL-compatible (like `grep -P`) |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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38 # - "r": extended grep patterns (like `grep -E`) |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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39 # use what case sensitivity? |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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40 # - "i": case insensitive matching (like `grep -i`) |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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41 groupFilterMode: !r c("r", "ri", "p", "pi", "f", "fi")[1] |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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42 # what pattern should be used for the first column |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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43 # (extended grep pattern, case sensitive) |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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44 firstDataColumn: "^Intensity[^_]" |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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45 # for small random value imputation, what percentile should be center? |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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46 meanPercentile: 50 |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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47 #meanPercentile: 1 |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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48 # for small random value imputation, what should `s / mean(x)` ratio be? |
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657663e89728
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49 sdPercentile: 1.0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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50 # output path for imputed data file |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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51 imputedDataFilename: "test-data/limbo/imputedDataFilename.txt" |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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52 # output path for imputed/quantile-normalized/log-transformed data file |
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657663e89728
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53 imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt" |
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29775869faba
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54 # output path for contents of `stats_metadata_v` table |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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55 anovaKseaMetadata: "test-data/limbo/anovaKseaMetadata.txt" |
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56 # how to test one variable with > 2 categories (e.g., aov or kruskal.test) |
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657663e89728
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57 oneWayManyCategories: !r c("aov", "kruskal.test", "oneway.test")[1] |
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29775869faba
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58 # how to test one variable with 2 categories (e.g., oneway.test) |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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59 oneWayTwoCategories: !r c("aov", "kruskal.test", "oneway.test")[3] |
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60 # what should be the minimum quality for consideration in both |
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61 minQuality: 0 |
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62 # correct KSEA with FDR (recommended) or raw p-value |
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63 kseaCutoffStatistic: !r c("FDR", "p.value")[1] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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64 # correct KSEA threshold 0.05 (conventional) or higher (perhaps better) |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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65 # "perhaps better" meaning that KSEA is an hypothesis-generator, not -test |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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66 #kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5)[1] |
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29775869faba
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67 # minimum number of substrates required for a kinase to be considered in KSEA |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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68 kseaMinSubstrateCount: 1 |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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69 # Should KSEA be performed aggregating signed log2FC or absolute? |
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70 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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71 # TRUE use abs(log2FC) for KSEA as Justin Drake requested; this is a |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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72 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm. |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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73 kseaUseAbsoluteLog2FC: TRUE |
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74 #kseaUseAbsoluteLog2FC: FALSE |
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75 # minimum number of observed values per sample-group |
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76 intensityMinValuesPerGroup: 1 |
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77 # maximum number of heatmap rows (result are poor when > 50) |
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78 intensityHeatmapRows: 50 |
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79 # what should be the primary criterion to eliminate excessive heatmap rows |
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80 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1] |
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81 # should correlation among substrates be used (rather than covariance) |
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82 correlateSubstrates: TRUE |
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83 # only show covariance among variables having variance > 1 |
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84 filterCovVarGT1: TRUE |
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85 # maximum number of residues to display for ppeps in rownames or columnames |
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86 ppepTruncN: 10 |
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87 # maximum number of characters of subgenes to display in rownames or columnames |
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88 subgeneTruncN: 10 |
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89 # maximum number of characters for paste(subgene, ppep) for enrichment plots |
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90 substTruncN: 20 |
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91 # should boxplots use variable-width boxes to reflect # of samples |
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92 boxPlotVarWidth: TRUE |
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93 # should boxplots use notched boxes to reflect difference between samples |
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94 boxPlotNotch: TRUE |
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95 # look-up tables for kinase descriptions |
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96 kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2" |
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97 kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2" |
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98 # should debugging trace messages be printed? |
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99 showEnrichedSubstrates: FALSE |
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100 |
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101 # should debugging nb/nbe messages be printed? |
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102 printNBMsgs: FALSE |
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103 # should debugging trace messages be printed? |
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104 printTraceMsgs: FALSE |
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105 # when debugging files are needed, set debugFileBasePath to the path |
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106 # to the directory where they should be writtn |
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107 debugFileBasePath: !r if (TRUE) NULL else "test-data" |
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24
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108 --- |
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109 <!-- |
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110 alphaFile: "test-data/alpha_levels.tabular" |
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27
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111 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" |
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112 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" |
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113 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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114 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" |
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115 regexSampleGrouping: "\\w+" |
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116 groupFilterPatterns: ".+" |
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117 groupFilter: !r c("none", "exclude", "include")[3] |
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118 imputationMethod: !r c("group-median", "median", "mean", "random")[1] |
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119 kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[1] |
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120 ut_alphaFile: "test-data/alpha_levels.tabular" |
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121 ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" |
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122 ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" |
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123 ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] |
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124 ut_regexSampleNames: "\\.\\d+[A-Z]$" |
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125 ut_regexSampleGrouping: "\\d+" |
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126 ut_groupFilterPatterns: ".+,.*" |
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127 ut_groupFilter: !r c("none", "exclude", "include")[1] |
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128 ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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129 ut_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1] |
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130 tst_alphaFile: "test-data/alpha_levels.tabular" |
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131 tst_inputFile: "test-data/test_input_for_anova.tabular" |
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132 tst_preprocDb: "test-data/test_input_for_anova.sqlite" |
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133 tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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134 tst_regexSampleNames: "\\.\\d+[A-Z]$" |
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135 tst_regexSampleGrouping: "\\d+" |
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136 tst_groupFilterPatterns: ".+" |
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137 tst_groupFilter: !r c("none", "exclude", "include")[1] |
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138 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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139 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5] |
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140 |
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141 tst_alphaFile: "test-data/alpha_levels.tabular" |
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142 tst_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" |
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143 tst_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" |
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144 tst_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] |
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145 tst_regexSampleNames: "\\.\\d+[A-Z]$" |
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146 tst_regexSampleGrouping: "\\d+" |
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147 tst_groupFilterPatterns: ".+,.*" |
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148 tst_groupFilter: !r c("none", "exclude", "include")[1] |
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149 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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150 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5] |
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151 px_alphaFile: "test-data/alpha_levels.tabular" |
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152 px_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" |
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153 px_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" |
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154 px_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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155 px_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" |
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156 px_regexSampleGrouping: "\\w+" |
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157 px_groupFilterPatterns: ".+" |
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158 px_groupFilter: !r c("none", "exclude", "include")[3] |
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159 px_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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160 px_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5] |
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161 pdx_alphaFile: "test-data/alpha_levels.tabular" |
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162 pdx_inputFile: "test-data/PDX012970_pST.preproc_tab.tabular" |
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163 pdx_preprocDb: "test-data/PDX012970_pST.preproc.sqlite" |
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164 pdx_kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2] |
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165 pdx_regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$" |
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166 pdx_regexSampleGrouping: "\\.\\w+\\K\\.\\w+" |
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167 pdx_groupFilterPatterns: "AdCa,AVPC" |
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168 pdx_groupFilter: !r c("none", "exclude", "include")[3] |
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169 pdx_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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170 pdx_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1] |
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171 tst_alphaFile: "test-data/alpha_levels.tabular" |
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172 tst_inputFile: "test-data/test_input_for_anova.tabular" |
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173 tst_preprocDb: "test-data/test_input_for_anova.sqlite" |
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174 tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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175 tst_regexSampleNames: "\\.\\d+[A-Z]$" |
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176 tst_regexSampleGrouping: "\\d+" |
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177 tst_groupFilterPatterns: ".+" |
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178 tst_groupFilter: !r c("none", "exclude", "include")[1] |
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179 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5] |
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180 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[1] |
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181 ut_alphaFile: "test-data/alpha_levels.tabular" |
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182 ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" |
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183 ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" |
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184 ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] |
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185 ut_regexSampleNames: "\\.\\d+[A-Z]$" |
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186 ut_regexSampleGrouping: "\\d+" |
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187 ut_groupFilterPatterns: ".+,.*" |
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188 ut_groupFilter: !r c("none", "exclude", "include")[1] |
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189 ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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190 alphaFile: "test-data/alpha_levels.tabular" |
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191 inputFile: "test-data/test_input_for_anova.tabular" |
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192 preprocDb: "test-data/test_input_for_anova.sqlite" |
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193 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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194 regexSampleNames: "\\.\\d+[A-Z]$" |
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195 regexSampleGrouping: "\\d+" |
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196 groupFilterPatterns: ".+,.*" |
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197 groupFilter: !r c("none", "exclude", "include")[1] |
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198 imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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199 nd_alphaFile: "test-data/alpha_levels.tabular" |
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200 nd_inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular" |
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201 nd_preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite" |
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202 nd_kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2] |
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203 nd_regexSampleNames: "\\.\\d+[A-Z]$" |
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204 nd_regexSampleGrouping: "\\d+" |
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205 nd_groupFilterPatterns: ".+,.*" |
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206 nd_groupFilter: !r c("none", "exclude", "include")[1] |
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207 nd_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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208 pxd_alphaFile: "test-data/alpha_levels.tabular" |
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209 pxd_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" |
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210 pxd_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" |
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211 pxd_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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212 pxd_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" |
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213 pxd_regexSampleGrouping: "\\w+" |
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214 pxd_groupFilterPatterns: ".+" |
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215 pxd_groupFilter: !r c("none", "exclude", "include")[3] |
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216 pxd_imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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217 |
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218 alphaFile: "test-data/alpha_levels.tabular" |
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219 inputFile: "test-data/test_input_for_anova.tabular" |
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220 preprocDb: "test-data/test_input_for_anova.sqlite" |
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221 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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222 regexSampleNames: "\\.\\d+[A-Z]$" |
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223 regexSampleGrouping: "\\d+" |
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224 groupFilterPatterns: ".+,.*" |
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225 groupFilter: !r c("none", "exclude", "include")[1] |
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226 |
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227 alphaFile: "test-data/alpha_levels.tabular" |
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228 inputFile: "test-data/PDX012970_pST.preproc_tab.tabular" |
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229 preprocDb: "test-data/PDX012970_pST.preproc.sqlite" |
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230 kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2] |
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231 regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$" |
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232 regexSampleGrouping: "\\.\\w+\\K\\.\\w+" |
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233 groupFilterPatterns: "AdCa,AVPC" |
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234 groupFilter: !r c("none", "exclude", "include")[3] |
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235 |
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236 alphaFile: "test-data/alpha_levels.tabular" |
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237 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular" |
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238 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite" |
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239 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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240 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$" |
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241 regexSampleGrouping: "\\w+" |
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242 groupFilterPatterns: ".+,.*" |
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243 groupFilter: !r c("none", "exclude", "include")[3] |
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25
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244 |
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245 kseaCutoffStatistic: !r c("p.value", "FDR")[2] |
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246 kseaCutoffThreshold: !r c(0.05, 0.1)[1] |
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247 |
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248 alphaFile: "test-data/alpha_levels.tabular" |
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249 inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular" |
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250 preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite" |
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251 kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2] |
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252 regexSampleNames: "\\.\\d+[A-Z]$" |
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253 regexSampleGrouping: "\\d+" |
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254 |
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255 alphaFile: "test-data/alpha_levels.tabular" |
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256 inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular" |
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257 preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite" |
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258 kseaAppPrepDb: !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2] |
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259 regexSampleNames: "\\.\\d+[A-Z]$" |
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260 regexSampleGrouping: "\\d+" |
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261 groupFilterPatterns: ".+,.*" |
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262 groupFilter: !r c("none", "exclude", "include")[3] |
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263 |
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264 alphaFile: "test-data/alpha_levels.tabular" |
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265 inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular" |
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266 preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite" |
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267 kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2] |
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268 regexSampleNames: "\\.\\d+[A-Z]$" |
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269 regexSampleGrouping: "\\d+" |
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270 groupFilterPatterns: ".+,.*" |
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271 groupFilter: !r c("none", "exclude", "include")[1] |
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272 |
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273 --> |
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274 ```{r setup, include = FALSE, results = 'asis'} |
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275 |
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276 # simple debug messaging |
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277 print_nb_messages <- params$printNBMsgs |
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278 |
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279 nb <- if (!print_nb_messages) { |
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280 function(...) invisible() |
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281 } else { |
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282 function(..., f = cat) f("\n$\\exists{}\\supset\\forall{}$", ...) |
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283 } |
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284 |
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285 nbe <- if (!print_nb_messages) { |
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286 function(...) invisible() |
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287 } else { |
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288 function(..., f = cat, file = stderr()) { |
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289 cat( |
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290 stringi::stri_unescape_unicode("\nNBE \\u2203\\u2283\\u2200"), |
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291 ..., |
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292 file = file |
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293 ) |
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294 } |
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295 } |
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296 |
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297 #ref for debugging: https://yihui.org/tinytex/r/#debugging |
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298 options(tinytex.verbose = TRUE) |
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299 |
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300 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285 |
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301 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355 |
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302 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10), dpi = 300) |
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303 |
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304 # freeze the random number generator so the same results will be produced |
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305 # from run to run |
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306 set.seed(28571) |
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307 |
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308 ### LIBRARIES |
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309 |
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310 if (print_nb_messages) nbe("library(gplots)") |
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311 library(gplots) |
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312 if (print_nb_messages) nbe("library(caret)") |
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313 # load caret for nearZeroVar |
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314 if (print_nb_messages) nbe("Please ignore the messages about systemd, if any.\n") |
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315 library(caret) |
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316 if (print_nb_messages) nbe("library(DBI)") |
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317 library(DBI) |
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318 if (print_nb_messages) nbe("library(RSQLite)") |
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319 library(RSQLite) |
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320 if (print_nb_messages) nbe("library(sqldf)\n") |
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321 # Suppress "Warning: no DISPLAY variable so Tk is not available" |
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322 suppressWarnings(suppressMessages(library(sqldf))) |
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323 |
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324 # required but not added to search list: |
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325 # - DBI |
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326 # - RSQLite |
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327 # - ggplot2 |
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328 # - knitr |
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329 # - latex2exp |
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330 # - preprocessCore |
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331 # - reshape2 |
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332 # - vioplot |
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333 |
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334 ### CONSTANTS |
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335 |
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336 const_boxplot_fill <- "grey94" |
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337 const_ksea_astrsk_kinases <- 1 |
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338 const_ksea_nonastrsk_kinases <- 2 |
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339 const_ksea_all_kinases <- 3 |
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340 const_log10_e <- log10(exp(1)) |
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341 const_stripchart_cex <- 0.5 |
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342 const_stripchart_jitter <- 0.3 |
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343 const_table_anchor_bp <- "bp" |
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344 const_table_anchor_ht <- "ht" |
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345 const_table_anchor_p <- "p" |
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346 const_table_anchor_t <- "t" |
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347 const_table_anchor_tbp <- "tbp" |
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348 |
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349 |
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350 ### GLOBAL VARIABLES (params) |
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351 |
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352 ## functions to process params |
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353 |
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354 is_string_null_or_empty <- function(x) { |
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355 # N. B. non-strings are intentionally treated as NULL |
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356 if (is.null(x)) |
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357 TRUE |
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358 else if (!is.character(x)) |
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359 TRUE |
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360 else x == "" |
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361 } |
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362 |
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363 ##' Catch *and* save both errors and warnings, and in the case of |
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364 ##' a warning, also keep the computed result. |
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365 ##' return result as list(value = ..., warning = ...) |
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366 ##' - value will be: |
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367 ##' - the result if no exception is thrown |
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368 ##' - the exception if an exception is caught |
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369 ##' - warning will be a string except perhaps when warning argument is not NULL |
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370 ##' |
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371 ##' adapted from `demo(error.catching)` |
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372 ##' |
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373 ##' @title tryCatch both warnings (with value) and errors |
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374 ##' @param expr an \R expression to evaluate |
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375 ##' @return a list with 'value' and 'warning', where |
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376 ##' 'value' may be an error caught. |
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377 ##' @author Martin Maechler; |
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378 ##' Copyright (C) 2010-2012 The R Core Team |
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379 try_catch_w_e <- |
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380 function(expr, error = function(e) e, warning = NULL) { |
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381 wrn <- NULL |
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382 # warning handler |
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383 w_handler <- |
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384 if (is.function(warning)) |
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385 warning |
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386 else |
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387 function(w) { |
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388 wrn <<- w |
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389 invokeRestart("muffleWarning") |
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390 } |
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391 e_handler <- |
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392 if (is.function(error)) |
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393 error |
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394 else |
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395 function(e) e |
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396 # return result as list(value = ..., warning = ...) |
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397 # - value will be: |
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398 # - the result if no exception is thrown |
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399 # - the exception if an exception is caught |
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400 list( |
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401 value = withCallingHandlers( |
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402 tryCatch( |
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403 expr, |
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404 error = e_handler |
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405 ), |
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406 warning = w_handler |
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407 ), |
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408 warning = wrn |
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409 ) |
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410 } |
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411 |
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412 see_kvp <- |
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413 function(format, key, value, suffix = "") { |
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414 if ( |
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415 !all( |
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416 is.character(format), |
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417 is.character(key), |
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418 is.character(value), |
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419 is.character(suffix) |
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420 ) |
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421 ) { |
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422 cat("all arguments to see_kvp should be character") |
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423 knitr::knit_exit() |
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424 } |
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425 result <- sprintf(format, value) |
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426 if (length(result) > 1) { |
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427 sprintf( |
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428 "%s = c(%s)%s", |
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429 whack_underscores(key), |
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430 paste(result, collapse = ", "), |
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431 suffix |
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432 ) |
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433 } else { |
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434 sprintf( |
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435 "%s = %s%s", |
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436 key, |
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437 result, |
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438 suffix |
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439 ) |
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440 } |
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441 } |
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442 |
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443 see_logical <- |
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444 function(x, suffix = "", xprssn = deparse1(substitute(x))) { |
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445 result <- as.character(as.logical(x)) |
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446 # handle NAs and NaNs |
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447 result[is.na(result)] <- "NA" |
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448 see_kvp( |
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449 format = "%s", |
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450 key = xprssn, |
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451 value = result, |
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452 suffix = suffix |
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453 ) |
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454 } |
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455 |
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456 see_numeric <- |
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457 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) { |
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458 if (is.numeric(digits) && is.numeric(x)) { |
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459 digits <- as.integer(digits) |
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460 digits <- min(16, max(0, digits)) |
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461 format <- paste0("%0.", as.character(digits), "g") |
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462 result <- sprintf(format, x) |
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463 see_kvp( |
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464 format = "%s", |
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465 key = xprssn, |
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466 value = result, |
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467 suffix = suffix |
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468 ) |
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469 } |
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470 } |
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471 |
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472 see_character <- |
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473 function(x, suffix = "", xprssn = deparse1(substitute(x))) { |
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474 if (is.character(x)) { |
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475 see_kvp( |
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476 format = "%s", |
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477 key = xprssn, |
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478 value = sprintf("\"%s\"", x), |
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479 suffix = suffix |
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480 ) |
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481 } |
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482 } |
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483 |
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484 see_variable <- |
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485 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) { |
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486 if (is.character(x)) { |
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487 see_character(x, suffix, xprssn) |
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488 } else if (is.numeric(x)) { |
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489 see_numeric(x, suffix, digits, xprssn) |
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490 } else if (is.logical(x)) { |
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491 see_logical(x, suffix, xprssn) |
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492 } else { |
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493 f <- file("") |
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494 sink(f) |
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495 str(x) |
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496 msg <- paste(readLines(f), collapse = "\n") |
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497 sink() |
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498 close(f) |
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499 paste0( |
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500 "see_variable - str(", |
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501 xprssn, |
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502 "):\n", |
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503 msg, "\n" |
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504 ) |
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505 } |
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506 } |
|
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507 |
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508 # ref: https://tug.org/texinfohtml/latex2e.html |
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509 # LaTeX sets aside the following characters for special purposes. |
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510 # For example, the percent sign % is for comments. |
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511 # They are called reserved characters or special characters. |
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512 # They are all discussed elsewhere in this manual. |
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513 # |
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514 # $ % & { } _ ~ ^ \ # |
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515 # |
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516 # If you want a reserved character to be printed as itself, in the text body |
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517 # font, for all but the final three characters in that list simply put |
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518 # a backslash \ in front of the character. |
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519 # Thus, typing \$1.23 will produce $1.23 in your output. |
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520 # |
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521 # As to the last three characters, to get a tilde in the text body font, |
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522 # use \~{} (omitting the curly braces would result in the next character |
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523 # receiving a tilde accent). |
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524 # Similarly, to get a text body font circumflex use \^{}. |
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525 # To get a backslash in the font of the text body enter \textbackslash{}. |
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526 whack_math <- |
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527 function(v) { |
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528 v <- as.character(v) |
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529 w <- gsub("\\", "\\textbackslash ", v, fixed = TRUE) |
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530 w <- Reduce( |
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531 f = function(l, r) { |
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532 gsub(r, paste0("\\", r), l, fixed = TRUE) |
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533 }, |
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534 x = c("#", "$", "%", "&", "{", "}", "_"), |
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535 init = w |
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536 ) |
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537 w <- gsub("^", "\\^{}", w, fixed = TRUE) |
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538 return(w) |
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539 if (all(v == w)) |
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540 v |
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541 else |
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542 paste0("\\texttt{", w, "}") |
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24
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543 } |
|
27
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544 whack_underscores <- whack_math |
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545 |
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546 ## dump params to stderr (remove this eventually) |
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547 |
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548 if (FALSE) nbe(see_variable(params)) |
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549 |
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550 ## unlist params for eventual output |
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551 |
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552 param_unlist <- unlist(as.list(params)) |
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553 |
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554 # no need to whack underscores and dollars because this is verbatim |
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555 param_df <- data.frame( |
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556 parameter = paste0("\\verb@", names(param_unlist), "@"), |
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557 value = paste0( |
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558 "\n\\begin{tiny}\n\\verb@", |
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559 param_unlist, |
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560 "@\n\\end{tiny}" |
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561 ) |
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562 ) |
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563 param_df <- data.frame( |
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564 parameter = names(param_unlist), |
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565 value = param_unlist |
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566 ) |
|
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567 param_df <- param_df[order(param_df$parameter), ] |
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568 |
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569 ## general output control |
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|
570 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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571 debug_file_base_path <- params$debugFileBasePath |
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572 print_trace_messages <- params$printTraceMsgs |
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573 show_enriched_substrates <- params$showEnrichedSubstrates |
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574 boxplot_varwidth <- params$boxPlotVarWidth |
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575 boxplot_notch <- params$boxPlotNotch |
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576 |
|
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577 ## parameters for static data |
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578 |
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579 kinase_name_uprt_lut_bz2 <- params$kinaseNameUprtLutBz2 |
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580 kinase_uprt_desc_lut_bz2 <- params$kinaseUprtDescLutBz2 |
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581 |
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|
582 ## parameters for input file |
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583 |
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584 preproc_db <- params$preprocDb |
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585 alpha_file <- params$alphaFile |
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586 input_file <- params$inputFile |
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587 |
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588 # First data column - ideally, this could be detected via |
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589 # regexSampleNames, but for now leave it as is. |
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590 first_data_column <- params$firstDataColumn |
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591 fdc_is_integer <- is.integer(first_data_column) |
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592 if (fdc_is_integer) { |
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593 first_data_column <- as.integer(params$firstDataColumn) |
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|
594 } |
|
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|
595 |
|
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changeset
|
596 ## parameters for output files |
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|
597 |
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598 ksea_app_prep_db <- params$kseaAppPrepDb |
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599 imputed_data_filename <- params$imputedDataFilename |
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600 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile |
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601 anova_ksea_mtdt_file <- params$anovaKseaMetadata |
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602 |
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603 ## parameters for imputation |
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604 |
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605 # Imputation method, should be one of |
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606 # "random", "group-median", "median", or "mean" |
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607 imputation_method <- params$imputationMethod |
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608 |
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609 # Selection of percentile of logvalue data to set the mean for random number |
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610 # generation when using random imputation |
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611 mean_percentile <- params$meanPercentile / 100.0 |
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612 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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613 # deviation adjustment-factor for random values; real number. |
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614 sd_percentile <- params$sdPercentile |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
615 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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616 ## parameters for group parsing and filtering |
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617 |
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29775869faba
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618 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$" |
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619 regex_sample_names <- params$regexSampleNames |
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620 # Regular expression to extract Sample Grouping from Sample Name; |
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29775869faba
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621 # if error occurs, compare smpl_trt vs. sample_name_matches |
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29775869faba
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622 # to see if groupings/pairs line up |
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623 # e.g., "(\\d+)" |
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624 |
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625 regex_sample_grouping <- params$regexSampleGrouping |
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626 # What are the patterns for filtering sample groups? |
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627 # How should sample groups be filtered? |
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628 # - none: do not filter |
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629 # - include: include sample groups matching filter |
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630 # - exclude: include sample groups not matching filter |
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631 |
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632 sample_group_filter <- params$groupFilter |
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633 if (grepl("f", params$groupFilterMode, fixed = TRUE)) { |
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634 sample_group_filter_perl <- FALSE |
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635 sample_group_filter_fixed <- TRUE |
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636 } else if (grepl("p", params$groupFilterMode, fixed = TRUE)) { |
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637 sample_group_filter_perl <- TRUE |
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638 sample_group_filter_fixed <- FALSE |
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639 } else { # normal regex |
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640 sample_group_filter_perl <- FALSE |
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641 sample_group_filter_fixed <- FALSE |
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642 } |
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643 |
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29775869faba
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644 sample_group_filter_nocase <- |
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645 grepl("i", params$groupFilterMode, fixed = TRUE) |
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646 |
|
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647 # What PCRE patterns should be included or excluded |
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648 group_filter_patterns_csv <- params$groupFilterPatterns |
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649 sample_group_filter_patterns <- strsplit( |
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650 x = group_filter_patterns_csv, |
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651 split = ",", |
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652 fixed = TRUE |
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29775869faba
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653 )[[1]] |
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654 |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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655 ## parameters for hypothesis testing |
|
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656 |
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657 one_way_all_categories_fname <- params$oneWayManyCategories |
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658 |
|
29775869faba
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659 one_way_all_categories <- try_catch_w_e( |
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660 match.fun(one_way_all_categories_fname)) |
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|
661 |
|
29775869faba
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662 if (!is.function(one_way_all_categories$value)) { |
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663 write("fatal error for parameter oneWayManyCategories:", stderr()) |
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664 write(one_way_all_categories$value$message, stderr()) |
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665 if (sys.nframe() > 0) { |
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666 cat("Cannot continue and quit() failed. Goodbye.") |
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667 knitr::knit_exit() |
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668 quit(save = "no", status = 1) |
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669 } |
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670 } |
|
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671 |
|
29775869faba
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672 one_way_all_categories <- one_way_all_categories$value |
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|
673 |
|
29775869faba
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674 one_way_two_categories_fname <- params$oneWayManyCategories |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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675 one_way_two_categories <- try_catch_w_e( |
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676 match.fun(one_way_two_categories_fname)) |
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|
677 if (!is.function(one_way_two_categories$value)) { |
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678 cat("fatal error for parameter oneWayTwoCategories: \n") |
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679 cat(one_way_two_categories$value$message, fill = TRUE) |
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680 if (sys.nframe() > 0) { |
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681 cat("Cannot continue and quit() failed. Goodbye.") |
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682 knitr::knit_exit() |
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683 quit(save = "no", status = 1) |
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684 } |
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685 } |
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686 one_way_two_categories <- one_way_two_categories$value |
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687 |
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688 ## parameters for KSEA |
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689 |
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690 ksea_cutoff_statistic <- params$kseaCutoffStatistic |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
691 ksea_cutoff_threshold <- params$kseaCutoffThreshold |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
692 ksea_min_substrate_count <- params$kseaMinSubstrateCount |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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changeset
|
693 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
694 ## parameters for global variables consumed by functions |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
695 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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696 # intensityHeatmapCriteria: !r c("na_count", "p_value")[2] # TODO switch to 1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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697 # TODO Validate within list |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
698 g_intensity_hm_criteria <- params$intensityHeatmapCriteria |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
699 if (is_string_null_or_empty(g_intensity_hm_criteria)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
700 cat("invalid intensityHeatmapCriteria parameter (must be string)") |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
701 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
702 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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changeset
|
703 switch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
704 g_intensity_hm_criteria, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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705 "quality" = NULL, |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
706 "na_count" = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
707 "p_value" = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
708 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
709 with( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
710 params, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
711 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
712 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
713 "invalid %s (must be %s)", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
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|
714 see_variable(intensityHeatmapCriteria), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
715 "one of quality or na_count or p_value" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
716 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
717 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
718 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
719 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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changeset
|
720 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
721 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
722 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
723 # intensityHeatmapRows: 50 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
724 # TODO Validate >> 0 < 75 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
725 g_intensity_hm_rows <- params$intensityHeatmapRows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
726 if (!is.integer(g_intensity_hm_rows) || g_intensity_hm_rows < 1) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
727 cat("invalid intensityHeatmapRows (must be integer > 0)") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
728 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
729 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
730 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
731 g_intensity_min_per_class <- params$intensityMinValuesPerGroup |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
732 if (!is.integer(g_intensity_min_per_class) || g_intensity_min_per_class < 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
733 cat("invalid intensityMinValuesPerGroup (must be integer > -1") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
734 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
735 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
736 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
737 if (is.na(as.logical(g_correlate_substrates <- params$correlateSubstrates))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
738 cat("invalid correlateSubstrates (must be TRUE or FALSE)") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
739 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
740 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
741 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
742 if (is.na(as.logical(g_filter_cov_var_gt_1 <- params$filterCovVarGT1))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
743 cat("invalid filterCovVarGT1 parameter (must be TRUE or FALSE)") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
744 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
745 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
746 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
747 # TODO Validate >> 0 < 30 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
748 g_ppep_trunc_n <- params$ppepTruncN |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
749 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
750 # TODO Validate >> 0 < 30 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
751 g_subgene_trunc_n <- params$subgeneTruncN |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
752 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
753 # TODO Validate >> 0 < 30 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
754 g_sbstr_trunc_n <- params$substTruncN |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
755 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
756 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
757 ### OPERATORS |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
758 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
759 # Test for exclusion |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
760 # ref: https://www.reneshbedre.com/blog/in-operator-r.html |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
761 `%notin%` <- Negate(`%in%`) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
762 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
763 # Augmented assignment |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
764 # ref: https://www2.cs.arizona.edu/icon/refernce/infix2.htm#aug_assign |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
765 `%||:=%` <- function(lvalue, ...) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
766 pf <- parent.frame() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
767 rvalue <- Reduce(paste0, x = ..., init = lvalue) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
768 assign( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
769 x = as.character(substitute(lvalue)), |
|
29775869faba
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|
770 value = rvalue, |
|
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|
771 pos = pf |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
772 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
773 invisible(rvalue) |
|
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|
774 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
775 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
776 ### FUNCTIONS |
|
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|
777 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
778 no_op <- |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
779 function() { |
|
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|
780 } |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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781 # this function is not used in this file and should be removed while |
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782 # factoring out reusable code |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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783 all_apply <- function(f, v, na_rm = TRUE, ...) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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784 Reduce( |
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|
785 f = function(l, r) if (na_rm && is.na(r)) TRUE else l && r, |
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|
786 x = sapply(X = v, FUN = f, ...), |
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|
787 init = TRUE |
|
24
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788 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
789 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
790 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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791 write_debug_file <- function(data_frame) { |
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792 if (!is.null(debug_file_base_path)) { |
|
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|
793 s_path <- |
|
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|
794 sprintf( |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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795 "%s/%s.txt", |
|
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|
796 debug_file_base_path, |
|
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|
797 deparse(substitute(data_frame)) |
|
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|
798 ) |
|
24
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|
799 write.table( |
|
27
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|
800 data_frame, |
|
24
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changeset
|
801 file = s_path, |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
802 sep = "\t", |
|
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|
803 col.names = TRUE, |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
804 row.names = TRUE, |
|
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|
805 quote = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
806 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
807 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
808 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
809 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
810 # ref: http://adv-r.had.co.nz/Environments.html |
|
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|
811 # "When creating your own environment, note that you should set its parent |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
812 # environment to be the empty environment. This ensures you don't |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
813 # accidentally inherit objects from somewhere else." |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
814 # Caution: this prevents `with(my_env, expr)` from working when `expr` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
815 # contains anything from the global environment, even operators! |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
816 # Hence, `x <- 1; get("x", new_env())` fails by design. |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
817 new_env <- function() { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
818 new.env(parent = emptyenv()) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
819 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
820 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
821 # make apply readable for rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
822 row_apply <- function(x, fun, ..., simplify = TRUE) { |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
823 apply(x, MARGIN = 1, fun, ..., simplify = TRUE) |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
824 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
825 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
826 # make apply readable for columns |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
827 column_apply <- function(x, fun, ..., simplify = TRUE) { |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
828 apply(x, MARGIN = 2, fun, ..., simplify = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
829 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
830 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
831 ##' Produce a vector of boolean values whose i-th value is TRUE when any |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
832 ##' member of v matches the i-th membr of s, where i in 1:seq_len(length(s)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
833 ##' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
834 ##' @title Search multiple strings for matches of multiple substrings |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
835 ##' @param v a vector of substrings to match |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
836 ##' @param s a vector of strings to search for matches |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
837 ##' @param ... additional arguments to grepl |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
838 ##' @return a list with keys in s and valuse that are vectors of elements of v |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
839 ##' @author Art Eschenlauer |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
840 ##' Copyright (C) 2022 Art Eschenlauer; |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
841 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
842 mgrepl <- function(v, s, ...) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
843 grpl_rslt <- rep_len(0, length(s)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
844 for (vi in v) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
845 grpl_rslt_v <- sapply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
846 X = s, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
847 FUN = function(t) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
848 Reduce( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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849 f = function(l, r) if (is.null(l)) r else c(l, r), |
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850 x = sapply( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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851 X = vi, |
|
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|
852 FUN = function(f) grepl(f, t, ...) |
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changeset
|
853 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
854 init = c() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
855 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
856 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
857 simplify = "array" |
|
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diff
changeset
|
858 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
859 grpl_rslt <- grpl_rslt + grpl_rslt_v |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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|
860 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
861 rslt <- unname(grpl_rslt > 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
862 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
863 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
864 ##' Produce positions in a vector where succeeding value != current valus |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
865 ##' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
866 ##' @title Search vector for neighboring positions having different values |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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867 ##' @param v a vector of comparable numeric values (e.g. integers) |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
868 ##' @return a vector of positions i where v[i] != v[i + 1] |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
869 ##' @author Art Eschenlauer |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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870 ##' Copyright (C) 2022 Art Eschenlauer; |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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871 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms |
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|
872 transition_positions <- function(v) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
873 Reduce( |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
874 f = function(l, i) if ((i != 1) && (v[i - 1] != v[i])) c(l, i - 1) else l, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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875 x = seq_along(v)[-1:0], |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
876 init = c() |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
877 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
878 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
879 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
880 ### figure debug functions |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
881 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
882 cat_par_vector <- function(par_name, lbl = "", newlines = TRUE) { |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
883 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
884 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
885 "%spar(%s) = c(%s)%s", |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
886 lbl, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
887 par_name, |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
888 paste(par(par_name), collapse = ", "), |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
889 if (newlines) "\n\n" else "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
890 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff
changeset
|
891 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
892 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
893 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
894 cat_margins <- function(lbl = NULL) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
895 for (p in c("fig", "fin", "mar", "mai", "omd", "omi", "oma")) |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
896 cat_par_vector(p, if (!is.null(lbl)) paste0(lbl, " ") else NULL) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
897 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
898 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
899 cat_variable <- |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
900 function(x, suffix = "", digits = 3, force_str = FALSE) { |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
901 xprssn <- deparse1(substitute(x)) |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
902 if (force_str || is.matrix(x) || is.list(x) || is.data.frame(x)) { |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
903 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
904 paste0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
905 "\n\\texttt{\\textbf{", |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
906 whack_underscores(xprssn), |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
907 "}} [", |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
908 typeof(x), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
909 ",", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
910 mode(x), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
911 "] =\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
912 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff
changeset
|
913 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
914 cat("\n\\begin{verbatim}\n") |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
915 str(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
916 cat("\n\\end{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
917 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
918 cat("\n", see_variable(x, suffix, digits, xprssn)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
919 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
920 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
921 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
922 ### structure helper functions |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
923 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
924 # ref: staque.R - Icon-oriented stack and queue operations |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
925 # - https://gist.github.com/eschen42/917690355e53918b9e7ba7138a02d1f8 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
926 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
927 # sq_get(v):x produces the leftmost element of v and removes it from v, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
928 # but produces NA if v is empty |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
929 sq_get <- function(v) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
930 if (length(v) == 0) return(NA) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
931 assign(as.character(substitute(v)), v[-1], parent.frame()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
932 return(v[1]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
933 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
934 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
935 # sq_put(v,x1,...,xn):v puts x1, x2, ..., xn onto the right end of v, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
936 # producing v. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
937 # Values are pushed in order from left to right, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
938 # so xn becomes the last (rightmost) value on v. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
939 # sq_put(v) with no second argument does nothing. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
940 sq_put <- function(v, x = NA, ...) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
941 pf <- parent.frame() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
942 if (is.null(x)) return(pf$v) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
943 if ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
944 !(length(x) > 1) && |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
945 !rlang::is_closure(x) && |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
946 is.na(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
947 ) return(pf$v) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
948 assign(as.character(substitute(v)), c(v, x, ...), pf) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
949 pf[[as.character(substitute(v))]] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
950 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
951 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
952 ### numerical/statistical helper functions |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
953 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
954 any_nan <- function(x) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
955 !any(x == "NaN") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
956 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
957 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
958 # determine standard deviation of quantile to impute |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
959 sd_finite <- function(x) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
960 ok <- is.finite(x) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
961 sd(x[ok]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
962 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
963 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
964 # compute anova raw p-value |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
965 anova_func <- function(x, grouping_factor, one_way_f) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
966 subject <- data.frame( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
967 intensity = x |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
968 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
969 x_aov <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
970 one_way_f( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
971 formula = intensity ~ grouping_factor, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
972 data = subject |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
973 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
974 pvalue <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
975 if (identical(one_way_f, aov)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
976 summary(x_aov)[[1]][["Pr(>F)"]][1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
977 else |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
978 pvalue <- x_aov$p.value |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
979 pvalue |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
980 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
981 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
982 # This code adapted from matrixcalc::is.positive.definite |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
983 # Notably, this simply tests without calling stop() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
984 is_positive_definite <- function(x, tol = 1e-08) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
985 if (!is.matrix(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
986 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
987 if (!is.numeric(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
988 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
989 if (nrow(x) < 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
990 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
991 if (ncol(x) < 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
992 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
993 if (nrow(x) != ncol(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
994 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
995 sum_symm <- sum(x == t(x), na.rm = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
996 value_count <- Reduce("*", dim(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
997 if (sum_symm != value_count) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
998 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
999 eigenvalues <- eigen(x, only.values = TRUE)$values |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1000 n <- nrow(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1001 for (i in 1:n) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1002 if (abs(eigenvalues[i]) < tol) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1003 eigenvalues[i] <- 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1004 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1005 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1006 if (any(eigenvalues <= 0)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1007 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1008 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1009 return(TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1010 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1011 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1012 ### LaTeX functions |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1013 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1014 # Use this like print.data.frame, from which it is adapted: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1015 data_frame_table_latex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1016 function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1017 x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1018 # digits to pass to format.data.frame |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1019 digits = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1020 # TRUE -> right-justify columns; FALSE -> left-justify |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1021 right = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1022 # maximumn number of rows to print |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1023 max = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1024 # string with justification of each column |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1025 justification = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1026 # TRUE to center on page |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1027 centered = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1028 # optional caption |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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changeset
|
1029 caption = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1030 # h(inline); b(bottom); t (top) or p (separate page) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1031 anchor = "h", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1032 # set underscore_whack to TRUE to escape underscores |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1033 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1034 # how to emit results |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1035 emit = cat |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1036 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1037 if (is.null(justification)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1038 justification <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1039 Reduce( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1040 f = paste, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
1041 x = rep_len(if (right) "r" else "l", length(colnames(x))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1042 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
1043 n <- length(rownames(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1044 if (length(x) == 0L) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1045 emit( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1046 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1047 # if n is one, use singular 'row', else use plural 'rows' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1048 ngettext( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1049 n, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1050 "data frame with 0 columns and %d row", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1051 "data frame with 0 columns and %d rows" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1052 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1053 n |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1054 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1055 "\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1056 sep = "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1057 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
1058 } else if (n == 0L) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1059 emit("0 rows for:\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1060 latex_itemized_list( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1061 v = names(x), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1062 underscore_whack = underscore_whack |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1063 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1064 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1065 if (is.null(max)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1066 max <- getOption("max.print", 99999L) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1067 if (!is.finite(max)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1068 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1069 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1070 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1071 omit <- (n0 <- max %/% length(x)) < n |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1072 m <- as.matrix( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1073 format.data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1074 if (omit) x[seq_len(n0), , drop = FALSE] else x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1075 digits = digits, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1076 na.encode = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1077 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1078 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1079 emit( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1080 # h(inline); b(bottom); t (top) or p (separate page) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1081 paste0("\\begin{table}[", anchor, "]"), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1082 "\\leavevmode", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1083 sep = "\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1084 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1085 if (!is.null(caption)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1086 emit(paste0(" \\caption{", caption, "}")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1087 if (centered) emit("\\centering\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1088 emit( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1089 paste( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1090 " \\begin{tabular}{", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1091 justification, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1092 "}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
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changeset
|
1093 sep = "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1094 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1095 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1096 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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changeset
|
1097 # ref for top and bottom struts (\T and \B): |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1098 # https://tex.stackexchange.com/a/50355 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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changeset
|
1099 if (!is.null(caption)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1100 emit("\\B \\\\\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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changeset
|
1101 latex_table_row( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1102 v = colnames(m), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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changeset
|
1103 extra = " \\T \\B", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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changeset
|
1104 underscore_whack = underscore_whack |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1105 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
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changeset
|
1106 emit("\\hline \\\\\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1107 for (i in seq_len(length(m[, 1]))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1108 latex_table_row( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
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changeset
|
1109 v = m[i, ], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
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changeset
|
1110 underscore_whack = underscore_whack |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1111 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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changeset
|
1112 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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changeset
|
1113 emit( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1114 paste( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1115 " \\end{tabular}", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1116 "\\end{table}", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1117 sep = "\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1118 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1119 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1120 if (omit) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1121 emit(" [ reached 'max' / getOption(\"max.print\") -- omitted", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1122 n - n0, "rows ]\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1123 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1124 invisible(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1125 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1126 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1127 # Use this like print.data.frame, from which it is adapted: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1128 data_frame_tabbing_latex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1129 function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1130 x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1131 # vector of tab stops, in inches |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1132 tabstops, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1133 # vector of headings, registered with tab-stops |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1134 headings = colnames(x), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1135 # digits to pass to format.data.frame |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1136 digits = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1137 # maximumn number of rows to print |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1138 max = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1139 # optional caption |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1140 caption = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1141 # set underscore_whack to TRUE to escape underscores |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1142 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1143 # flag for landscape mode |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1144 landscape = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1145 # flag indicating that subsubsection should be used for caption |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1146 # rather than subsection |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1147 use_subsubsection_header = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1148 # character-size indicator; for possible values, see: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1149 # https://tug.org/texinfohtml/latex2e.html#Font-sizes |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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changeset
|
1150 charactersize = "small", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1151 # set verbatim to TRUE to debug output |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1152 verbatim = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1153 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1154 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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changeset
|
1155 hlinport <- if (landscape) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1156 function() cat("\\hlinlscp \\\\\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1157 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1158 function() cat("\\hlinport \\\\\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1159 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1160 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1161 tabstops_tex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1162 Reduce( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1163 f = function(l, r) paste0(l, r), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1164 x = sprintf("\\hspace{%0.2fin}\\=", tabstops), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1165 init = "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1166 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1167 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1168 n <- length(rownames(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1169 if (length(x) == 0L) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1170 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1171 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1172 # if n is one, use singular 'row', else use plural 'rows' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1173 ngettext( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1174 n, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1175 "data frame with 0 columns and %d row", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1176 "data frame with 0 columns and %d rows" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1177 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1178 n |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1179 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1180 "\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1181 sep = "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1182 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1183 } else if (n == 0L) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1184 cat("0 rows for:\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1185 latex_itemized_list( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1186 v = names(x), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1187 underscore_whack = underscore_whack |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1188 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1189 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1190 if (is.null(max)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1191 max <- getOption("max.print", 99999L) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1192 if (!is.finite(max)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1193 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1194 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1195 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1196 omit <- (n0 <- max %/% length(x)) < n |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1197 m <- as.matrix( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1198 format.data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1199 if (omit) x[seq_len(n0), , drop = FALSE] else x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1200 digits = digits, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1201 na.encode = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1202 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1203 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1204 if (landscape) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1205 cat("\n\\begin{landscape}") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1206 tex_caption <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1207 if (!is.null(caption)) sprintf("\\captionof{table}{%s}\n", caption) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1208 else "\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1209 # build the column names, which have multiple lines when |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1210 # length(headings) is a multiple of the number of columns |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1211 column_names <- "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1212 while (length(headings) > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1213 my_row <- c() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1214 for (i in 1:(1 + length(tabstops))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1215 my_field <- sq_get(headings) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1216 sq_put(my_row, if (is.na(my_field)) "" else my_field) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1217 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1218 column_names %||:=% latex_tabbing_row( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1219 v = my_row, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1220 underscore_whack = underscore_whack, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1221 action = paste0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1222 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1223 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1224 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1225 # Begin tabbing environment after beginning charactersize environment |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1226 if (verbatim) cat("\n\\begin{verbatim}") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1227 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1228 paste0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1229 "\n\\begin{", charactersize, "}", tex_caption, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1230 "\\begin{tabwrap}{", tabstops_tex, "}\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1231 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1232 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1233 # emit column names |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1234 cat(column_names) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1235 # emit hline |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1236 hlinport() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1237 for (i in seq_len(length(m[, 1]))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1238 my_row <- latex_tabbing_row( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1239 v = m[i, ], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1240 underscore_whack = underscore_whack, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1241 action = paste0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1242 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1243 if (FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1244 cat(my_row) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1245 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1246 cat(my_row) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1247 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1248 hlinport() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1249 if (omit) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1250 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1251 n - n0, "rows ]\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1252 # End charactersize environment after ending tabbing environment |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1253 cat(paste0("\\end{tabwrap}\n\\end{", charactersize, "}\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1254 if (verbatim) cat("\\end{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1255 if (landscape) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1256 cat("\\end{landscape}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1257 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1258 invisible(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1259 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1260 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1261 param_df_noexit <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1262 function(e = NULL) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1263 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1264 x = param_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1265 tabstops = c(1.75), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1266 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1267 caption = "Input parameters", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1268 verbatim = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1269 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1270 if (!is.null(e)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1271 sink(stderr()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1272 cat("Caught fatal error:\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1273 str(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1274 sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1275 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1276 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1277 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1278 param_df_exit <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1279 function(e = NULL) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1280 param_df_noexit(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1281 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1282 exit(-1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1283 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1284 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1285 # exit with exit code (default 0) and optional msg |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1286 exit <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1287 function(code = 0, msg = NULL, use_stderr = FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1288 if (!is.null(msg)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1289 if (use_stderr) sink(stderr()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1290 cat("\n\n", msg, "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1291 if (use_stderr) sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1292 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1293 q(save = "no", status = code) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1294 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1295 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1296 # make control sequences into printable latex sequences |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1297 latex_printable_control_seqs <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1298 function(s) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1299 s <- gsub("[\\]", "xyzzy_plugh", s) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1300 s <- gsub("[$]", "\\\\$", s) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1301 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1302 return(s) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1303 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1304 nolatex_verbatim <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1305 function(expr) eval(expr) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1306 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1307 latex_verbatim <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1308 function(expr) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1309 arg_string <- deparse1(substitute(expr)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1310 cat("\n\\begin{verbatim}\n___\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1311 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1312 expr = expr, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1313 error = param_df_exit, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1314 #ACE error = |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1315 #ACE function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1316 #ACE cat("Caught error:\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1317 #ACE str(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1318 #ACE knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1319 #ACE stop(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1320 #ACE }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1321 finally = cat("...\n\\end{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1322 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1323 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1324 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1325 latex_samepage <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1326 function(expr) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1327 arg_string <- deparse1(substitute(expr)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1328 cat("\n\\begin{samepage}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1329 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1330 expr = expr, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1331 error = param_df_exit, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1332 #ACE error = |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1333 #ACE function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1334 #ACE cat("Caught error:\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1335 #ACE str(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1336 #ACE knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1337 #ACE stop(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1338 #ACE }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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changeset
|
1339 finally = cat("\n\\end{samepage}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1340 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1341 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1342 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1343 # return the result of invocation after showing parameters |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1344 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1345 latex_show_invocation <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1346 function(f, f_name = deparse1(substitute(f)), head_patch = FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1347 function(...) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
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changeset
|
1348 my_env <- (as.list(environment())) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1349 va <- list(...) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1350 my_rslt <- new_env() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1351 my_rslt$rslt <- NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1352 latex_verbatim( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1353 expr = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1354 cat(sprintf("\n .. Local variables for '%s':\n\n", f_name)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1355 str(va) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1356 if (!head_patch) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1357 # return this result |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1358 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1359 cat(sprintf("\n .. Invoking '%s'\n", f_name)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1360 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1361 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1362 cat("\n\\end{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1363 rslt <- do.call(f, va) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1364 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1365 error = param_df_exit, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1366 #ACE error = function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1367 #ACE cat("\n\\begin{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1368 #ACE str(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1369 #ACE cat("\n\\end{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1370 #ACE knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1371 #ACE stop(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1372 #ACE }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1373 finally = cat("\n\\begin{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1374 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1375 cat(sprintf("\n .. '%s' returned:\n", f_name)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1376 str(rslt) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1377 my_rslt$rslt <- rslt |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1378 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1379 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1380 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1381 # return the result of invocation with the shown parameters |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1382 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1383 if (head_patch) my_rslt$rslt <- do.call(f, va) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1384 (my_rslt$rslt) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1385 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1386 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1387 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1388 latex_collapsed_vector <- function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1389 collapse_string, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1390 v, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1391 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
1392 action = cat0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1393 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1394 v_sub <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1395 if (underscore_whack) whack_underscores(v) else v |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1396 action( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1397 paste0( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1398 v_sub, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1399 collapse = collapse_string |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1400 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1401 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1402 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1403 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1404 latex_itemized_collapsed <- function(collapse_string, v, underscore_whack = TRUE) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1405 cat("\\begin{itemize}\n\\item ") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1406 latex_collapsed_vector(collapse_string, v, underscore_whack) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1407 cat("\n\\end{itemize}\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1408 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1409 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1410 latex_itemized_list <- function(v, underscore_whack = TRUE) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1411 latex_itemized_collapsed("\n\\item ", v, underscore_whack) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1412 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1413 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1414 latex_enumerated_collapsed <- function(collapse_string, v, underscore_whack = TRUE) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1415 cat("\\begin{enumerate}\n\\item ") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1416 latex_collapsed_vector(collapse_string, v, underscore_whack) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1417 cat("\n\\end{enumerate}\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1418 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1419 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1420 latex_enumerated_list <- function(v) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1421 latex_enumerated_collapsed("\n\\item ", v) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1422 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1423 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1424 latex_table_row <- function(v, extra = "", underscore_whack = TRUE) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1425 latex_collapsed_vector(" & ", v, underscore_whack) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1426 cat(extra) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1427 cat(" \\\\\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1428 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1429 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1430 latex_tabbing_row <- function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1431 v, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1432 extra = "", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1433 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1434 action = cat0 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1435 ) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1436 # latex_collapsed_vector applies action to result of paste0; |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1437 # by default, action = cat; |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1438 # hence, a scalar string is assigned to v_collapsed |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1439 v_collapsed <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1440 latex_collapsed_vector( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1441 "} \\> \\tabfill{", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1442 v, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1443 underscore_whack, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1444 action = paste0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1445 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1446 action( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1447 "\\tabfill{", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1448 v_collapsed, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1449 "}", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1450 extra, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1451 " \\\\\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1452 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1453 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1454 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1455 # N.B. use con = "" to emulate regular cat |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1456 fcat0 <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1457 function(..., sprtr = " ", cnnctn = file()) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1458 cat0(..., sep = sprtr, file = cnnctn) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1459 invisible(cnnctn) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1460 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1461 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1462 hypersub <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1463 function(s) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1464 hyper <- tolower(s) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1465 hyper <- gsub("[^a-z0-9]+", "-", hyper) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1466 hyper <- gsub("[-]+", "-", hyper) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1467 hyper <- gsub("[_]+", "-", hyper) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1468 hyper <- sub("^[-]", "", hyper) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1469 hyper <- sub("[-]$", "", hyper) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1470 return(hyper) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1471 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1472 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1473 table_href <- function(s = "offset", caption = "") { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1474 paste0("\\hyperlink{table.\\arabic{", s, "}}{Table \\arabic{", s, "}}") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1475 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1476 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1477 table_offset <- function(i = 0, s = "offset", new = FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1478 paste0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1479 if (new) paste0("\\newcounter{", s, "}\n") else "", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1480 "\\setcounter{", s, "}{\\value{table}}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1481 paste0(if (i > 0) rep(paste0("\\stepcounter{", s, "}"), i), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1482 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1483 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1484 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1485 a_section_header <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1486 function(s, prefix = "") { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1487 hyper <- hypersub(s) |
|
27
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|
1488 my_subsection_header <- sprintf( |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1489 "\\hypertarget{%s}{\\%ssection{%s}\\label{%s}}\n", |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1490 hyper, |
|
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changeset
|
1491 prefix, |
|
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|
1492 gsub("_", "\\_", s, fixed = TRUE), |
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|
1493 hyper |
|
24
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|
1494 ) |
|
27
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1495 my_subsection_header |
|
24
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|
1496 } |
|
27
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|
1497 section_header <- function(s) a_section_header(s, "") |
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|
1498 subsection_header <- function(s) a_section_header(s, "sub") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1499 subsubsection_header <- function(s) a_section_header(s, "subsub") |
|
24
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|
1500 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1501 ### SQLite functions |
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|
1502 |
|
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|
1503 ddl_exec <- function(db, sql) { |
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|
1504 discard <- DBI::dbExecute(conn = db, statement = sql) |
|
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|
1505 if (FALSE && discard != 0) { |
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|
1506 need_newpage <- TRUE |
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|
1507 if (need_newpage) { |
|
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|
1508 need_newpage <<- FALSE |
|
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|
1509 cat("\\newpage\n") |
|
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|
1510 } |
|
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|
1511 o_file <- stdout() |
|
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|
1512 cat("\n\\begin{verbatim}\n") |
|
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|
1513 cat(sql, file = o_file) |
|
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|
1514 cat(sprintf("\n%d rows affected by DDL\n", discard), file = o_file) |
|
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|
1515 cat("\n\\end{verbatim}\n") |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1516 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1517 } |
|
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|
1518 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1519 dml_no_rows_exec <- function(db, sql) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1520 discard <- DBI::dbExecute(conn = db, statement = sql) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1521 if (discard != 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1522 need_newpage <- TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1523 if (need_newpage) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1524 need_newpage <<- FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1525 cat("\\newpage\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1526 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1527 cat("\n\\begin{verbatim}\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1528 o_file <- stdout() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1529 cat(sql, file = o_file) |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1530 cat(sprintf("\n%d rows affected by DML\n", discard), file = o_file) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
1531 cat("\n\\end{verbatim}\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1532 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1533 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1534 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
1535 ### KSEA functions and helpers |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1536 |
|
27
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diff
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|
1537 #' The KSEA App Analysis (KSEA Kinase Scores Only) |
|
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|
1538 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1539 #' Compute KSEA kinase scores and statistics from phoshoproteomics data input |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1540 #' Adapted from KSEAapp::KSEA.Scores to allow retrieval of maximum log2(FC) |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1541 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1542 #' Result is an R data.frame with column names |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1543 #' "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1544 #' "Please refer to the original Casado et al. publication for detailed |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1545 #' description of these columns and what they represent: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1546 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1547 #' - Kinase.Gene indicates the gene name for each kinase. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1548 #' - mS represents the mean log2(fold change) of all the |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1549 #' kinase's substrates. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1550 #' - Enrichment is the background-adjusted value of the kinase's mS. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1551 #' - m is the total number of detected substrates |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1552 #' from the experimental dataset for each kinase. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1553 #' - z.score is the normalized score for each kinase, weighted by |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1554 #' the number of identified substrates. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1555 #' - p.value represents the statistical assessment for the z.score. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1556 #' - FDR is the p-value adjusted for multiple hypothesis testing |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1557 #' using the Benjamini & Hochberg method." |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1558 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1559 #' @param ksdata the Kinase-Substrate dataset uploaded from the file |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1560 #' prefaced with "PSP&NetworKIN_" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1561 #' available from github.com/casecpb/KSEA/ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1562 #' @param px the experimental data file formatted as described in |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1563 #' the KSEA.Complete() documentation |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1564 #' @param networkin a binary input of TRUE or FALSE, indicating whether |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1565 #' or not to include NetworKIN predictions, where |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1566 #' \code{NetworKIN = TRUE} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1567 #' means include NetworKIN predictions |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1568 #' @param networkin_cutoff a numeric value between 1 and infinity setting |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1569 #' the minimum NetworKIN score |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1570 #' (this can be omitted if NetworKIN = FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1571 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1572 #' @return creates a new R data.frame with all the KSEA kinase |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1573 #' scores, along with each one's statistical |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1574 #' assessment, as described herein. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1575 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1576 #' @references |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1577 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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1578 #' Casado et al. (2013) Sci Signal. 6(268):rs6 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
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1579 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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1580 #' Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
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1581 #' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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1582 #' Horn et al. (2014) Nature Methods 11(6):603-4 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1583 #' |
|
24
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changeset
|
1584 ksea_scores <- function( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1585 # For human data, typically, ksdata = KSEAapp::ksdata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1586 ksdata, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1587 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1588 # Input data file having columns: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
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1589 # - Protein : abbreviated protein name |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
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1590 # - Gene : HUGO gene name |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
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1591 # - Peptide : peptide sequence without indications of phosphorylation |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1592 # - Reside.Both : position(s) of phosphorylation within Gene sequence |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
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1593 # - First letter designates AA that is modified |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1594 # - Numbers indicate position within Gene |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
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1595 # - Multiple values are separated by semicolons |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1596 # - p : p-value |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
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1597 # - FC : fold-change |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1598 px, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1599 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1600 # A binary input of TRUE or FALSE, indicating whether or not to include |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1601 # NetworKIN predictions |
|
657663e89728
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1602 networkin, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1603 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1604 # A numeric value between 1 and infinity setting the minimum NetworKIN |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1605 # score (can be left out if networkin = FALSE) |
|
27
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1606 networkin_cutoff, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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1607 |
|
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1608 # Minimum substrate count, necessary to adjust the p-value appropriately. |
|
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|
1609 minimum_substrate_count |
|
24
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1610 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1611 ) { |
|
27
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1612 # no px$FC should be <= 0, but abs(px$FC) is used below as a precaution. |
|
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1613 if (length(grep(";", px$Residue.Both)) == 0) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1614 # There are no Residue.Both entries having semicolons, so new is |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1615 # simply px except two columns are renamed and a column is added |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1616 # for log2(abs(fold-change)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1617 new <- px |
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657663e89728
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1618 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD") |
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657663e89728
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|
1619 new$log2_fc <- log2(abs(as.numeric(as.character(new$FC)))) |
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657663e89728
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|
1620 new <- new[complete.cases(new$log2_fc), ] |
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1621 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1622 # Split each row having semicolons in Residue.Both into rows that are |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1623 # duplicated in all respects except that each row has a single |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1624 # member of the set "split-on-semicolon-Residue.Both" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1625 px_double <- px[grep(";", px$Residue.Both), ] |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1626 residues <- as.character(px_double$Residue.Both) |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1627 residues <- as.matrix(residues, ncol = 1) |
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657663e89728
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1628 split <- strsplit(residues, split = ";") |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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1629 # x gets count of residues in each row, |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1630 # i.e., 1 + count of semicolons |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1631 x <- sapply(split, length) |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1632 # Here is the set of split rows |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1633 px_single <- data.frame( |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1634 Protein = rep(px_double$Protein, x), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1635 Gene = rep(px_double$Gene, x), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1636 Peptide = rep(px_double$Peptide, x), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1637 Residue.Both = unlist(split), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1638 p = rep(px_double$p, x), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1639 FC = rep(px_double$FC, x) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1640 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1641 # new first gets the split rows |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1642 new <- px[-grep(";", px$Residue.Both), ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1643 # to new, append the rows that didn't need splitting in the first place |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1644 new <- rbind(new, px_single) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1645 # map Gene to SUB_GENE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1646 # map Residue.Both to SUB_MOD_RSD |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1647 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1648 # Eliminate any non-positive values to prevent introduction of |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1649 # infinite or NaN values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1650 new[(0 <= new$log2_fc), "log2_fc"] <- NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
1651 # Because of preceding step, there is no need for abs in the next line |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
1652 new$log2_fc <- log2(as.numeric(as.character(new$FC))) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
1653 # Convert any illegal values from NaN to NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1654 new[is.nan(new$log2_fc), "log2_fc"] <- NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
1655 # Eliminate rows having missing values (e.g., non-imputed data) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1656 new <- new[complete.cases(new$log2_fc), ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1657 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1658 # At this point, new$log2_fc is signed according to which contrast has |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1659 # the greater intensity |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1660 # To take the magnitude into account without taking the direction into |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1661 # account, set params$kseaUseAbsoluteLog2FC to TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1662 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1663 # Should KSEA be performed aggregating signed log2FC or absolute? |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1664 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1665 if (params$kseaUseAbsoluteLog2FC) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
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|
1666 # TRUE use abs(log2FC) for KSEA as Justin requested; this is a |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1667 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1668 new$log2_fc <- abs(new$log2_fc) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1669 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1670 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1671 monitor_filtration_on_stderr <- TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1672 if (monitor_filtration_on_stderr) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1673 # set to TRUE to monitor filtration on stderr |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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|
1674 sink(stderr()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1675 cat(see_variable(networkin, "\n")) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
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|
1676 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1677 ksdata_filtered <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1678 sqldf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1679 sprintf("%s %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1680 "select * from ksdata where not Source = 'NetworKIN'", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1681 if (networkin) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1682 sprintf("or networkin_score >= %d", networkin_cutoff) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
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|
1683 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1684 "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1685 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1686 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
1687 if (monitor_filtration_on_stderr) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
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|
1688 cat(see_variable(sqldf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1689 "select count(*), Source from ksdata group by Source"), "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
1690 cat(see_variable(sqldf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
1691 "select count(*), Source from ksdata_filtered group by Source"), "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1692 sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1693 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1694 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1695 ############################################################################ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1696 # Line numbers below refer to lines of: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
1697 # https://github.com/casecpb/KSEAapp/blob/master/R/KSEA.Scores.R |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1698 # I would put the original line in a comment but then lint would complain... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1699 # - Indeed, I had to rename all the variables because lint didn't like names |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1700 # containing periods or capital letters. |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1701 # ACE |
|
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|
1702 ############################################################################ |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1703 # |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1704 # (1) Join the two data.frames on common columns SUB_GENE and SUB_MOD_RSD |
|
24
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|
1705 # colnames of ksdata_filtered: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1706 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" "SUB_GENE_ID" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1707 # "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" "SITE_GRP_ID" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1708 # "SITE_...7_AA" "networkin_score" "Source" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1709 # colnames of new: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
1710 # "Protein" "SUB_GENE" "Peptide" "SUB_MOD_RSD" "p" "FC" "log2_fc" |
|
657663e89728
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|
1711 # Equivalent to: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1712 # SELECT a.*. b.Protein, b.Peptide, b.p, b.FC, b.log2_fc |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1713 # FROM ksdata_filtered a |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1714 # INNER JOIN new b |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1715 # ON a.SUB_GENE = b.SUB_GENE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
1716 # AND a.SUB_MOD_RSD = b.SUB_MOD_RSD |
|
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|
1717 # (KSEA.Scores.R line # 105) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1718 # "Extract KSData.filtered annotations that are only found in new" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1719 ksdata_dataset <- base::merge(ksdata_filtered, new) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1720 # colnames of ksdata_dataset: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1721 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1722 # "SUB_GENE_ID" "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1723 # "SITE_GRP_ID" "SITE_...7_AA" "networkin_score" "Source" "Protein" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1724 # "Peptide" "p" "FC" "log2_fc" (uniprot_no_isoform) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1725 # Re-order dataset; prior to accounting for isoforms |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1726 # (KSEA.Scores.R line # 106) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1727 ksdata_dataset <- ksdata_dataset[order(ksdata_dataset$GENE), ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1728 # Extract non-isoform accession in UniProtKB |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1729 # (KSEA.Scores.R line # 107) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1730 ksdata_dataset$uniprot_no_isoform <- sapply( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1731 ksdata_dataset$KIN_ACC_ID, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1732 function(x) unlist(strsplit(as.character(x), split = "-"))[1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1733 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1734 # "last expression collapses isoforms ... for easy processing" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1735 # Discard previous results while selecting interesting columns ... |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
1736 # (KSEA.Scores.R line # 110) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1737 ksdata_dataset_abbrev <- ksdata_dataset[, c(5, 1, 2, 16:19, 14)] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1738 # Column names are now: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1739 # "GENE" "SUB_GENE" "SUB_MOD_RSD" "Peptide" "p" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1740 # "FC" "log2_fc" "Source" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
1741 # Make column names human-readable |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
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|
1742 # (KSEA.Scores.R line # 111) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1743 colnames(ksdata_dataset_abbrev) <- c( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1744 "Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1745 "FC", "log2FC", "Source" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1746 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1747 # SELECT * FROM ksdata_dataset_abbrev |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1748 # ORDER BY Kinase.Gene, Substrate.Gene, Substrate.Mod, p |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
1749 # (KSEA.Scores.R line # 112) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1750 # "Extract KSData.filtered annotations that are only found in new" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1751 ksdata_dataset_abbrev <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1752 ksdata_dataset_abbrev[ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1753 order( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1754 ksdata_dataset_abbrev$Kinase.Gene, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1755 ksdata_dataset_abbrev$Substrate.Gene, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1756 ksdata_dataset_abbrev$Substrate.Mod, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1757 ksdata_dataset_abbrev$p), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1758 ] |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
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|
1759 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev)) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1760 # First aggregation step to account for multiply phosphorylated peptides |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1761 # and differing peptide sequences; the goal here is to combine results |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1762 # for all measurements of the same substrate. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1763 # SELECT `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1764 # `Source`, avg(log2FC) AS log2FC |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1765 # FROM ksdata_dataset_abbrev |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1766 # GROUP BY `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1767 # `Source` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1768 # ORDER BY `Kinase.Gene`; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1769 # in two steps: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1770 # (1) compute average log_2(fold-change) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
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|
1771 # "take the mean of the log2FC amongst phosphosite duplicates" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1772 # (KSEA.Scores.R line # 115) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1773 ksdata_dataset_abbrev <- aggregate( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1774 log2FC ~ Kinase.Gene + Substrate.Gene + Substrate.Mod + Source, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
1775 data = ksdata_dataset_abbrev, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1776 FUN = mean |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1777 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1778 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev)) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1779 # (2) order by Kinase.Gene |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
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|
1780 # (KSEA.Scores.R line # 117) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1781 ksdata_dataset_abbrev <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1782 ksdata_dataset_abbrev[order(ksdata_dataset_abbrev$Kinase.Gene), ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1783 # SELECT `Kinase.Gene`, count(*) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1784 # FROM ksdata_dataset_abbrev |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1785 # GROUP BY `Kinase.Gene`; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1786 # in two steps: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
1787 # (1) Extract the list of Kinase.Gene names |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1788 # "@@@@@@@@@@@@@@@@@@@@" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
1789 # "Do analysis for KSEA" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
1790 # "@@@@@@@@@@@@@@@@@@@@" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
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|
1791 # (KSEA.Scores.R line # 124) |
|
24
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1792 kinase_list <- as.vector(ksdata_dataset_abbrev$Kinase.Gene) |
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1793 # (2) Convert to a named list of counts of kinases in ksdata_dataset_abrev, |
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1794 # named by Kinase.Gene |
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1795 # (KSEA.Scores.R line # 125) |
|
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1796 kinase_list <- as.matrix(table(kinase_list)) |
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1797 # Second aggregation step to account for all substrates per kinase |
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1798 # CREATE TABLE mean_fc |
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1799 # AS |
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1800 # SELECT `Kinase.Gene`, avg(log2FC) AS log2FC |
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1801 # FROM ksdata_dataset_abbrev |
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1802 # GROUP BY `Kinase.Gene` |
|
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1803 # (KSEA.Scores.R line # 127) |
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1804 if (print_nb_messages) nb(see_variable(ksdata_dataset_abbrev), "\n") |
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1805 mean_fc <- |
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1806 aggregate( |
|
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1807 log2FC ~ Kinase.Gene, |
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1808 data = ksdata_dataset_abbrev, |
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1809 FUN = mean |
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1810 ) |
|
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1811 if (print_nb_messages) nbe(see_variable(mean_fc), "\n") |
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1812 |
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1813 # for contrast j |
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1814 # for each kinase i |
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1815 # extract log2 of fold-change (from `new` above) |
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1816 # (used in KSEA.Scores.R lines # 130 & 132) |
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1817 log2_fc_j_each_i <- |
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1818 new$log2_fc |
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1819 |
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1820 # for contrast j |
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1821 # for all kinases i |
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1822 # compute mean of abs(log2 of fold-change) |
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1823 # (used in KSEA.Scores.R lines # 130) |
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1824 mean_abs_log2_fc_j_all_i <- |
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1825 mean(abs(log2_fc_j_each_i), na.rm = TRUE) |
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1826 |
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1827 # for contrast j |
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1828 # for all kinases i |
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1829 # compute mean of log2 of fold-change |
|
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1830 # (used in KSEA.Scores.R lines # 132) |
|
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1831 mean_log2_fc_j_all_i <- |
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1832 mean(log2_fc_j_each_i, na.rm = TRUE) |
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1833 |
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1834 # Reorder mean_fc, although I don't see why |
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1835 # (KSEA.Scores.R line 128 |
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1836 mean_fc <- mean_fc[order(mean_fc[, 1]), ] |
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1837 # mean_fc columns so far: "Kinase.Gene", "log2FC" |
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1838 # - Kinase.Gene |
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1839 # indicates the gene name for each kinase. |
|
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1840 |
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1841 # Create column 3: mS |
|
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1842 # - mS |
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1843 # represents the mean log2(fold change) of all the |
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1844 # kinase's substrates. |
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1845 # (KSEA.Scores.R line # 129) |
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1846 mean_fc$m_s <- |
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1847 mean_fc_m_s <- mean_fc[, 2] |
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|
1848 |
|
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1849 # Create column 4: Enrichment |
|
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1850 # - Enrichment |
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1851 # is the background-adjusted value of the kinase's mS. |
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1852 # (KSEA.Scores.R line # 130) |
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|
1853 mean_fc$enrichment <- |
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1854 mean_fc_m_s / mean_abs_log2_fc_j_all_i |
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1855 |
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1856 # Create column 5: m, count of substrates of kinase (count of j for i) |
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1857 # - m |
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1858 # is the total number of detected substrates |
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1859 # from the experimental dataset for each kinase. |
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1860 # (KSEA.Scores.R line # 131) |
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1861 mean_fc$m <- |
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1862 mean_fc_m <- kinase_list |
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1863 |
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1864 |
|
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1865 # Create column 6: z-score |
|
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1866 # - z.score |
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1867 # is the normalized score for each kinase, weighted by |
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1868 # the number of identified substrates. |
|
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|
1869 # (KSEA.Scores.R line # 132) |
|
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|
1870 mean_fc$z_score <- |
|
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1871 (mean_fc_m_s - mean_log2_fc_j_all_i) * sqrt(mean_fc_m) / |
|
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1872 sd(log2_fc_j_each_i, na.rm = TRUE) |
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|
1873 |
|
24
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|
1874 # Create column 7: p-value, deduced from z-score |
|
27
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|
1875 # - p.value |
|
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|
1876 # represents the statistical assessment for the z.score. |
|
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1877 # (KSEA.Scores.R line # 133) |
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|
1878 # "one-tailed p-value" |
|
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|
1879 mean_fc$p_value <- |
|
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1880 pnorm(-abs(mean_fc$z_score)) |
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1881 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
1882 # zap excluded kinases; this must be done before adjusting p-value |
|
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1883 if (TRUE) { |
|
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1884 mean_fc <- |
|
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1885 mean_fc[ |
|
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1886 mean_fc$m >= minimum_substrate_count, |
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1887 , |
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|
1888 drop = FALSE |
|
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1889 ] |
|
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1890 } |
|
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1891 |
|
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1892 #ACE nb(see_variable(nrow(mean_fc)), "\n") |
|
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1893 # Create column 8: FDR, deduced by Benjamini-Hochberg adustment from p-value |
|
27
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1894 # - FDR |
|
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1895 # is the p-value adjusted for multiple hypothesis testing |
|
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1896 # using the Benjamini & Hochberg method." |
|
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1897 # (KSEA.Scores.R line # 134) |
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1898 mean_fc$fdr <- |
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1899 p.adjust(mean_fc$p_value, method = "fdr") |
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1900 |
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1901 # It makes no sense to leave Z-scores negative when using |
|
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1902 # absolute value of fold-change |
|
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1903 if (params$kseaUseAbsoluteLog2FC) { |
|
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1904 mean_fc$z_score <- abs(mean_fc$z_score) |
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1905 } |
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1906 |
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1907 # Remove second column (log2FC), which is duplicated as mS |
|
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1908 # (KSEA.Scores.R line # 136) |
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1909 mean_fc <- |
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1910 mean_fc[order(mean_fc$Kinase.Gene), -2] |
|
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1911 # Correct the column names which we had to hack because of the linter... |
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1912 colnames(mean_fc) <- c( |
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1913 "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR" |
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1914 ) |
|
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1915 # (KSEA.Scores.R line # 138) |
|
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1916 return(mean_fc) |
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1917 } |
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1918 |
|
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1919 ksea_low_fdr_barplot_factory <- function( |
|
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1920 rslt, |
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1921 i_cntrst, |
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1922 i, |
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1923 a_level, |
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1924 b_level, |
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1925 fold_change, |
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1926 caption |
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1927 ) { |
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1928 rslt_score_list_i <- rslt$score_list[[i]] |
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1929 if (!is.null(rslt_score_list_i)) { |
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1930 rslt_score_list_i_nrow <- nrow(rslt_score_list_i) |
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1931 k <- data.frame( |
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1932 contrast = as.integer(i_cntrst), |
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1933 a_level = rep.int(a_level, rslt_score_list_i_nrow), |
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1934 b_level = rep.int(b_level, rslt_score_list_i_nrow), |
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1935 kinase_gene = rslt_score_list_i$Kinase.Gene, |
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1936 mean_log2_fc = rslt_score_list_i$mS, |
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1937 enrichment = rslt_score_list_i$Enrichment, |
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1938 substrate_count = rslt_score_list_i$m, |
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1939 z_score = rslt_score_list_i$z.score, |
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1940 p_value = rslt_score_list_i$p.value, |
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1941 fdr = rslt_score_list_i$FDR |
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1942 ) |
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1943 selector <- switch( |
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1944 ksea_cutoff_statistic, |
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1945 "FDR" = { |
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1946 k$fdr |
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1947 }, |
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1948 "p.value" = { |
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1949 k$p_value |
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1950 }, |
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1951 { |
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1952 cat( |
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1953 sprintf( |
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1954 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
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1955 ksea_cutoff_statistic |
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1956 ) |
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1957 ) |
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1958 param_df_exit() |
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1959 knitr::knit_exit() |
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1960 } |
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1961 ) |
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1962 |
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1963 k <- k[selector < ksea_cutoff_threshold, ] |
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1964 nrow_k <- nrow(k) |
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1965 |
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1966 #ACE nbe(see_variable(fdr_barplot_dataframe <- k)) |
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1967 |
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1968 if (nrow_k > 0) { |
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1969 max_nchar_rowname <- max(nchar(rownames(k))) |
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1970 my_cex_names <- 1.0 / (1 + nrow_k / 50) |
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1971 |
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1972 if (print_trace_messages) cat_margins("Initially") |
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1973 if (print_trace_messages) cat_variable(nrow_k, "\n\n", 0) |
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1974 if (print_trace_messages) cat_variable(my_cex_names, "\n\n", 0) |
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1975 if (print_trace_messages) cat_variable(max_nchar_rowname, "\n\n", 0) |
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1976 |
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1977 # fin: The figure region dimensions, (width, height), in inches. |
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1978 # mar: A numerical vector of the form c(bottom, left, top, right) |
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1979 # that gives the number of lines of margin to be specified |
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1980 # on the four sides of the plot; default: c(5, 4, 4, 2) + 0.1 |
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1981 |
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1982 # mar: The figure region dimensions, (width, height), in inches. |
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1983 numeric_z_score <- as.numeric(k$z_score) |
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1984 bar_order <- order(-as.numeric(k$p_value)) |
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1985 kinase_name <- k$kinase_gene |
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1986 long_caption <- |
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1987 sprintf( |
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1988 "Kinase z-score, %s, KSEA %s < %s", |
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1989 caption, |
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1990 ksea_cutoff_statistic, |
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1991 ksea_cutoff_threshold |
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1992 ) |
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1993 my_cex_caption <- 65.0 / max(65.0, nchar(long_caption)) |
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1994 # return a function that draws the plot |
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1995 function() { |
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1996 par_fin <- par("fin") # vector of width_in_inches and height_in_inches) |
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1997 op <- par( |
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1998 bg = if (print_trace_messages) "yellow" else "white", |
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1999 fin = c(par_fin[1], min(par_fin[2], 2.5 + nrow_k / 6)), |
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2000 mar = par("mar") + |
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2001 c(3 / nrow_k, (1 + max_nchar_rowname * my_cex_names) / 2, 0, 0) |
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2002 # bottom, left, top, right |
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2003 ) |
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2004 on.exit(par(op)) |
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2005 if (print_trace_messages) cat_margins("Eventually") |
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2006 |
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2007 barplot( |
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2008 height = numeric_z_score[bar_order], |
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2009 border = NA, |
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2010 xpd = FALSE, |
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2011 cex.names = my_cex_names, |
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2012 main = long_caption, |
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2013 cex.main = my_cex_caption, |
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2014 names.arg = kinase_name[bar_order], |
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2015 horiz = TRUE, |
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2016 srt = 45, |
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2017 las = 1, |
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2018 cex.axis = 0.9 |
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|
2019 ) |
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2020 } |
|
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2021 } |
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27
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2022 } else { |
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2023 no_op |
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2024 } |
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changeset
|
2025 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2026 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2027 # note that this adds elements to the global variable `ksea_asterisk_hash` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2028 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2029 ksea_low_fdr_print <- function( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2030 rslt, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2031 i_cntrst, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2032 i, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2033 a_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2034 b_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2035 fold_change, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2036 caption, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2037 write_db = TRUE, # if TRUE, write to DB, else print table |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2038 anchor = c(const_table_anchor_p, const_table_anchor_t) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2039 ) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2040 rslt_score_list_i <- rslt$score_list[[i]] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2041 if (!is.null(rslt_score_list_i)) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
2042 rslt_score_list_i_nrow <- nrow(rslt_score_list_i) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
2043 k <- contrast_ksea_scores <- data.frame( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2044 contrast = as.integer(i_cntrst), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2045 a_level = rep.int(a_level, rslt_score_list_i_nrow), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2046 b_level = rep.int(b_level, rslt_score_list_i_nrow), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2047 kinase_gene = rslt_score_list_i$Kinase.Gene, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2048 mean_log2_fc = rslt_score_list_i$mS, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2049 enrichment = rslt_score_list_i$Enrichment, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2050 substrate_count = rslt_score_list_i$m, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2051 z_score = rslt_score_list_i$z.score, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2052 p_value = rslt_score_list_i$p.value, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
2053 fdr = rslt_score_list_i$FDR |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2054 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2055 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2056 selector <- switch( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2057 ksea_cutoff_statistic, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2058 "FDR" = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2059 k$fdr |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2060 }, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2061 "p.value" = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2062 k$p_value |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2063 }, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2064 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2065 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2066 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2067 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2068 ksea_cutoff_statistic |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2069 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2070 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2071 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2072 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2073 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2074 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2075 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2076 k <- k[selector < ksea_cutoff_threshold, ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2077 # save kinase names to ksea_asterisk_hash |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2078 for (kinase_name in k$kinase_gene) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2079 ksea_asterisk_hash[[kinase_name]] <- 1 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2080 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2081 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2082 if (write_db) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2083 db_write_table_overwrite <- (i_cntrst < 2) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2084 db_write_table_append <- !db_write_table_overwrite |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2085 RSQLite::dbWriteTable( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2086 conn = db, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2087 name = "contrast_ksea_scores", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2088 value = contrast_ksea_scores, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2089 append = db_write_table_append |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2090 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2091 "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2092 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2093 selector <- switch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2094 ksea_cutoff_statistic, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2095 "FDR" = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2096 contrast_ksea_scores$fdr |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2097 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2098 "p.value" = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2099 contrast_ksea_scores$p_value |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2100 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2101 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2102 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2103 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2104 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2105 ksea_cutoff_statistic |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2106 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2107 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2108 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2109 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2110 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2111 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2112 if (print_nb_messages) nbe(see_variable(contrast_ksea_scores)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2113 output_df <- contrast_ksea_scores[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2114 selector < ksea_cutoff_threshold, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2115 c("kinase_gene", "mean_log2_fc", "enrichment", "substrate_count", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2116 "z_score", "p_value", "fdr") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2117 ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2118 output_df$kinase_gene <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2119 gsub( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2120 "_", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2121 "\\\\_", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2122 output_df$kinase_gene |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2123 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2124 colnames(output_df) <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2125 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2126 colnames(output_df)[1], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2127 colnames(output_df)[2], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2128 "enrichment", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2129 "m_s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2130 "z_score", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2131 "p_value", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2132 "fdr" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2133 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2134 #ACE output_order <- with(output_df, order(fdr)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2135 output_order <- with(output_df, order(p_value)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2136 output_df <- output_df[output_order, ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2137 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2138 output_df[, 2] <- sprintf("%0.3g", output_df[, 2]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2139 output_df$fdr <- sprintf("%0.4f", output_df$fdr) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2140 output_df$p_value <- sprintf("%0.2e", output_df$p_value) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2141 output_df$z_score <- sprintf("%0.2f", output_df$z_score) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
2142 output_df$m_s <- sprintf("%d", output_df$m_s) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
2143 output_df$enrichment <- sprintf("%0.3g", output_df$enrichment) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2144 output_ncol <- ncol(output_df) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2145 colnames(output_df) <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2146 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2147 "Kinase", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2148 "\\(\\overline{{\\lvert}\\log_2 (\\text{fold-change}){\\rvert}}\\)", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2149 "Enrichment", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2150 "Substrates", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2151 "z-score", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2152 "p-value", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2153 "FDR" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2154 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2155 selector <- switch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2156 ksea_cutoff_statistic, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2157 "FDR" = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2158 rslt$score_list[[i]]$FDR |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2159 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2160 "p.value" = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2161 rslt$score_list[[i]]$p.value |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2162 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2163 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2164 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2165 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2166 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2167 ksea_cutoff_statistic |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2168 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2169 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2170 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2171 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2172 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2173 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2174 if (sum(selector < ksea_cutoff_threshold) > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2175 if (print_nb_messages) nbe(see_variable(output_df)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2176 math_caption <- gsub("{", "\\{", caption, fixed = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2177 math_caption <- gsub("}", "\\}", math_caption, fixed = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2178 # with ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2179 # output_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
2180 # ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2181 if (TRUE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2182 output_df$Kinase <- whack_underscores(output_df$Kinase) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2183 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2184 x = output_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2185 # vector of tab stops, in inches |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2186 tabstops = c(1.0, 1.2, 1.0, 1.0, 1.0, 1.0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2187 # vector of headings, registered with tab-stops |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2188 headings = colnames(output_df), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2189 # digits to pass to format.data.frame |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2190 digits = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2191 # maximumn number of rows to print |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2192 max = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2193 # optional caption |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2194 caption = sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2195 "\\text{%s}, KSEA %s < %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2196 math_caption, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2197 ksea_cutoff_statistic, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2198 ksea_cutoff_threshold |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2199 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2200 # set underscore_whack to TRUE to escape underscores |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2201 underscore_whack = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2202 # flag for landscape mode |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2203 landscape = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2204 # flag indicating that subsubsection should be used for caption |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2205 # rather than subsection |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2206 use_subsubsection_header = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2207 # character-size indicator; for possible values, see: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2208 # https://tug.org/texinfohtml/latex2e.html#Font-sizes |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2209 charactersize = "small", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2210 # set verbatim to TRUE to debug output |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2211 verbatim = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2212 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2213 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2214 data_frame_table_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2215 x = output_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2216 justification = "l c c c c c c", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2217 centered = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2218 caption = sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2219 "\\text{%s}, KSEA %s < %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2220 math_caption, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2221 ksea_cutoff_statistic, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2222 ksea_cutoff_threshold |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2223 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2224 anchor = anchor, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2225 underscore_whack = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2226 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2227 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2228 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2229 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2230 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2231 "\\break |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2232 No kinases had |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2233 \\(\\text{KSEA %s}_\\text{enrichment} < %s\\) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2234 for contrast %s\\hfill\\break\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2235 ksea_cutoff_statistic, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2236 ksea_cutoff_threshold, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2237 caption |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2238 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2239 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2240 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2241 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2242 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2243 "" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2244 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2245 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2246 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2247 # create_breaks is a helper for ksea_heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2248 create_breaks <- function(merged_scores) { |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2249 if (sum(!is.na(merged_scores)) < 2) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2250 return(NULL) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2251 if (min(merged_scores, na.rm = TRUE) < -1.6) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2252 breaks_neg <- seq(-1.6, 0, length.out = 30) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2253 breaks_neg <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2254 append( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2255 seq(min(merged_scores, na.rm = TRUE), -1.6, length.out = 10), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2256 breaks_neg |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2257 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2258 breaks_neg <- sort(unique(breaks_neg)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2259 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2260 breaks_neg <- seq(-1.6, 0, length.out = 30) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2261 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2262 if (max(merged_scores, na.rm = TRUE) > 1.6) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2263 breaks_pos <- seq(0, 1.6, length.out = 30) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2264 breaks_pos <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2265 append( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2266 breaks_pos, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2267 seq(1.6, max(merged_scores, na.rm = TRUE), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2268 length.out = 10) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2269 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2270 breaks_pos <- sort(unique(breaks_pos)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2271 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2272 breaks_pos <- seq(0, 1.6, length.out = 30) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2273 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2274 breaks_all <- unique(append(breaks_neg, breaks_pos)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2275 mycol_neg <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2276 gplots::colorpanel(n = length(breaks_neg), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2277 low = "blue", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2278 high = "white") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2279 mycol_pos <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2280 gplots::colorpanel(n = length(breaks_pos) - 1, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2281 low = "white", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2282 high = "red") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2283 mycol <- unique(append(mycol_neg, mycol_pos)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2284 color_breaks <- list(breaks_all, mycol) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2285 return(color_breaks) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2286 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2287 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2288 hm2plus <- function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2289 x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2290 mat = matrix( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2291 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2292 c(0, 4, 0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2293 c(0, 3, 3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2294 c(2, 1, 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2295 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2296 nrow = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2297 ncol = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2298 byrow = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2299 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2300 denwid = 0.5, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2301 denhgt = 0.15, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2302 widths = c(0.5, 2.5, 1.5), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2303 heights = c(0.4, 0.15, 3.95), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2304 divergent = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2305 notecol = "grey50", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2306 trace = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2307 margins = c(6, 20), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2308 srtcol = 90, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2309 srtrow = 0, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2310 density_info = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2311 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2312 key_par = list(), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2313 hclustfun = hclust, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2314 ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2315 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2316 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2317 varargs <- list(...) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2318 if (FALSE) # this is to avoid commenting out code to pass linting... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2319 my_hm2 <- latex_show_invocation(heatmap.2, head_patch = FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2320 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2321 my_hm2 <- heatmap.2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2322 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2323 x <- as.matrix(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2324 if (sum(!is.na(x)) < 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2325 return(NULL) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2326 color_count <- 1 + max(64, length(as.vector(x))) # 8 was not enough |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2327 break_count <- 1 + color_count |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2328 min_nonax <- min(x, na.rm = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2329 max_nonax <- max(x, na.rm = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2330 if (print_nb_messages) nb("within hm2plus", see_variable(divergent), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2331 if (divergent) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2332 zlim <- max(abs(min_nonax), abs(max_nonax)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2333 if (print_nb_messages) nb(see_variable(pre_zlim <- zlim, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2334 breaks <- (zlim) / (break_count:1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2335 if (print_nb_messages) nb(see_variable(breaks, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2336 breaks <- breaks - median(breaks) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2337 zlim <- c(-zlim, zlim) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2338 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2339 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2340 zlim <- max(abs(min_nonax), abs(max_nonax)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2341 if (print_nb_messages) nb(see_variable(pre_zlim <- zlim, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2342 breaks <- zlim / (break_count:1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2343 if (print_nb_messages) nb(see_variable(breaks, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2344 if (max_nonax < 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2345 breaks <- breaks - zlim |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2346 zlim <- c(-zlim, 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2347 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2348 zlim <- c(0, zlim) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2349 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2350 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2351 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2352 nonax <- x |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2353 nonax[is.na(x)] <- min_nonax |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2354 if (is.null(widths)) widths <- c(denwid, 4 - denwid, 1.5) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2355 if (is.null(heights)) heights <- c(0.4, denhgt, 4.0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2356 colors <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2357 if (divergent && min_nonax < 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2358 # divergent colors on both sides of zero |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2359 colorRampPalette(c("red", "white", "blue"))(color_count) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2360 } else if (divergent && min_nonax > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2361 # "divergent" colors > zero |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2362 colorRampPalette(c("white", "blue"))(color_count) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2363 } else if (divergent && max_nonax < 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2364 # "divergent" colors < zero |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2365 colorRampPalette(c("red", "white"))(color_count) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2366 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2367 # "non-divergent" colors including zero |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2368 hcl.colors(color_count, "YlOrRd", rev = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2369 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2370 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2371 #ACE if (print_nb_messages) nb("within hm2plus", see_variable(key_par), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2372 #ACE if (print_nb_messages) nb(see_variable(colors, "\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2373 #ACE key_par$col = colors |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2374 #ACE key_par$breaks = breaks |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2375 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2376 if (print_nb_messages) nb(see_variable(par(), "\n")) #ACE TODO remove me |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2377 if (print_nb_messages) cat("\\leavevmode\n\\linebreak\n") #ACE TODO remove me |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2378 suppressWarnings( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2379 my_hm2( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2380 x = x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2381 col = colors, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2382 #ACE symkey = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2383 density.info = density_info, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2384 srtCol = srtcol, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2385 srtRow = srtrow, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2386 margins = margins, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2387 lwid = widths, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2388 lhei = heights, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2389 key.title = NA, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2390 key.xlab = key_xlab, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2391 key.par = key_par, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2392 lmat = mat, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2393 notecol = notecol, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2394 trace = trace, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2395 bg = "yellow", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2396 hclustfun = hclustfun, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2397 #ACE breaks = breaks, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2398 oldstyle = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2399 ... # varargs |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2400 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2401 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2402 # implicitly returning value returned by heatmap.2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2403 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2404 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2405 # draw_kseaapp_summary_heatmap is a helper function for ksea_heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2406 draw_kseaapp_summary_heatmap <- function( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2407 x, # matrix with row/col names already formatted |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2408 sample_cluster, # a binary input of TRUE or FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2409 # indicating whether or not to perform |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
2410 # hierarchical clustering of the sample columns |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2411 merged_asterisk, # matrix having dimensions of x, values "*" or "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2412 color_breaks, # breaks for color gradation, from create_breaks |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
2413 # passed to `breaks` argument of `image` |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
2414 margins = c(8, 15), # two integers setting the bottom and right margins |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
2415 # to accommodate row and column labels |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
2416 master_cex = 0.7, # basis for text sizes |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2417 ... |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2418 ) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2419 merged_scores <- x |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2420 if (!is.matrix(x)) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2421 cat( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2422 paste0( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2423 "No plot because \\texttt{typeof(x)} is '", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2424 typeof(x), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2425 "' rather than 'matrix'.\n\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2426 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2427 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2428 cat_variable(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2429 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2430 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2431 if (print_trace_messages) cat(sprintf("master_cex = %03f\n\n", master_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2432 nrow_x <- nrow(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2433 ncol_x <- ncol(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2434 #if (nrow_x < 2) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2435 if (nrow_x < 1) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2436 cat("No plot because matrix has no rows.\n\n") |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2437 return(FALSE) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2438 } else if (nrow_x < 2) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2439 cat("No plot because matrix has one row. Matrix looks like this:\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2440 cat("\n\\begin{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2441 print(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2442 cat("\n\\end{verbatim}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2443 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2444 } else if (ncol_x < 2) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2445 cat("No plot because matrix x has ", ncol_x, " columns.\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2446 cat_variable(x) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2447 return(FALSE) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2448 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2449 max_nchar_rowname <- max(nchar(rownames(x))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2450 max_nchar_colname <- max(nchar(colnames(x))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2451 my_limit <- g_intensity_hm_rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2452 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2453 my_row_cex_scale <- master_cex * 150 / nrow_x |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2454 my_col_cex_scale <- 3.0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2455 my_asterisk_scale <- 0.4 * my_row_cex_scale |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2456 my_row_warp <- 1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2457 my_note_warp <- 2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2458 my_row_warp <- 1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2459 my_row_cex_asterisk <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2460 master_cex * my_row_warp * my_asterisk_scale |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2461 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2462 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2463 my_col_cex <- my_col_cex_scale * master_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2464 my_row_cex <- min(3.5 * my_row_cex_asterisk, my_col_cex) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2465 my_key_cex <- 1.286 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2466 my_hm2_cex <- 1 * master_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2467 my_offset <- (4.8 / (9 + nrow_x / 10)) - 0.4 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2468 if (print_trace_messages) cat(sprintf("nrow_x = %03f\n\n", nrow_x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2469 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2470 my_offset <- 0.05 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2471 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2472 my_scale <- 3.0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2473 if (ncol_x < 10 && nrow_x < 10) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2474 my_scale <- my_scale * 10 / (10 - nrow_x) * 10 / (10 - ncol_x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2475 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2476 my_heights <- c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2477 0.15, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2478 3.85 - my_offset, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2479 0.5 + my_offset |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2480 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2481 my_margins <- c(1, 1) + |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2482 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2483 margins[1] * 0.08 * max_nchar_colname * my_col_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2484 margins[2] * 0.04 * max_nchar_rowname * my_row_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2485 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2486 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2487 my_notecex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2488 my_scale * |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2489 min( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2490 1.1, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2491 my_row_cex_asterisk * my_note_warp, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2492 my_col_cex * my_note_warp |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2493 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2494 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2495 if (print_trace_messages) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2496 cat_variable(my_heights, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2497 cat_variable(my_margins, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2498 cat_variable(my_row_cex_scale, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2499 cat_variable(my_col_cex_scale, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2500 cat_variable(my_row_cex_asterisk, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2501 cat_variable(my_row_cex, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2502 cat_variable(my_col_cex, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2503 cat_variable(my_row_cex, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2504 cat_variable(my_col_cex, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2505 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2506 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2507 hm2plus( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2508 x = merged_scores, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2509 Colv = sample_cluster, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2510 cellnote = merged_asterisk, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2511 cex = my_hm2_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2512 cexCol = my_col_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2513 cexRow = my_row_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2514 denhgt = 0.15, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2515 density_info = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2516 denwid = 0.5, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2517 divergent = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2518 key_par = list(cex = my_key_cex), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2519 key_xlab = "Z-score", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2520 margins = my_margins, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2521 notecex = my_scale * min( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2522 1.5, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2523 my_row_cex_asterisk * my_note_warp, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2524 my_col_cex * my_note_warp |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2525 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2526 notecol = "white", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2527 scale = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2528 srtcol = 90, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2529 srtrow = 0, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2530 trace = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2531 mat = matrix( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2532 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2533 c(0, 3, 3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2534 c(2, 1, 1), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2535 c(0, 4, 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2536 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2537 nrow = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2538 ncol = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2539 byrow = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2540 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2541 widths = c(0.5, 3.1, 0.9), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2542 heights = my_heights, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2543 ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2544 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2545 return(TRUE) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2546 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2547 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2548 # function drawing heatmap of contrast fold-change for each kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2549 # adapted from KSEAapp::KSEA.Heatmap |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2550 ksea_heatmap <- function( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2551 # the data frame outputs from the KSEA.Scores() function, in list format |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2552 score_list, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2553 # a character vector of all the sample names for heatmap annotation: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2554 # - the names must be in the same order as the data in score_list |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2555 # - please avoid long names, as they may get cropped in the final image |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2556 sample_labels, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2557 # character string of either "p.value" or "FDR" indicating the data column |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2558 # to use for marking statistically significant scores |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2559 stats, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2560 # a numeric value between 0 and infinity indicating the min. number of |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2561 # substrates a kinase must have to be included in the heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2562 m_cutoff, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2563 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2564 # for indicating significant kinases in the heatmap |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2565 p_cutoff = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2566 cat("argument 'p_cutoff' is required for function 'ksea_heatmap'") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2567 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2568 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2569 }, |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2570 # a binary input of TRUE or FALSE, indicating whether or not to perform |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2571 # hierarchical clustering of the sample columns |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2572 sample_cluster, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2573 # a binary input of TRUE or FALSE, indicating whether or not to export |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2574 # the heatmap as a .png image into the working directory |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2575 export = FALSE, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2576 # bottom and right margins; adjust as needehttps://tex.stackexchange.com/a/56795d if contrast names are too long |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2577 margins = c(6, 6), |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2578 # print which kinases? |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2579 # - Mandatory argument, must be one of const_ksea_.*_kinases |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2580 which_kinases, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2581 # additional arguments to gplots::heatmap.2, such as: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2582 # - main: main title of plot |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2583 # - xlab: x-axis label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2584 # - ylab: y-axis label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2585 ... |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2586 ) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2587 filter_m <- function(dataset, m_cutoff) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2588 filtered <- dataset[(dataset$m >= m_cutoff), ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2589 return(filtered) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2590 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2591 score_list_m <- lapply(score_list, function(...) filter_m(..., m_cutoff)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2592 for (i in seq_len(length(score_list_m))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2593 names <- colnames(score_list_m[[i]])[c(2:7)] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2594 colnames(score_list_m[[i]])[c(2:7)] <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2595 paste(names, i, sep = ".") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2596 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2597 master <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2598 Reduce( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2599 f = function(...) { |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
24
diff
changeset
|
2600 base::merge(..., by = "Kinase.Gene", all = TRUE) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2601 }, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2602 x = score_list_m |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2603 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2604 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2605 row.names(master) <- master$Kinase.Gene |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2606 columns <- as.character(colnames(master)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2607 merged_scores <- as.matrix(master[, grep("z.score", columns), drop = FALSE]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2608 colnames(merged_scores) <- sample_labels |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2609 merged_stats <- as.matrix(master[, grep(stats, columns)]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2610 asterisk <- function(mtrx, p_cutoff) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2611 new <- data.frame() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2612 for (i in seq_len(nrow(mtrx))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2613 for (j in seq_len(ncol(mtrx))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2614 my_value <- mtrx[i, j] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2615 if (!is.na(my_value) && my_value < p_cutoff) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2616 new[i, j] <- "*" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2617 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2618 new[i, j] <- "" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2619 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2620 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2621 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2622 return(new) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2623 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2624 merged_asterisk <- as.matrix(asterisk(merged_stats, p_cutoff)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2625 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2626 asterisk_rows <- rowSums(merged_asterisk == "*") > 0 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2627 all_rows <- rownames(merged_stats) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2628 names(asterisk_rows) <- all_rows |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2629 non_asterisk_rows <- names(asterisk_rows[asterisk_rows == FALSE]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
2630 asterisk_rows <- names(asterisk_rows[asterisk_rows == TRUE]) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
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diff
changeset
|
2631 merged_scores_asterisk <- merged_scores[names(asterisk_rows), , drop = FALSE] |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
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diff
changeset
|
2632 merged_scores_non_asterisk <- merged_scores[names(non_asterisk_rows), , drop = FALSE] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2633 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2634 row_list <- list() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2635 row_list[[const_ksea_astrsk_kinases]] <- asterisk_rows |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2636 row_list[[const_ksea_all_kinases]] <- all_rows |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2637 row_list[[const_ksea_nonastrsk_kinases]] <- non_asterisk_rows |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2638 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2639 i <- which_kinases |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2640 my_row_names <- row_list[[i]] |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
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diff
changeset
|
2641 scrs <- merged_scores[my_row_names, , drop = FALSE] |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
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diff
changeset
|
2642 stts <- merged_stats[my_row_names, , drop = FALSE] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2643 merged_asterisk <- as.matrix(asterisk(stts, p_cutoff)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2644 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2645 color_breaks <- create_breaks(scrs) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
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diff
changeset
|
2646 if (is.null(color_breaks)) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2647 cat("No plot because matrix has too few rows.\n\n") |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
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diff
changeset
|
2648 return(NULL) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2649 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2650 plot_height <- nrow(scrs) ^ 0.55 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2651 plot_width <- ncol(scrs) ^ 0.7 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2652 if (export == "TRUE") { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2653 png( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2654 "KSEA.Merged.Heatmap.png", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2655 width = plot_width * 300, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2656 height = 2 * plot_height * 300, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2657 res = 300, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2658 pointsize = 14 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2659 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2660 } |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2661 did_draw <- draw_kseaapp_summary_heatmap( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2662 x = scrs, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2663 sample_cluster = sample_cluster, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2664 merged_asterisk = merged_asterisk, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2665 color_breaks = color_breaks, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2666 margins = margins |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2667 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2668 if (export == "TRUE") { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2669 dev.off() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2670 } |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2671 if (!did_draw) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2672 return(NULL) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2673 return(my_row_names) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2674 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2675 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2676 # helpers for heatmaps of phosphopeptide intensities |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2677 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2678 # factory producing function to truncate string after n characters |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2679 trunc_n <- function(n) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2680 function(x) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2681 sapply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2682 X = x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2683 FUN = function(s) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2684 if (is.na(s)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2685 return("NA") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2686 cond <- try_catch_w_e(nchar(s) > n) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2687 if (!is.logical(cond$value)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2688 return(cond$value$message) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2689 } else if (cond$value) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2690 paste0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2691 strtrim(s, n), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2692 "..." |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2693 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2694 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2695 s |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2696 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2697 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2698 USE.NAMES = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2699 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2700 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2701 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2702 trunc_long_ppep <- function(x) trunc_n(40)(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2703 trunc_ppep <- function(x) trunc_n(g_ppep_trunc_n)(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2704 trunc_subgene <- function(x) trunc_n(g_subgene_trunc_n)(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2705 trunc_enriched_substrate <- function(x) trunc_n(g_sbstr_trunc_n)(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2706 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2707 # factory producing a function that returns a covariance |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2708 # matrix's rows (and columns) having variance > v_min |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2709 keep_cov_w_var_gtr_min <- function(v_min) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2710 function(x) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2711 if (!is.matrix(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2712 return(NULL) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2713 keepers <- sapply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2714 X = seq_len(nrow(x)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2715 FUN = function(i) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2716 if (x[i, i] < v_min) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2717 NA |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2718 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2719 x[i, i] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2720 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2721 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2722 names(keepers) <- rownames(x) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2723 keepers <- keepers[!is.na(keepers)] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2724 keepers <- names(keepers) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2725 if (length(keepers) == 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2726 return(NULL) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2727 x[keepers, keepers] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2728 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2729 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2730 # function that returns a matrix's rows having variance > 1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2731 keep_cov_w_var_gtr_1 <- keep_cov_w_var_gtr_min(1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2732 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2733 # factory producing a function that returns |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2734 # - either a matrix's rows (rows = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2735 # - or a matrix's columns (rows = FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2736 # having variance > v_min |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2737 keep_var_gtr_min <- function(v_min) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2738 function(x, rows = TRUE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2739 nrowcol <- if (rows) nrow else ncol |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2740 if (!is.matrix(x)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2741 return(NULL) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2742 keepers <- sapply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2743 X = seq_len(nrowcol(x)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2744 FUN = function(i) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2745 row_var <- var( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2746 if (rows) x[i, ] else x[, i], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2747 na.rm = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2748 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2749 if (is.na(row_var) || row_var <= v_min) NA else i |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2750 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2751 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2752 keepers <- keepers[!is.na(keepers)] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2753 if (rows) x[keepers, ] else x[, keepers] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2754 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2755 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2756 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2757 keep_var_gtr_0 <- keep_var_gtr_min(0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2758 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2759 # function drawing heatmap of phosphopeptide intensities |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2760 ppep_heatmap <- |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2761 function( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2762 m, # matrix with rownames already formatted |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2763 cutoff, # cutoff used by hm_heading_function |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2764 hm_heading_function, # construct $ cat heading from m and cutoff |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2765 hm_main_title, # main title for plot (drawn below heading) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2766 suppress_row_dendrogram = TRUE, # set to false to show dendrogram |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2767 max_peptide_count = # experimental: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2768 g_intensity_hm_rows, # values of 50 and 75 worked well |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2769 master_cex = 1.0, # basis for text sizes |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2770 margins = NULL, # optional margins (bottom, right) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2771 cellnote = NULL, # optional matrix of character; dim = dim(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2772 adj = 0.5, # adjust text: 0 left, 0.5 middle, 1 right |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2773 ... # passthru to hm2plus or heatmap.2 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2774 ) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2775 use_heatmap_1 <- FALSE |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2776 peptide_count <- 0 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2777 # emit the heading for the heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2778 if (hm_heading_function(m, cutoff)) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2779 nrow_m <- nrow(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2780 peptide_count <- min(max_peptide_count, nrow_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
2781 if (nrow_m > 1) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2782 m_margin <- m[peptide_count:1, ] |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2783 # Margin was heuristically derived to accommodate the widest label |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2784 row_mchar_max <- max(nchar(rownames(m_margin))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2785 col_mchar_max <- max(nchar(colnames(m_margin))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2786 row_margin <- master_cex * row_mchar_max * 2.6 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2787 col_margin <- master_cex * col_mchar_max * 2.6 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2788 if (print_trace_messages) cat(sprintf("row_margin = %0.3f; ", row_margin)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2789 if (print_trace_messages) cat(sprintf("col_margin = %0.3f; ", col_margin)) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
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diff
changeset
|
2790 hm_call <- NULL |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2791 tryCatch( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2792 { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2793 # set non-argument parameters for hm_call inner function |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2794 my_row_cex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2795 master_cex * 200000 / ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2796 (max(nchar(rownames(m_margin)))^2) * g_intensity_hm_rows |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2797 ) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff
changeset
|
2798 m_hm <- m[peptide_count:1, , drop = FALSE] |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2799 if (is.null(cellnote)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
2800 cellnote <- matrix("", nrow = nrow(m_hm), ncol = ncol(m_hm)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2801 cellnote[is.na(m_hm)] <- "NA" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
2802 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2803 cellnote <- cellnote[peptide_count:1, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2804 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
2805 m_hm[is.na(m_hm)] <- 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2806 nrow_m_hm <- nrow(m_hm) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2807 ncol_m_hm <- ncol(m_hm) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2808 if (nrow_m_hm < 1 || ncol_m_hm < 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2809 return(peptide_count) # return zero as initialized above |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2810 my_limit <- g_intensity_hm_rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2811 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2812 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2813 my_row_cex <- master_cex * (100 / (2 + row_mchar_max)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2814 my_col_cex <- master_cex * 6 * row_margin / col_margin |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2815 my_col_adj <- min(my_col_cex, my_row_cex) / my_col_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2816 my_col_cex <- min(my_col_cex, my_row_cex) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2817 col_margin <- sqrt(my_col_adj) * col_margin |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2818 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2819 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2820 if (is.null(margins)) my_margins <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2821 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2822 (my_col_cex + col_margin), # col |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2823 (my_row_cex + row_margin) / my_row_cex # row |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2824 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2825 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2826 my_margins <- margins |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2827 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2828 if (print_trace_messages) cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2829 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2830 "my_margins = c(%s)\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2831 paste(my_margins, collapse = ", ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2832 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2833 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2834 my_hm2_cex <- 2 * master_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2835 my_key_cex <- 0.9 - 0.1 * (g_intensity_hm_rows + nrow_m_hm) / g_intensity_hm_rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2836 my_key_warp <- 1.5 * 22.75 / row_margin |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2837 my_key_cex <- min(1.10, my_key_warp * my_key_cex) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2838 my_hgt_scale <- 3.70 - 0.4 * (max(1, 0.9 * my_row_cex) - 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2839 my_hgt_scale <- 3.75 # 3.615 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2840 my_hgt_scale <- 3.60 # 3.615 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2841 if (print_trace_messages) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2842 cat_variable(my_hgt_scale, "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2843 my_warp <- max(0.1, 1.4 * (7.5 + nrow_m) / g_intensity_hm_rows) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2844 if (print_trace_messages) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2845 cat_variable(my_warp, "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2846 # added 0.9 heuristically... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2847 my_plot_height <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2848 (0.566 + 0.354 * (nrow_m / g_intensity_hm_rows)) * |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2849 min(my_hgt_scale, my_hgt_scale * my_warp) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2850 my_plot_height <- min(3.65, my_plot_height * g_intensity_hm_rows / 50) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2851 my_heights <- c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2852 0.3, # title and top dendrogram |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2853 my_plot_height, # plot and bottom margin |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2854 4.15 - my_hgt_scale, # legend |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2855 0.05 + my_hgt_scale - my_plot_height # whitespace below legend |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2856 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2857 my_note_cex <- min(0.8, my_row_cex, my_col_cex) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2858 if (print_trace_messages) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2859 cat_variable(my_plot_height, "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2860 cat_variable(4.19 - my_hgt_scale, "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2861 cat_variable(nrow_m_hm, "; ", 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2862 cat_variable(ncol_m_hm, "; ", 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2863 cat_variable(my_row_cex, "; ", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2864 cat_variable(my_col_cex, "; ", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2865 cat_variable(my_note_cex, "; ", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2866 cat_variable(my_key_cex, "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2867 cat_variable(my_hgt_scale, "; ", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2868 cat_variable(my_plot_height, "; ", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2869 cat_variable(my_warp, "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2870 cat_variable(my_heights, "; ", 2) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2871 cat_variable(sum(my_heights), "\n\n", 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2872 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2873 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2874 # define hm_call inner function |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2875 hm_call <- function(x, scaling, title) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2876 my_cex_main <- min(5.0, 220 / nchar(title)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2877 op <- par( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2878 cex.main = my_cex_main * master_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2879 adj = adj |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2880 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2881 if ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2882 !is.null( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2883 hm2plus( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2884 x, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2885 Colv = NA, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2886 Rowv = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2887 cexRow = my_row_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2888 cexCol = my_col_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2889 dendrogram = "row", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2890 las = 1, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2891 main = title, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2892 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2893 cex = my_hm2_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2894 key_par = list(cex = my_key_cex), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2895 margins = my_margins, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2896 widths = c(0.4, 2.6, 1.5), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2897 heights = my_heights, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2898 mat = matrix( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2899 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2900 c(0, 3, 3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2901 c(2, 1, 1), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2902 c(0, 4, 0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2903 c(0, 0, 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2904 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2905 nrow = 4, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2906 ncol = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2907 byrow = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2908 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2909 na.rm = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2910 scale = scaling, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2911 srtcol = 90, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2912 srtrow = 0, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2913 xlab = "", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2914 cellnote = cellnote, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2915 notecex = my_note_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2916 ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2917 ) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2918 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2919 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2920 if (print_trace_messages) cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2921 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2922 "my_heights = c(%s); sum = %0.3f\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2923 paste( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2924 sprintf("%0.3f", my_heights), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2925 collapse = ", " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2926 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2927 sum(my_heights) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2928 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2929 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2930 if (print_trace_messages) cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2931 sprintf("my_key_cex = %0.3f\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2932 my_key_cex) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2933 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2934 if (print_trace_messages) cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2935 sprintf("my_key_cex/my_heights[3] = %0.3f\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2936 my_key_cex / my_heights[3]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2937 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2938 if (print_trace_messages) cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2939 sprintf("my_heights[2]/my_heights[3] = %0.3f\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2940 my_heights[2] / my_heights[3]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2941 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2942 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2943 par(op) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2944 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2945 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2946 # invoke hm_call inner function |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2947 if (sum(rowSums(!is.na(m_hm)) < 2)) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2948 hm_call( |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2949 m_hm, |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2950 "none", |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2951 "log(intensities), unscaled, unimputed, and unnormalized" |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2952 ) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2953 else |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2954 hm_call( |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2955 m_hm, |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2956 "row", |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2957 "log(intensities), row-scaled, unimputed, and unnormalized" |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2958 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2959 }, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2960 error = function(e) { |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2961 if (!is.null(hm_call)) { |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2962 m_hm[is.na(m_hm)] <- 0 |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2963 tryCatch( |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2964 { |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2965 if (nrow(m_hm) > 1) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2966 hm_call( |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2967 m_hm, |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2968 "none", |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2969 paste( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2970 "log(intensities), unscaled,", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2971 "zero-imputed, unnormalized" |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2972 ) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2973 ) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2974 else |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2975 cat("\nThere are too few peptides to produce a heatmap.\n") |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2976 }, |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2977 error = function(r) { |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2978 cat( |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2979 sprintf( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2980 "\n%s %s Internal message: %s\n\\newline\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2981 "Failure drawing heatmap,", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2982 "possibly because of too many missing values.\n\\newline\n\n", |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2983 r$message |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2984 ) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2985 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2986 cat_margins() |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2987 } |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2988 ) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2989 } else { |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2990 cat( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2991 "\nFailure drawing heatmap, possibly because of too many missing values.\n" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2992 ) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
2993 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2994 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2995 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2996 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
2997 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2998 # return value: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
2999 peptide_count |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3000 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3001 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3002 # function drawing heatmap of correlations if they exist, else covariances |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3003 cov_heatmap <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3004 function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3005 m, # matrix with rownames already formatted |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3006 top_substrates = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3007 ... # passthru to hm2plus or heatmap.2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3008 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3009 if (print_nb_messages) nbe(see_variable(m), " [", nrow(m), "x", ncol(m), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3010 #ACE nb(rowSums(m, na.rm = TRUE)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3011 #ACE bad_rows <- (rowSums(m, na.rm = TRUE) == 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3012 #ACE nb(see_variable(bad_rows)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3013 #ACE m <- m[-bad_rows, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3014 colnames_m <- colnames(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3015 is_na_m <- is.na(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3016 tmp <- m |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3017 tmp[is_na_m] <- 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3018 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3019 tmp <- m[, 0 < colSums(x = tmp)] # by default, na.rm is FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3020 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3021 colnames_tmp <- colnames(tmp) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3022 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3023 my_low_p_seq <- seq( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3024 from = min(g_intensity_hm_rows, nrow(m)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3025 to = 1, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3026 by = -1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3027 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3028 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3029 if (g_correlate_substrates) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3030 # zap samples having zero or near-zero variance |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3031 tmp[is.na(tmp)] <- 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3032 nzv <- caret::nearZeroVar( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3033 tmp, # matrix of values, samples x variables |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3034 freqCut = 1.01, # min(freq most prevalent value / |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3035 # freq second most prevalent) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3036 uniqueCut = 99 # max(number of unique values / |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3037 # total number of samples) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3038 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3039 tmp <- if (length(nzv) > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3040 m[, -nzv, drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3041 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3042 m |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3043 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3044 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3045 tmp <- m[my_low_p_seq, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3046 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3047 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3048 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3049 t_m <- t(tmp) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3050 t_m[is.na(t_m)] <- 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3051 prefiltered_nrow <- ncol(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3052 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3053 my_corcov <- cov(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3054 did_filter_rows <- did_filter_cols <- FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3055 if (g_correlate_substrates && !is_positive_definite(my_corcov)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3056 my_correlate_substrates <- FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3057 t_m <- t(m[my_low_p_seq, , drop = FALSE]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3058 t_m[is.na(t_m)] <- 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3059 unfiltered_row_count <- ncol(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3060 unfiltered_col_count <- nrow(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3061 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3062 # zap empty samples |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3063 t_m <- t_m[0 < rowSums(x = t_m), ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3064 # zap substrates present in fewer than two samples |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3065 foo <- t_m > 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3066 foo <- colSums(x = foo) > 1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3067 t_m <- t_m[, foo] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3068 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3069 did_filter_rows <- unfiltered_row_count > ncol(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3070 did_filter_cols <- unfiltered_col_count > nrow(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3071 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3072 colnames_tmp <- rownames(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3073 my_corcov <- cov(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3074 if (g_filter_cov_var_gt_1) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3075 my_corcov <- keep_cov_w_var_gtr_1(my_corcov) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3076 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3077 } else if (g_correlate_substrates) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3078 my_corcov <- cov2cor(my_corcov) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3079 my_correlate_substrates <- TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3080 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3081 my_correlate_substrates <- FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3082 if (g_filter_cov_var_gt_1) my_corcov <- keep_cov_w_var_gtr_1(my_corcov) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3083 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3084 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3085 omitted_samples <- colnames_m[colnames_m %notin% colnames_tmp] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3086 suffix <- if (length(omitted_samples) > 1) "s" else "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3087 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3088 f_omissions <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3089 function(is_corr) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3090 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3091 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3092 "Below is the %s plot for %s substrates", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3093 if (is_corr) "correlation" else "covariance", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3094 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3095 if (top_substrates) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3096 "%0.0f \"highest-quality\"" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3097 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3098 "%0.0f", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3099 ncol(t_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3100 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3101 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3102 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3103 if (did_filter_cols) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3104 cat(sprintf(", omitting sample%s ", suffix)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3105 latex_collapsed_vector(", ", omitted_samples) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3106 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3107 cat(".\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3108 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3109 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3110 if (is.null(my_corcov) || sum(!is.na(t_m)) < 2) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3111 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3112 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3113 "\\newline\n%s %s plot.\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3114 "Insufficient covariance to produce", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3115 if (my_correlate_substrates) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3116 "correlation" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3117 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3118 "covariance" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3119 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3120 "\\newpage\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3121 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3122 return(NULL) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3123 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3124 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3125 cat("\\leavevmode\n", "\\newpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3126 f_omissions(my_correlate_substrates) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3127 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3128 master_cex <- 0.4 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3129 max_nchar <- max(nchar(rownames(t_m))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3130 my_limit <- g_intensity_hm_rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3131 diminution <- sqrt(my_limit / (my_limit + ncol(t_m))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3132 my_row_cex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3133 my_col_cex <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3134 min(1.75, master_cex * 9 * diminution ^ 1.5) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3135 my_margin <- 3 + my_row_cex * 64 / (8 + max_nchar) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3136 my_key_cex <- 1.4 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3137 my_hm2_cex <- 1.0 * master_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3138 my_hgt_scale <- 3.50 - 0.26 * (max(0.4, my_key_cex) - 0.4) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3139 my_hgt_scale <- 2.7 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3140 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3141 my_legend_height <- 4.0 - my_hgt_scale |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3142 my_legend_height <- 0.5 * my_key_cex |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3143 my_warp <- 0.65 * (my_limit + ncol(t_m)) / my_limit |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3144 my_warp <- 0.8 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3145 my_legend_height <- 0.77 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3146 my_legend_height <- 0.67 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3147 my_plot_height <- my_hgt_scale + (1 - my_warp) * my_legend_height |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3148 my_legend_height <- my_warp * my_legend_height |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3149 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3150 parjust <- par(adj = 0.5) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3151 on.exit(par(parjust)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3152 my_corcov <- my_corcov[order(rownames(my_corcov)), ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3153 my_main <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3154 sprintf("%s among %s substrates %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3155 if (my_correlate_substrates) "Correlation" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3156 else "Covariance", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3157 kinase_name, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3158 if (!my_correlate_substrates && |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3159 g_filter_cov_var_gt_1 && |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3160 did_filter_rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3161 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3162 "having variance > 1" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3163 else "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3164 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3165 my_main_nchar <- nchar(my_main) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3166 my_heights <- c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3167 0.3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3168 my_plot_height, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3169 my_legend_height # was 4.0 - my_hgt_scale # was 4.19 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3170 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3171 if (print_trace_messages) cat(sprintf("max_nchar = %0.3f; ", max_nchar)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3172 if (print_trace_messages) cat(sprintf("my_margin = %0.3f; ", my_margin)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3173 if (print_trace_messages) cat(sprintf("my_plot_height = %0.3f\n\n", my_plot_height)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3174 if (print_trace_messages) cat(sprintf("master_cex = %0.3f; ", master_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3175 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3176 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3177 if (print_trace_messages) cat(sprintf("my_key_cex = %0.3f\n\n", my_key_cex)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3178 if (print_trace_messages) cat(sprintf("my_hgt_scale = %0.3f\n\n", my_hgt_scale)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3179 if (print_trace_messages) cat(sprintf("legend height = %0.3f\n\n", my_legend_height)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3180 if (print_trace_messages) cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3181 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3182 "my_heights = c(%s); sum = %0.3f\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3183 paste( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3184 sprintf("%0.3f", my_heights), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3185 collapse = ", " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3186 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3187 sum(my_heights) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3188 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3189 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3190 op <- par(cex.main = (30 + my_main_nchar) / my_main_nchar) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3191 on.exit(par(op)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3192 hm2plus( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3193 x = my_corcov, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3194 cex = my_hm2_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3195 cexCol = my_col_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3196 cexRow = my_row_cex, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3197 density_info = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3198 denhgt = 0.15, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3199 denwid = 0.5, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3200 divergent = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3201 key_par = list(cex = my_key_cex), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3202 key_xlab = if (my_correlate_substrates) "Correlation" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3203 else "Covariance", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3204 main = my_main, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3205 mat = matrix( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3206 c( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3207 c(0, 3, 3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3208 c(2, 1, 1), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3209 c(0, 4, 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3210 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3211 nrow = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3212 ncol = 3, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3213 byrow = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3214 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3215 heights = my_heights, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3216 margins = c(my_margin, my_margin), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3217 widths = c(0.5, 3.1, 0.9), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3218 scale = "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3219 symkey = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3220 symbreaks = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3221 symm = FALSE #TODO evaluate TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3222 # ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3223 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3224 } # end cov_heatmap |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3225 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3226 ### FILE IMPORT |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3227 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3228 # function reading bzipped file to data.frame |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3229 bzip2df <- function(d, f, ctor = bzfile) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3230 # read.delim file (by default, compressed by bzip2) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3231 if (file.exists(f)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3232 conn <- NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3233 pf <- parent.frame() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3234 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3235 assign( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3236 as.character(substitute(d)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3237 read.delim(conn <- bzfile(f, open = "r")), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3238 pf |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3239 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3240 finally = if (!is.null(conn)) close(conn) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3241 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3242 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3243 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3244 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3245 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3246 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3247 # Purpose |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3248 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3249 The purpose of this analysis is to perform for phosphopeptides: |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3250 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3251 - imputation of missing values, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3252 - quantile normalization, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3253 - ANOVA (using the R stats::`r params$oneWayManyCategories` function), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3254 - assignment of an FDR-adjusted $p$-value and a "quality score" to each phosphopeptide, and |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3255 - KSEA (Kinase-Substrate Enrichment Analysis) using code adapted from the CRAN `KSEAapp` package to search for kinase substrates from the following databases: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3256 - PhosphoSitesPlus [https://www.phosphosite.org](https://www.phosphosite.org) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3257 - The Human Proteome Database [http://hprd.org](http://hprd.org) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3258 - NetworKIN [http://networkin.science/](http://networkin.science/) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3259 - Phosida [http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx](http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3260 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3261 ```{r include = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3262 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3263 if (params$kseaUseAbsoluteLog2FC) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3264 sfc <- "|s|" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3265 pfc <- "|p|" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3266 pfc_txt <- "$\\text{absolute value}({\\log_2 (\\text{fold-change})})$" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
3267 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3268 sfc <- "s" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3269 pfc <- "p" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3270 pfc_txt <- "${\\log_2 (\\text{fold-change}})$" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
3271 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3272 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3273 ksea_heatmap_titles <- list() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3274 ksea_heatmap_titles[[const_ksea_astrsk_kinases]] <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3275 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3276 "Summary for all kinases enriched in one or more contrasts at %s < %s", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3277 ksea_cutoff_statistic, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3278 ksea_cutoff_threshold |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3279 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3280 ksea_heatmap_titles[[const_ksea_all_kinases]] <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3281 "Summary figure for all contrasts and all kinases" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3282 ksea_heatmap_titles[[const_ksea_nonastrsk_kinases]] <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3283 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3284 "Summary for all kinases not enriched at %s < %s in any contrast", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3285 ksea_cutoff_statistic, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3286 ksea_cutoff_threshold |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3287 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3288 # hash to hold names of significantly enriched kinases |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3289 ksea_asterisk_hash <- new_env() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3290 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3291 # PROCESS (mostly read) PARAMETERS |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3292 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3293 # False discovery rate adjustment for ANOVA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3294 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3295 val_fdr <- read.table(file = alpha_file, sep = "\t", header = FALSE, quote = "") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3296 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3297 if ( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3298 ncol(val_fdr) != 1 || |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3299 sum(!is.numeric(val_fdr[, 1])) || |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3300 sum(val_fdr[, 1] < 0) || |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3301 sum(val_fdr[, 1] > 1) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3302 ) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3303 cat("alphaFile should be one column of numbers within the range [0.0,1.0]") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3304 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3305 knitr::knit_exit() |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3306 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3307 val_fdr <- val_fdr[, 1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3308 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3309 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3310 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3311 ```{r echo = FALSE, results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3312 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3313 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3314 result <- file.copy( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3315 from = preproc_db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3316 to = ksea_app_prep_db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3317 overwrite = TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3318 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3319 if (!result) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3320 write( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3321 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3322 "fatal error copying initial database '%s' to output '%s'", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3323 preproc_db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3324 ksea_app_prep_db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3325 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3326 stderr() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3327 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3328 if (sys.nframe() > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3329 cat("Cannot continue and quit() failed. Goodbye.") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3330 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3331 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3332 # in case knit_exit doesn't exit |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3333 quit(save = "no", status = 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3334 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3335 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3336 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3337 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3338 write.table(x = param_df, file = "test-data/params.txt") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3339 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3340 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3341 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3342 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3343 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3344 ### READ DATA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3345 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3346 # read.table reads a file in table format and creates a data frame from it. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3347 # - note that `quote = ""` means that quotation marks are treated literally. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3348 full_data <- read.table( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3349 file = input_file, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3350 sep = "\t", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3351 header = TRUE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3352 quote = "", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3353 check.names = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3354 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3355 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3356 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3357 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3358 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3359 # Extraction of Sample Classes and Names from Input Data |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3360 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3361 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3362 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3363 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3364 my_column_names <- names(full_data) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3365 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3366 if (!fdc_is_integer) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3367 if (length(data_column_indices) > 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3368 first_data_column <- data_column_indices[1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3369 } else { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3370 cat(paste("failed to convert firstDataColumn:", first_data_column)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3371 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3372 knitr::knit_exit() |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3373 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3374 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3375 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3376 cat( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3377 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3378 paste( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3379 "\n\nThe input data file has peptide-intensity data", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3380 "in columns %d (\"%s\") through %d (\"%s\")." |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3381 ), |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3382 tmp <- min(data_column_indices), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3383 my_column_names[tmp], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3384 tmp <- max(data_column_indices), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3385 my_column_names[tmp] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3386 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3387 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3388 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3389 if (TRUE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3390 cat0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3391 table_offset(i = 1, new = TRUE), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3392 "Sample classes and names are shown in ", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3393 table_href(), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3394 ".\n\n" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3395 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3396 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3397 cat0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3398 "\\newcounter{offset}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3399 "\\setcounter{offset}{\\value{table}}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3400 "\\stepcounter{offset}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3401 "Sample classes and names are shown in ", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3402 table_href(), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3403 ".\n\n" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3404 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3405 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3406 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3407 #TODO remove this unused variable and assignment |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3408 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3409 # Write column names as a LaTeX enumerated list. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3410 column_name_df <- data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3411 column = seq_len(length(colnames(full_data))), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3412 name = paste0("\\verb@", colnames(full_data), "@") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3413 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3414 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3415 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3416 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3417 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3418 ```{r echo = FALSE, results = 'asis'} |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3419 # extract intensity columns from full_data to quant_data |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3420 quant_data <- full_data[first_data_column:length(full_data)] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3421 quant_data[quant_data == 0] <- NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3422 rownames(quant_data) <- rownames(full_data) <- full_data$Phosphopeptide |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3423 full_data_names <- colnames(quant_data) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3424 # Extract factors and trt-replicates using regular expressions. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3425 # Typically: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3426 # regex_sample_names is "\\.\\d+[A-Z]$" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3427 # regex_sample_grouping is "\\d+" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3428 # This would distinguish trt-replicates by terminal letter [A-Z] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3429 # in sample names and group them into trts by the preceding digits. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3430 # e.g.: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3431 # group .1A .1B .1C into group 1; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3432 # group .2A .2B .2C, into group 2; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3433 # etc. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3434 m <- regexpr(regex_sample_names, colnames(quant_data), perl = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3435 sample_name_matches <- regmatches(names(quant_data), m) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3436 colnames(quant_data) <- sample_name_matches |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3437 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3438 write_debug_file(quant_data) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3439 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3440 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3441 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3442 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3443 if (print_nb_messages) nbe(see_variable(smpl_trt, "\n\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3444 if (print_nb_messages) nbe(see_variable(sample_name_matches, "\n\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3445 if (print_nb_messages) nbe(see_variable(full_data_names, "\n\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3446 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3447 sample_treatment_df <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3448 save_sample_treatment_df <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3449 data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3450 class = smpl_trt, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3451 sample = sample_name_matches, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3452 full_sample_names = full_data_names |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3453 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3454 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3455 if (print_nb_messages) nbe(see_variable(sample_treatment_df, "\n\n")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3456 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3457 # reorder data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3458 my_order <- with(sample_treatment_df, order(class, sample)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3459 quant_data <- quant_data[, my_order] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3460 sample_name_matches <- sample_name_matches[my_order] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3461 smpl_trt <- smpl_trt[my_order] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3462 sample_treatment_df <- data.frame( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3463 class = smpl_trt, |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
3464 sample = sample_name_matches |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
3465 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3466 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3467 # filter smpl_trt as appropriate |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3468 if (sample_group_filter %in% c("include", "exclude")) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3469 include_sample <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3470 mgrepl( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3471 v = sample_group_filter_patterns, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3472 s = as.character(smpl_trt), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3473 fixed = sample_group_filter_fixed, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3474 perl = sample_group_filter_perl, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3475 ignore.case = sample_group_filter_nocase |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3476 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3477 if (sum(include_sample) < 2) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3478 errmsg <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3479 paste( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3480 "ERROR:", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3481 sum(include_sample), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3482 "samples are too few for analysis;", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3483 "check input parameters for sample-name parsing" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3484 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3485 cat0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3486 errmsg, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3487 "\\stepcounter{offset}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3488 " in ", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3489 table_href(), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3490 ".\n\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3491 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3492 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3493 x = save_sample_treatment_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3494 tabstops = c(1.25, 1.25), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3495 caption = "Sample classes", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3496 use_subsubsection_header = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3497 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3498 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3499 x = |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3500 param_df[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3501 c("regexSampleNames", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3502 "regexSampleGrouping", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3503 "groupFilterPatterns", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3504 "groupFilter", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3505 "groupFilterMode" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3506 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3507 ], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3508 tabstops = c(1.75), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3509 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3510 caption = "Input parameters for sample-name parsing", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
3511 verbatim = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3512 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3513 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3514 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3515 return(invisible(-1)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3516 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3517 sample_treatment_df <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3518 if (sample_group_filter == "include") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3519 sample_treatment_df[include_sample, ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3520 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3521 sample_treatment_df[!include_sample, ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3522 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3523 include_sample <- rep.int(TRUE, length(smpl_trt)) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
24
diff
changeset
|
3524 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3525 sample_name_matches <- sample_treatment_df$sample |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3526 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3527 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3528 sample_treatment_df$class <- smpl_trt |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3529 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3530 # filter quant_data as appropriate |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3531 number_of_samples <- length(sample_name_matches) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3532 quant_data <- quant_data[, sample_name_matches] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3533 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3534 sample_level_integers <- as.integer(smpl_trt) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3535 sample_treatment_levels <- levels(smpl_trt) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3536 count_of_treatment_levels <- length(sample_treatment_levels) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3537 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3538 # for each phosphopeptide, across treatment levels, compute minimum |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3539 # count of observed (i.e., non-missing) values |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3540 my_env <- new_env() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3541 for (l in sample_treatment_levels) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3542 my_env[[as.character(l)]] <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3543 as.vector(rowSums(!is.na(quant_data[l == smpl_trt]))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3544 min_group_obs_count <- row_apply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3545 x = Reduce( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3546 f = function(l, r) cbind(l, my_env[[r]]), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3547 x = sample_treatment_levels, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3548 init = c() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3549 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3550 fun = min |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3551 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3552 names(min_group_obs_count) <- rownames(quant_data) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3553 rm(my_env) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3554 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3555 # display (possibly-filtered) results |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3556 cat("\\newpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3557 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3558 if (sum(include_sample) > 1) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3559 data_frame_tabbing_latex( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3560 x = sample_treatment_df, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3561 tabstops = c(1.25), |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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24
diff
changeset
|
3562 caption = "Sample classes", |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3563 use_subsubsection_header = FALSE |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3564 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3565 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3566 sample_name_grow <- 10 / (10 + max(nchar(sample_name_matches) + 6)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3567 sample_colsep <- transition_positions(as.integer(sample_treatment_df$class)) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3568 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3569 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3570 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3571 cat("\\newpage\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3572 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3573 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
3574 ## Are the log-transformed sample distributions similar? |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
3575 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3576 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
24
657663e89728
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parents:
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changeset
|
3577 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
3578 quant_data[quant_data == 0] <- NA #replace 0 with NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
3579 quant_data_log <- log10(quant_data) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3580 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
3581 rownames(quant_data_log) <- rownames(quant_data) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
3582 colnames(quant_data_log) <- sample_name_matches |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3583 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3584 write_debug_file(quant_data_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
3585 |
|
27
29775869faba
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diff
changeset
|
3586 g_ppep_distrib_ctl <- new_env() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3587 g_ppep_distrib_ctl$xlab_line <- 3.5 + 11.86 * (0.67 - sample_name_grow) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3588 g_ppep_distrib_ctl$mai_bottom <- (0.5 + 3.95 * (0.67 - sample_name_grow)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3589 g_ppep_distrib_ctl$axis <- (0.6 + 0.925 * (0.67 - sample_name_grow)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3590 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3591 my_ppep_distrib_bxp <- function( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3592 x |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3593 , sample_name_grow = sample_name_grow |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3594 , main |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3595 , varwidth = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3596 , sub = NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3597 , xlab |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3598 , ylab |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3599 , col = const_boxplot_fill |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3600 , notch = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3601 , ppep_distrib_ctl = g_ppep_distrib_ctl |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3602 , ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3603 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3604 my_xlab_line <- g_ppep_distrib_ctl$xlab_line |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3605 my_mai_bottom <- g_ppep_distrib_ctl$mai_bottom |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3606 my_axis <- g_ppep_distrib_ctl$axis |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3607 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3608 if (print_trace_messages) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3609 cat_variable(my_xlab_line, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3610 cat_variable(my_mai_bottom, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3611 cat_variable(my_axis, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3612 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3613 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3614 old_par <- par( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3615 mai = par("mai") + c(my_mai_bottom, 0, 0, 0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3616 cex.axis = my_axis, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3617 cex.lab = 1.2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3618 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3619 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3620 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3621 # Vertical plot |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3622 boxplot( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3623 x |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3624 , las = 2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3625 , col = col |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3626 , main = main |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3627 , sub = NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3628 , ylab = ylab |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3629 , xlab = NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3630 , notch = notch |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3631 , varwidth = varwidth |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3632 , ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3633 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3634 title( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3635 sub = sub |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3636 , cex.sub = 1.0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3637 , line = my_xlab_line + 1 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3638 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3639 title( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3640 xlab = xlab |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3641 , line = my_xlab_line |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3642 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3643 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3644 finally = par(old_par) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3645 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3646 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3647 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3648 my_ppep_distrib_bxp( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3649 x = quant_data_log |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3650 , sample_name_grow = sample_name_grow |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3651 , main = "Peptide intensities for each sample" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3652 , varwidth = boxplot_varwidth |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3653 , sub = "Box widths reflect number of peptides for sample" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3654 , xlab = "Sample" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3655 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3656 , col = const_boxplot_fill |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3657 , notch = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3658 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3659 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
3660 cat("\n\n\n\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3661 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3662 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3663 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3664 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3665 if (nrow(quant_data_log) > 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3666 quant_data_log_stack <- stack(quant_data_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3667 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) + |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3668 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) + |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3669 ggplot2::ylab("Probability density") + |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3670 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3671 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3672 cat("No density plot because there are too few peptides.\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3673 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3674 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3675 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3676 ## Globally, are peptide intensities are approximately unimodal? |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3677 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3678 <!-- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3679 # bquote could be used as an alternative to latex2exp::TeX below particularly |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3680 # and when plotting math expressions generally, at the expense of mastering |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3681 # another syntax, which hardly seems worthwhile when I need to use TeX |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3682 # elsewhere; here's an introduction to bquote: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3683 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3684 --> |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3685 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3686 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3687 # identify the location of missing values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3688 fin <- is.finite(as.numeric(as.matrix(quant_data_log))) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3689 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3690 logvalues <- as.numeric(as.matrix(quant_data_log))[fin] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3691 logvalues_density <- density(logvalues) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3692 plot( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3693 x = logvalues_density, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3694 main = latex2exp::TeX( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3695 "Smoothed estimated probability density vs. $log_{10}$(peptide intensity)" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3696 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3697 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3698 ylab = "Probability density" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3699 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3700 hist( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3701 x = as.numeric(as.matrix(quant_data_log)), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3702 xlim = c(min(logvalues_density$x), max(logvalues_density$x)), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3703 breaks = 100, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3704 main = latex2exp::TeX("Frequency vs. $log_{10}$(peptide intensity)"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3705 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3706 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3707 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3708 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3709 # Characterization of Input Data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3710 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3711 ## Distribution of standard deviations of $log_{10}(\text{intensity})$, ignoring missing values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3712 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3713 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3714 # determine quantile |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3715 q1 <- quantile(logvalues, probs = mean_percentile)[1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3716 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3717 # 1 = row of matrix (ie, phosphopeptide) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3718 sds <- row_apply(quant_data_log, sd_finite) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3719 if (sum(!is.na(sds)) > 2) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3720 plot( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3721 density(sds, na.rm = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3722 , main = "Smoothed estimated probability density vs. std. deviation" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3723 , sub = "(probability estimation made with Gaussian smoothing)" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3724 , ylab = "Probability density" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3725 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3726 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3727 cat( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3728 "At least two non-missing values are required to plot", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3729 "probability density.\n\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3730 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3731 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3732 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3733 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3734 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3735 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3736 # Determine number of cells to impute |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3737 temp <- quant_data[is.na(quant_data)] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3738 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3739 # Determine number of values to impute |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3740 number_to_impute <- length(temp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3741 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3742 # Determine percent of missing values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3743 pct_missing_values <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3744 round(length(temp) / (length(logvalues) + length(temp)) * 100) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3745 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3746 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3747 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3748 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3749 # prep for trt-median based imputation |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3750 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3751 ``` |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3752 # Imputation of Missing Values |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3753 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3754 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3755 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3756 imp_smry_pot_peptides_before <- nrow(quant_data_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3757 imp_smry_missing_values_before <- number_to_impute |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3758 imp_smry_pct_missing <- pct_missing_values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3759 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3760 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3761 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3762 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3763 #Determine number of cells to impute |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3764 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3765 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3766 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3767 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3768 # Identify which values are missing and need to be imputed |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3769 ind <- which(is.na(quant_data), arr.ind = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3770 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3771 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3772 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3773 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3774 # Apply imputation |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3775 switch( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3776 imputation_method |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3777 , "group-median" = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3778 quant_data_imp <- quant_data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3779 imputation_method_description <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3780 paste("Substitute missing value with", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3781 "median peptide-intensity for sample group.\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3782 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3783 # Take the accurate ln(x+1) because the data are log-normally distributed |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3784 # and because median can involve an average of two measurements. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3785 quant_data_imp <- log1p(quant_data_imp) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3786 for (i in seq_len(count_of_treatment_levels)) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3787 # Determine the columns for this factor-level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3788 level_cols <- i == sample_level_integers |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3789 # Extract those columns |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3790 lvlsbst <- quant_data_imp[, level_cols, drop = FALSE] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3791 # assign to ind the row-column pairs corresponding to each NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3792 ind <- which(is.na(lvlsbst), arr.ind = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3793 # No group-median exists if there is only one sample |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3794 # a given ppep has no measurement; otherwise, proceed. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3795 if (ncol(lvlsbst) > 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3796 the_centers <- |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3797 row_apply(lvlsbst, median, na.rm = TRUE) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3798 for (j in seq_len(nrow(lvlsbst))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3799 for (k in seq_len(ncol(lvlsbst))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3800 if (is.na(lvlsbst[j, k])) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3801 lvlsbst[j, k] <- the_centers[j] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3802 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3803 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3804 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3805 quant_data_imp[, level_cols] <- lvlsbst |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3806 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3807 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3808 # Take the accurate e^x - 1 to match scaling of original input. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3809 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3810 good_rows <- !is.na(rowMeans(quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3811 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3812 , "median" = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3813 quant_data_imp <- quant_data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3814 imputation_method_description <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3815 paste("Substitute missing value with", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3816 "median peptide-intensity across all sample classes.\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3817 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3818 # Take the accurate ln(x+1) because the data are log-normally distributed |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3819 # and because median can involve an average of two measurements. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3820 quant_data_imp <- log1p(quant_data_imp) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3821 quant_data_imp[ind] <- row_apply(quant_data_imp, median, na.rm = TRUE)[ind[, 1]] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3822 # Take the accurate e^x - 1 to match scaling of original input. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3823 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3824 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3825 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3826 , "mean" = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3827 quant_data_imp <- quant_data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3828 imputation_method_description <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3829 paste("Substitute missing value with", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3830 "geometric-mean peptide intensity across all sample classes.\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3831 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3832 # Take the accurate ln(x+1) because the data are log-normally distributed, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3833 # so arguments to mean should be previously transformed. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3834 # this will have to be |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3835 quant_data_imp <- log1p(quant_data_imp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3836 # Assign to NA cells the mean for the row |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3837 quant_data_imp[ind] <- row_apply(quant_data_imp, mean, na.rm = TRUE)[ind[, 1]] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3838 # Take the accurate e^x - 1 to match scaling of original input. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3839 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3840 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3841 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3842 , "random" = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3843 quant_data_imp <- quant_data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3844 m1 <- median(sds, na.rm = TRUE) * sd_percentile #sd to be used is the median sd |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3845 # If you want results to be reproducible, you will want to call |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3846 # base::set.seed before calling stats::rnorm |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3847 imputation_method_description <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3848 paste("Substitute each missing value with random intensity", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3849 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3850 "random intensity $N \\sim (%0.2f, %0.2f)$.\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3851 q1, m1 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3852 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3853 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3854 cat(sprintf("mean_percentile (from input parameter) is %2.0f\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3855 100 * mean_percentile)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3856 cat(sprintf("sd_percentile (from input parameter) is %0.2f\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3857 sd_percentile)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3858 quant_data_imp[ind] <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3859 10 ^ rnorm(number_to_impute, mean = q1, sd = m1) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3860 quant_data_imp_ln <- log1p(quant_data_imp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3861 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3862 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3863 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3864 quant_data_imp_log10 <- quant_data_imp_ln * const_log10_e |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3865 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3866 if (length(good_rows) < 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3867 print("ERROR: Cannot impute data; there are no good rows!") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3868 return(-1) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3869 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3870 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3871 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3872 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3873 cat("\\quad\n\nImputation method:\n\n\n", imputation_method_description) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3874 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3875 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3876 ```{r echo = FALSE} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3877 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3878 imp_smry_pot_peptides_after <- sum(good_rows) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3879 imp_smry_rejected_after <- sum(!good_rows) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3880 imp_smry_missing_values_after <- sum(is.na(quant_data_imp[good_rows, ])) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3881 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3882 # From ?`%in%`, %in% is currently defined as function(x, table) match(x, table, nomatch = 0) > 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3883 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3884 sink(stderr()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3885 print("`%in%`:") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3886 print(`%in%`) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3887 sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3888 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3889 stock_in <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3890 names(good_rows) %in% |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3891 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3892 if (print_nb_messages) nbe(see_variable(stock_in), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3893 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3894 explicit_in <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3895 0 < match( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3896 names(good_rows), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3897 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3898 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3899 if (print_nb_messages) nbe(see_variable(explicit_in), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3900 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3901 great_enough_row_names <- good_rows[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3902 names(good_rows) %in% |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3903 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3904 ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3905 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3906 great_enough_row_names <- great_enough_row_names[great_enough_row_names] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3907 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3908 ``` |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3909 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3910 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3911 # ref: http://www1.maths.leeds.ac.uk/latex/TableHelp1.pdf |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3912 tabular_lines_fmt <- paste( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3913 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
3914 " \\leavevmode", |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3915 " \\caption{Imputation Results}", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3916 " \\centering", # \centering centers the table on the page |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3917 " \\begin{tabular}{l c c c}", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3918 " \\hline\\hline", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3919 " \\ & potential peptides & missing values & rejected", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3920 " peptides \\\\ [0.5ex]", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3921 " \\hline", |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3922 " before imputation & %d & %d (%d\\%s) & \\\\", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3923 " after imputation & %d & %d & %d \\\\", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3924 " after keep comparable & %d & & %d \\\\ [1ex]", |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3925 " \\hline", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3926 " \\end{tabular}", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3927 #" \\label{table:nonlin}", # may be used to refer this table in the text |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3928 "\\end{table}", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3929 sep = "\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3930 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3931 tabular_lines <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3932 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3933 tabular_lines_fmt, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3934 imp_smry_pot_peptides_before, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3935 imp_smry_missing_values_before, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3936 imp_smry_pct_missing, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3937 "%", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3938 imp_smry_pot_peptides_after, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3939 imp_smry_missing_values_after, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3940 imp_smry_rejected_after, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3941 length(great_enough_row_names), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
3942 imp_smry_pot_peptides_before - |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3943 length(great_enough_row_names) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3944 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3945 cat(tabular_lines) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3946 ``` |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3947 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3948 ```{r filter_good_rows, echo = FALSE} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3949 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3950 if (print_nb_messages) nbe("before name extraction, ", see_variable(length(good_rows)), " ", see_variable(good_rows), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3951 good_rows <- names(good_rows[names(great_enough_row_names)]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3952 if (print_nb_messages) nbe("after name extraction, ", see_variable(length(good_rows)), see_variable(good_rows), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
3953 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3954 #ACE min_group_obs_count <- min_group_obs_count[names(great_enough_row_names)] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
3955 #ACE nbe("good_rows") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3956 #ACE nbe(see_variable(good_rows)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3957 #ACE nbe("names(min_group_obs_count) before filter for good rows") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3958 #ACE nbe(see_variable(names(min_group_obs_count))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3959 min_group_obs_count <- min_group_obs_count[good_rows] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3960 #ACE nbe("min_group_obs_count after filter for good rows") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3961 #ACE nbe(see_variable(names(min_group_obs_count))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
3962 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3963 # Zap rows where imputation was insufficiently effective |
|
24
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changeset
|
3964 full_data <- full_data [good_rows, ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
3965 quant_data <- quant_data [good_rows, ] |
|
27
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diff
changeset
|
3966 quant_data_log <- quant_data_log [good_rows, ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3967 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3968 if (print_nb_messages) nbe("before row filter, ", see_variable(nrow(quant_data_imp)), "\n") |
|
24
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changeset
|
3969 quant_data_imp <- quant_data_imp[good_rows, ] |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
3970 if (print_nb_messages) nbe("after row filter, ", see_variable(nrow(quant_data_imp)), "\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
3971 write_debug_file(quant_data_imp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
3972 quant_data_imp_good_rows <- quant_data_imp |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
3973 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3974 write_debug_file(quant_data_imp_good_rows) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3975 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3976 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3977 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3978 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3979 can_plot_before_after_imp <- TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3980 d_combined <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3981 as.numeric( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3982 as.matrix( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3983 log10(quant_data_imp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3984 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3985 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3986 d_original <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3987 as.numeric( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3988 as.matrix( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3989 log10(quant_data_imp[!is.na(quant_data)]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3990 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3991 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3992 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3993 if (sum(!is.na(d_original)) > 2) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3994 d_original <- density(d_original) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3995 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3996 can_plot_before_after_imp <- FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3997 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3998 if (can_plot_before_after_imp && sum(is.na(d_combined)) < 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
3999 d_combined <- density(d_combined) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4000 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4001 can_plot_before_after_imp <- FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4002 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4003 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4004 if (sum(is.na(quant_data)) > 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4005 # There ARE missing values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4006 d_imputed <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4007 as.numeric( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4008 as.matrix( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4009 log10(quant_data_imp[is.na(quant_data)]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4010 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4011 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4012 if (can_plot_before_after_imp && sum(is.na(d_imputed)) < 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4013 d_imputed <- (density(d_imputed)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4014 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4015 can_plot_before_after_imp <- FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4016 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4017 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4018 # There are NO missing values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4019 d_imputed <- d_combined |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4020 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4021 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4022 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4023 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4024 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4025 zero_sd_rownames <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4026 rownames(quant_data_imp)[ |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4027 is.na((row_apply(quant_data_imp, sd, na.rm = TRUE)) == 0) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4028 ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4029 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4030 if (length(zero_sd_rownames) >= nrow(quant_data_imp)) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4031 cat("All peptides have zero standard deviation. Cannot continue.") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4032 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4033 knitr::knit_exit() |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4034 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4035 if (length(zero_sd_rownames) > 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4036 cat( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4037 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4038 "%d %s %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4039 length(zero_sd_rownames), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4040 "peptides with zero variance", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4041 "were removed from statistical consideration" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4042 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4043 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4044 zap_named_rows <- function(df, nms) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4045 return(df[!(row.names(df) %in% nms), ]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4046 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4047 quant_data_imp <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4048 zap_named_rows(quant_data_imp, zero_sd_rownames) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4049 quant_data <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4050 zap_named_rows(quant_data, zero_sd_rownames) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4051 full_data <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4052 zap_named_rows(full_data, zero_sd_rownames) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4053 min_group_obs_count <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4054 min_group_obs_count[names(min_group_obs_count) %notin% zero_sd_rownames] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4055 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4056 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4057 if (sum(is.na(quant_data)) > 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4058 cat("\\leavevmode\\newpage\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4059 # Copy quant data to x |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4060 x <- quant_data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4061 # x gets to have values of: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4062 # - NA for observed values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4063 # - 1 for missing values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4064 x[is.na(x)] <- 0 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4065 x[x > 1] <- NA |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4066 x[x == 0] <- 1 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4067 # Log-transform imputed data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4068 # update variable because rows may have been eliminated from quant_data_imp |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4069 quant_data_imp_log10 <- log10(quant_data_imp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4070 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4071 write_debug_file(quant_data_imp_log10) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4072 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4073 # Set blue_dots to log of quant data or NA for NA quant data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4074 blue_dots <- log10(quant_data) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4075 # Set red_dots to log of imputed data or NA for observed quant data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4076 red_dots <- quant_data_imp_log10 * x |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4077 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4078 count_red <- sum(!is.na(red_dots)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4079 count_blue <- sum(!is.na(blue_dots)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4080 ylim_save <- ylim <- c( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4081 min(red_dots, blue_dots, na.rm = TRUE), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4082 max(red_dots, blue_dots, na.rm = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4083 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4084 show_stripchart <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4085 50 > (count_red + count_blue) / length(sample_name_matches) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4086 if (show_stripchart) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4087 boxplot_sub <- "Light blue = data before imputation; Red = imputed data;" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4088 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4089 boxplot_sub <- "" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4090 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4091 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4092 # Vertical plot |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4093 colnames(blue_dots) <- sample_name_matches |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4094 my_ppep_distrib_bxp( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4095 x = blue_dots |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4096 , sample_name_grow = sample_name_grow |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4097 , main = "Peptide intensities after eliminating unusable peptides" |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4098 , varwidth = boxplot_varwidth |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4099 , sub = paste(boxplot_sub, "Box widths reflect number of peptides for sample") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4100 , xlab = "Sample" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4101 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4102 , col = const_boxplot_fill |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4103 , notch = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4104 , ylim = ylim |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4105 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4106 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4107 if (show_stripchart) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4108 # Points |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4109 # ref: https://r-charts.com/distribution/add-points-boxplot/ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4110 # NA values are not plotted |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4111 stripchart( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4112 blue_dots, # Data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4113 method = "jitter", # Random noise |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4114 jitter = const_stripchart_jitter, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4115 pch = 19, # Pch symbols |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4116 cex = const_stripchart_cex, # Size of symbols reduced |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4117 col = "lightblue", # Color of the symbol |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4118 vertical = TRUE, # Vertical mode |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4119 add = TRUE # Add it over |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4120 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4121 stripchart( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4122 red_dots, # Data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4123 method = "jitter", # Random noise |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4124 jitter = const_stripchart_jitter, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4125 pch = 19, # Pch symbols |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4126 cex = const_stripchart_cex, # Size of symbols reduced |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4127 col = "red", # Color of the symbol |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4128 vertical = TRUE, # Vertical mode |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4129 add = TRUE # Add it over |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4130 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4131 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4132 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4133 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4134 ``` |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4135 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4136 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4137 if (sum(is.na(quant_data)) > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4138 # show measured values in blue on left half-violin plot |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4139 cat("\\leavevmode\n\\quad\n\n\\quad\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4140 old_par <- par( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4141 mai = par("mai") + c(g_ppep_distrib_ctl$mai_bottom, 0, 0, 0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4142 cex.axis = g_ppep_distrib_ctl$axis, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4143 cex.lab = 1.2 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4144 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4145 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4146 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4147 vioplot::vioplot( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4148 x = lapply(blue_dots, function(x) x[!is.na(x)]), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4149 col = "lightblue1", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4150 side = "left", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4151 plotCentre = "line", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4152 ylim = ylim_save, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4153 main = "Distributions of observed and imputed data", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4154 sub = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4155 las = 2, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4156 xlab = NULL, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4157 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4158 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4159 title( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4160 sub = "Light blue = observed data; Pink = imputed data", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4161 cex.sub = 1.0, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4162 line = g_ppep_distrib_ctl$xlab_line + 1 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4163 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4164 title( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4165 xlab = "Sample", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4166 line = g_ppep_distrib_ctl$xlab_line |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4167 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4168 red_violins <- lapply(red_dots, function(x) x[!is.na(x)]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4169 cols_to_delete <- c() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4170 for (ix in seq_len(length(red_violins))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4171 if (length(red_violins[[ix]]) < 1) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4172 cols_to_delete <- c(cols_to_delete, ix) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4173 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4174 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4175 # destroy any unimputable columns |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4176 if (!is.null(cols_to_delete)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4177 red_violins <- red_violins[-cols_to_delete] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4178 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4179 # plot imputed values in red on right half-violin plot |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4180 vioplot::vioplot( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4181 x = red_violins, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4182 col = "lightpink1", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4183 side = "right", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4184 plotCentre = "line", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4185 add = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4186 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4187 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4188 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4189 finally = par(old_par) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4190 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4191 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4192 # density plot |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4193 cat("\\leavevmode\n\n\n\n\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4194 if (can_plot_before_after_imp) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4195 ylim <- c( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4196 0, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4197 max( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4198 if (is.list(d_combined)) d_combined$y else d_combined, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4199 if (is.list(d_original)) d_original$y else d_original, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4200 if (is.list(d_imputed)) d_imputed$y else d_imputed, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4201 na.rm = TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4202 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4203 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4204 plot( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4205 d_combined, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4206 ylim = ylim, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4207 sub = |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4208 paste( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4209 "Blue = data before imputation; Red = imputed data;", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4210 "Black = combined" |
|
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|
4211 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4212 main = "Density of peptide intensity before and after imputation", |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4213 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4214 ylab = "Probability density" |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4215 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4216 lines(d_original, col = "blue") |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4217 lines(d_imputed, col = "red") |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4218 } else { |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4219 cat( |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4220 "There are too few points to plot the density of peptide intensity", |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4221 "before and after imputation." |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4222 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4223 } |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4224 cat("\\leavevmode\\newpage\n") |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4225 } |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4226 ``` |
|
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|
4227 |
|
27
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diff
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|
4228 # Quantile Normalization |
|
24
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|
4229 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4230 The excellent `normalize.quantiles` function from |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4231 *[the `preprocessCore` Bioconductor package](http://bioconductor.org/packages/release/bioc/html/preprocessCore.html)* |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4232 performs "quantile normalization" as described Bolstad *et al.* (2003), |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4233 DOI *[10.1093/bioinformatics/19.2.185](https://doi.org/10.1093%2Fbioinformatics%2F19.2.185)* |
|
27
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|
4234 and its supplementary material [http://bmbolstad.com/misc/normalize/normalize.html](http://bmbolstad.com/misc/normalize/normalize.html), |
|
24
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|
4235 i.e., it assumes that the goal is to detect |
|
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|
4236 subtle differences among grossly similar samples (having similar distributions) |
|
27
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diff
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|
4237 by equalizing intra-quantile quantitations^[Unfortunately, |
|
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diff
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|
4238 one software library upon which `preprocessCore` depends |
|
24
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4239 *[suffers from a concurrency defect](https://support.bioconductor.org/p/122925/#9135989)* |
|
27
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|
4240 that requires that a specific, non-concurrent version of the library (`openblas` version $0.3.3$) be |
|
24
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|
4241 installed. The installation command equivalent to what was used to install the library to produce the results presented here is: |
|
27
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|
4242 \linebreak |
|
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|
4243 ` conda install bioconductor-preprocesscore openblas=0.3.3`]. |
|
24
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|
4244 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4245 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4246 <!-- |
|
27
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|
4247 # Apply quantile normalization using preprocessCore::normalize.quantiles |
|
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|
4248 # --- |
|
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|
4249 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html |
|
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|
4250 # except this: https://support.bioconductor.org/p/122925/#9135989 |
|
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|
4251 # says to install it like this: |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
4252 # ``` |
|
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|
4253 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1]) |
|
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|
4254 # ``` |
|
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diff
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|
4255 # conda installation (necessary because of a bug in recent openblas): |
|
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|
4256 # conda install bioconductor-preprocesscore openblas=0.3.3 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
4257 # ... |
|
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diff
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|
4258 # --- |
|
29775869faba
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diff
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|
4259 # normalize.quantiles {preprocessCore} -- Quantile Normalization |
|
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|
4260 # |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
4261 # Description: |
|
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diff
changeset
|
4262 # Using a normalization based upon quantiles, this function normalizes a |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
4263 # matrix of probe level intensities. |
|
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|
4264 # |
|
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|
4265 # THIS FUNCTIONS WILL HANDLE MISSING DATA (ie NA values), based on the |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
4266 # assumption that the data is missing at random. |
|
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|
4267 # |
|
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|
4268 # Usage: |
|
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|
4269 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE) |
|
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|
4270 # |
|
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|
4271 # Arguments: |
|
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|
4272 # |
|
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|
4273 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe. |
|
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|
4274 # |
|
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|
4275 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy, |
|
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|
4276 # but in certain situations not making a copy of the matrix, but instead normalizing |
|
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|
4277 # it in place will be more memory friendly. |
|
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|
4278 # |
|
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|
4279 # - keep.names: Boolean option to preserve matrix row and column names in output. |
|
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|
4280 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
4281 # Details: |
|
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|
4282 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions. |
|
29775869faba
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|
4283 # No special allowances are made for outliers. If you make use of quantile normalization |
|
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|
4284 # please cite Bolstad et al, Bioinformatics (2003). |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
4285 # |
|
29775869faba
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changeset
|
4286 # This functions will handle missing data (ie NA values), based on |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
4287 # the assumption that the data is missing at random. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4288 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
4289 # Note that the current implementation optimizes for better memory usage |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4290 # at the cost of some additional run-time. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4291 # |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4292 # Value: A normalized matrix. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4293 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4294 # Author: Ben Bolstad, bmbolstad.com |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4295 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4296 # References |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
4297 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4298 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4299 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf |
|
29775869faba
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diff
changeset
|
4300 # |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4301 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of |
|
29775869faba
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diff
changeset
|
4302 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4303 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185 |
|
29775869faba
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diff
changeset
|
4304 # http://bmbolstad.com/misc/normalize/normalize.html |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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changeset
|
4305 # ... |
|
24
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changeset
|
4306 --> |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4307 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4308 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4309 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp)), "\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4310 if (nrow(quant_data_imp) > 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4311 quant_data_imp_qn <- preprocessCore::normalize.quantiles( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4312 as.matrix(quant_data_imp), keep.names = TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4313 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4314 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4315 quant_data_imp_qn <- as.matrix(quant_data_imp) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4316 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4317 |
|
27
29775869faba
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diff
changeset
|
4318 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn)), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
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|
4319 |
|
24
657663e89728
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changeset
|
4320 quant_data_imp_qn <- as.data.frame(quant_data_imp_qn) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4321 write_debug_file(quant_data_imp_qn) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4322 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4323 quant_data_imp_qn_log <- log10(quant_data_imp_qn) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4324 write_debug_file(quant_data_imp_qn_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4325 |
|
27
29775869faba
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diff
changeset
|
4326 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4327 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n") |
|
29775869faba
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diff
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|
4328 |
|
24
657663e89728
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changeset
|
4329 quant_data_imp_qn_ls <- t(scale(t(log10(quant_data_imp_qn)))) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4330 |
|
27
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|
4331 sel <- row_apply(quant_data_imp_qn_ls, any_nan) |
|
24
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|
4332 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4333 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4334 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls2[which(sel), ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4335 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4336 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4337 quant_data_imp_qn_ls <- as.data.frame(quant_data_imp_qn_ls) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4338 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4339 write_debug_file(quant_data_imp_qn_ls) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4340 write_debug_file(quant_data_imp_qn_ls2) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4341 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4342 # Create data.frame used by ANOVA analysis |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4343 data_table_imp_qn_lt <- cbind(full_data[1:9], quant_data_imp_qn_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4344 ``` |
|
657663e89728
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changeset
|
4345 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4346 ## Are normalized, imputed, log-transformed sample distributions similar? |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4347 |
|
27
29775869faba
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diff
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|
4348 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
24
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|
4349 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4350 # Save unimputed quant_data_log for plotting below |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
4351 unimputed_quant_data_log <- quant_data_log |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4352 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4353 # log10 transform (after preparing for zero values, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4354 # which should never happen...) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4355 quant_data_imp_qn[quant_data_imp_qn == 0] <- .000000001 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4356 quant_data_log <- log10(quant_data_imp_qn) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4357 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4358 how_many_peptides <- nrow(quant_data_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4359 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4360 if ((how_many_peptides) > 0) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
4361 cat( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
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changeset
|
4362 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
4363 "Intensities for %d peptides:\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4364 how_many_peptides |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4365 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4366 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4367 cat("\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4368 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4369 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4370 # data visualization |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4371 if (TRUE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4372 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4373 my_ppep_distrib_bxp( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4374 x = quant_data_log |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4375 , sample_name_grow = sample_name_grow |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4376 , main = "Peptide intensities for each sample" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4377 , varwidth = boxplot_varwidth |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4378 , sub = NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4379 , xlab = "Sample" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4380 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4381 , col = const_boxplot_fill |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4382 , notch = boxplot_notch |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4383 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4384 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4385 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4386 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4387 old_par <- par( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4388 mai = par("mai") + c(0.5, 0, 0, 0) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4389 , oma = par("oma") + c(0.5, 0, 0, 0) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4390 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4391 # ref: https://r-charts.com/distribution/add-points-boxplot/ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4392 # Vertical plot |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4393 colnames(quant_data_log) <- sample_name_matches |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4394 boxplot( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4395 quant_data_log |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4396 , las = 2 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4397 , cex.axis = 0.9 * sample_name_grow |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4398 , col = const_boxplot_fill |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4399 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4400 , xlab = "Sample" |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4401 , notch = boxplot_notch |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4402 , varwidth = boxplot_varwidth |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4403 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4404 par(old_par) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4405 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4406 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4407 cat("There are no peptides to plot\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4408 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4409 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4410 cat("\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4411 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4412 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4413 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4414 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4415 if (nrow(quant_data_log) > 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4416 quant_data_log_stack <- stack(quant_data_log) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4417 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) + |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4418 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) + |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4419 ggplot2::ylab("Probability density") + |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4420 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4421 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4422 cat("No density plot because there are fewer than two peptides to plot.\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4423 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4424 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4425 ```{r echo = FALSE, results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4426 cat("\\leavevmode\\newpage\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4427 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4428 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
4429 # ANOVA Analysis |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
4430 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4431 ## Assignment of $p$-value and quality score |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4432 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4433 For each phosphopeptide, ANOVA analysis was performed to compute a $p$-value representing the evidence against the "null hypothesis" ($H_0$) that the intensity does not vary significantly among sample groups. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4434 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4435 However, because as more and more phosphopeptides are tested, there is increasd probability that, by random chance, a given peptide will have a $p$-value that appears to indicate significance. For this reason, the $p$-values were adjusted by applying the False Discovery Rate (FDR) correction from Benjamini and Hochberg (1995) [doi:10.1111/j.2517-6161.1995.tb02031.x](https:/doi.org/10.1111/j.2517-6161.1995.tb02031.x). |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4436 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
4437 Furthermore, to give more weight to phosphopeptides having fewer missing values, an (arbitrarily defined) quality score was assigned to each, defined as: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4438 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
4439 $$ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4440 \textit{quality}_j |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
4441 = \frac{1 + o_{j}}{v_{j}(1 + o_{j}) + 0.005} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4442 $$ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4443 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4444 where: |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4445 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4446 - $o_j$ is the minimum number of non-missing observations per sample group for substrate $j$ for all sample groups, and |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4447 - $v_j$ is the FDR-adjusted ANOVA $p$-value for substrate $j$. |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4448 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4449 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4450 ```{r, echo = FALSE, results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4451 cat("\\newpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4452 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4453 # Make new data frame containing only Phosphopeptides |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4454 # to connect preANOVA to ANOVA (connect_df) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4455 connect_df <- data.frame( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4456 data_table_imp_qn_lt$Phosphopeptide |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4457 , data_table_imp_qn_lt[, first_data_column] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4458 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4459 colnames(connect_df) <- c("Phosphopeptide", "Intensity") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4460 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4461 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4462 ```{r anova, echo = FALSE, fig.dim = c(10, 12), results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4463 g_can_run_ksea <- FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4464 old_oma <- par("oma") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4465 if (count_of_treatment_levels < 2) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4466 cat( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4467 "ERROR!!!! Cannot perform ANOVA analysis", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4468 "(see next page)\\newpage\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4469 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4470 cat( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4471 "ERROR: ANOVA analysis", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4472 "requires two or more factor levels!\n\n\n" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4473 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4474 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4475 cat("\n\n\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4476 cat("Unparsed sample names are:\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4477 "\\begin{quote}\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4478 paste(names(quant_data_imp_qn_log), collapse = "\n\n\n"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4479 "\n\\end{quote}\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4480 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4481 regex_sample_names <- latex_printable_control_seqs(regex_sample_names) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4482 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4483 cat("\\leavevmode\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4484 cat("Parsing rule for SampleNames is", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4485 "\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4486 "\\text{'", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4487 regex_sample_names, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4488 "'}\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4489 sep = "" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4490 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4491 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4492 cat("\nParsed sample names are:\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4493 "\\begin{quote}\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4494 paste(sample_name_matches, collapse = "\n\n\n"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4495 "\n\\end{quote}\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4496 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4497 regex_sample_grouping <- latex_printable_control_seqs(regex_sample_grouping) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4498 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4499 cat("\\leavevmode\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4500 cat("Parsing rule for SampleGrouping is", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4501 "\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4502 "\\text{'", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4503 regex_sample_grouping, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4504 "'}\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4505 sep = "" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4506 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4507 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4508 cat("\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4509 cat("Sample group assignments are:\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4510 "\\begin{quote}\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4511 paste(regmatches(sample_name_matches, rx_match), collapse = "\n\n\n"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4512 "\n\\end{quote}\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4513 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4514 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4515 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4516 if (print_nb_messages) nbe("computing p_value_data_anova_ps\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4517 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4518 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4519 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log[, ".NE.7C"]), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4520 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4521 if (print_nb_messages) nbe(see_variable(anova_func), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4522 if (print_nb_messages) nbe(see_variable(smpl_trt), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4523 if (print_nb_messages) nbe(see_variable(one_way_all_categories), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4524 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4525 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4526 p_value_data_anova_ps <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4527 row_apply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4528 quant_data_imp_qn_log, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4529 anova_func, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4530 grouping_factor = smpl_trt, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4531 one_way_f = one_way_all_categories |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4532 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4533 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4534 error = function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4535 mesg <- paste("Could not compute ANOVA because", e$message) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4536 cat("\n\n", mesg, "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4537 param_df_noexit(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4538 sink(stderr()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4539 cat("\n\n", mesg, "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4540 values <- paste(param_df$parameter, "=", param_df$value, collapse = "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4541 cat(values) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4542 sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4543 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4544 exit(code = 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4545 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4546 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4547 if (print_nb_messages) nbe(see_variable(p_value_data_anova_ps), "\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4548 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4549 p_value_data_anova_ps_fdr <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4550 p.adjust(p_value_data_anova_ps, method = "fdr") |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4551 my_ppep_v <- full_data[, 1] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4552 p_value_data <- list( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4553 phosphopeptide = my_ppep_v, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4554 raw_anova_p = p_value_data_anova_ps, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4555 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4556 missing_values = rowSums(is.na(quant_data)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4557 min_group_obs_count = min_group_obs_count |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4558 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4559 p_value_data <- data.frame( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4560 phosphopeptide = my_ppep_v, |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4561 raw_anova_p = p_value_data_anova_ps, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4562 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4563 missing_values = rowSums(is.na(quant_data)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4564 min_group_obs_count = min_group_obs_count |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4565 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4566 p_value_data$quality <- 1.0 / with( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4567 p_value_data, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4568 fdr_adjusted_anova_p + 0.005 / (1 + min_group_obs_count) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4569 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4570 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4571 p_value_data$ranking <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4572 with( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4573 p_value_data, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4574 switch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4575 g_intensity_hm_criteria, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4576 "quality" = order(-quality), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4577 "na_count" = order(missing_values, fdr_adjusted_anova_p), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4578 # the default is "p_value" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4579 order(fdr_adjusted_anova_p) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4580 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4581 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4582 p_value_data <- p_value_data[p_value_data$ranking, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4583 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4584 write.table( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4585 p_value_data, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4586 file = "p_value_data.txt", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4587 sep = "\t", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4588 col.names = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4589 row.names = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4590 quote = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4591 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4592 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4593 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4594 # output ANOVA file to constructed filename, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4595 # e.g. "Outputfile_pST_ANOVA_STEP5.txt" |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4596 # becomes "Outputfile_pST_ANOVA_STEP5_FDR0.05.txt" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4597 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4598 # Re-output datasets to include p-values |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4599 metadata_plus_p <- cbind(full_data[1:9], p_value_data[, 2:ncol(p_value_data)]) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4600 write.table( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4601 cbind(metadata_plus_p, quant_data_imp), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4602 file = imputed_data_filename, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4603 sep = "\t", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4604 col.names = TRUE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4605 row.names = FALSE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4606 quote = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4607 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4608 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4609 write.table( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4610 cbind(metadata_plus_p, quant_data_imp_qn_log), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4611 file = imp_qn_lt_data_filenm, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4612 sep = "\t", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4613 col.names = TRUE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4614 row.names = FALSE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4615 quote = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4616 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4617 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4618 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4619 first_page_suppress <- 1 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4620 number_of_peptides_found <- 0 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4621 cutoff <- val_fdr[1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4622 for (cutoff in val_fdr) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4623 #loop through FDR cutoffs |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4624 if (number_of_peptides_found > g_intensity_hm_rows - 1) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4625 cat("\\leavevmode\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4626 break |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4627 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4628 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4629 bool_1 <- (p_value_data$fdr_adjusted_anova_p < cutoff) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4630 bool_2 <- (p_value_data$min_group_obs_count >= g_intensity_min_per_class) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4631 g_can_run_ksea <- g_can_run_ksea || (sum(bool_2) > 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4632 bool_4 <- (p_value_data$quality >= params$minQuality) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4633 bool_3 <- as.logical( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4634 as.integer(bool_1) * |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4635 as.integer(bool_2) * |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4636 as.integer(bool_4) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4637 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4638 if (print_trace_messages) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4639 if (length(bool_1) > 30) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4640 cat_variable(bool_1, force_str = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4641 cat_variable(bool_2, force_str = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4642 cat_variable(bool_3, force_str = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4643 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4644 cat_variable(bool_1, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4645 cat_variable(bool_2, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4646 cat_variable(bool_3, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4647 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4648 cat_variable(length(bool_3), digits = 0, suffix = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4649 cat_variable(sum(bool_3), digits = 0, suffix = "\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4650 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4651 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4652 filtered_p <- |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4653 p_value_data[bool_3, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4654 filtered_p <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4655 filtered_p[!is.na(filtered_p$phosphopeptide), , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4656 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4657 if (print_trace_messages) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4658 cat_variable(filtered_p, force_str = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4659 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4660 have_remaining_peptides <- sum(bool_3, na.rm = TRUE) > 0 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4661 filter_result_string <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4662 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4663 "%s, %s of %0.0f peptides remained having both %s and %s.\n\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4664 "After filtering for ANOVA results", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4665 if (have_remaining_peptides) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4666 as.character(sum(bool_3, na.rm = TRUE)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4667 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4668 "none", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4669 length(bool_3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4670 sprintf("adjusted p-value < %s", as.character(signif(cutoff, 2))), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4671 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4672 "more than %0.0f observations in some groups", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4673 max(0, g_intensity_min_per_class - 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4674 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4675 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4676 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4677 filtered_data_filtered <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4678 quant_data_imp_qn_log[ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4679 rownames(filtered_p), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4680 , drop = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4681 ] |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4682 # order by p-value |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4683 filtered_data_filtered <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4684 filtered_data_filtered[ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4685 order(filtered_p$fdr_adjusted_anova_p), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4686 , drop = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4687 ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4688 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4689 if (have_remaining_peptides && nrow(filtered_p) > 0 && nrow(filtered_data_filtered) > 0) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4690 if (first_page_suppress == 1) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4691 first_page_suppress <- 0 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4692 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4693 cat("\\newpage\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4694 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4695 latex_samepage({ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4696 cat(filter_result_string) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4697 if (nrow(filtered_data_filtered) > 1) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4698 cat(subsection_header(sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4699 "Intensity distributions for %d phosphopeptides\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4700 nrow(filtered_data_filtered) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4701 ))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4702 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4703 cat(subsection_header(sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4704 "Intensity distribution for one phosphopeptide (%s)\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4705 rownames(filtered_data_filtered)[1] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4706 ))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4707 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4708 }) # end latex_samepage |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4709 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4710 old_par <- par( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4711 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4712 oma = old_oma * c(1, 1, 0.3, 1), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4713 cex.main = 0.9, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4714 cex.axis = 0.7, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4715 fin = c(9, 7.25) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4716 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4717 # Vertical plot |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4718 colnames(filtered_data_filtered) <- sample_name_matches |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4719 tryCatch( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4720 boxplot( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4721 filtered_data_filtered, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4722 main = "Imputed, normalized intensities", # no line plot |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4723 las = 2, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4724 cex.axis = 0.9 * sample_name_grow, |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4725 col = const_boxplot_fill, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4726 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4727 notch = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4728 varwidth = boxplot_varwidth |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4729 ), |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4730 error = function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4731 print(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4732 cat_margins() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4733 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4734 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4735 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4736 par(old_par) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4737 } else { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4738 cat(sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4739 "%s < %0.2f\n\n\n\n\n", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4740 "No peptides were found to have cutoff adjusted p-value", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4741 cutoff |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4742 )) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4743 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4744 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4745 if (have_remaining_peptides && nrow(filtered_data_filtered) > 0) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4746 # Add Phosphopeptide column to anova_filtered table |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4747 # The assumption here is that the first intensity is unique; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4748 # this is a hokey assumption but almost definitely will |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4749 # be true in the real world unless there is a computation |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4750 # error upstream. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4751 anova_filtered_merge <- base::merge( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4752 x = connect_df, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4753 y = filtered_data_filtered, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4754 by.x = "Intensity", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4755 by.y = 1 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4756 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4757 anova_filtered_merge_order <- rownames(filtered_p) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4758 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4759 anova_filtered <- data.frame( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4760 ppep = anova_filtered_merge$Phosphopeptide, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4761 intense = anova_filtered_merge$Intensity, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4762 data = anova_filtered_merge[, 2:number_of_samples + 1] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4763 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4764 colnames(anova_filtered) <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4765 c("Phosphopeptide", colnames(filtered_data_filtered)) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4766 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4767 # Merge qualitative columns into the ANOVA data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4768 output_table <- data.frame(anova_filtered$Phosphopeptide) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4769 output_table <- base::merge( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4770 x = output_table, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4771 y = data_table_imp_qn_lt, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4772 by.x = "anova_filtered.Phosphopeptide", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4773 by.y = "Phosphopeptide" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4774 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4775 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4776 # Produce heatmap to visualize significance and the effect of imputation |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4777 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4778 cat_hm_heading <- function(m, cutoff) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4779 if (nrow(m) > g_intensity_hm_rows) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4780 cat("\\clearpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4781 cat(subsection_header( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4782 paste( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4783 sprintf("Heatmap for the %d most-significant peptides", |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4784 g_intensity_hm_rows), |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4785 sprintf("whose adjusted p-value < %0.2f\n", cutoff) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4786 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4787 )) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4788 } else { |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4789 if (nrow(m) == 0) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4790 return(FALSE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4791 } else { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4792 cat(subsection_header( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4793 paste( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4794 sprintf("Heatmap for %d usable peptide genes whose", nrow(m)), |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4795 sprintf("adjusted p-value < %0.2f\n", cutoff) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4796 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4797 )) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4798 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4799 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4800 cat("\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4801 cat("\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4802 return(TRUE) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4803 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4804 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4805 # construct matrix with appropriate rownames |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4806 m <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4807 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ]) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4808 nrow_m <- nrow(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4809 ncol_m <- ncol(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4810 if (nrow_m > 0) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4811 rownames_m <- rownames(m) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4812 q <- data.frame(pepname = rownames_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4813 g <- sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4814 SELECT q.pepname, substr(met.Gene_Name, 1, 30) AS gene_name |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4815 FROM q, metadata_plus_p AS met |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4816 WHERE q.pepname = met.Phosphopeptide |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4817 ORDER BY q.rowid |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4818 ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4819 tmp <- sapply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4820 X = seq_len(nrow(g)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4821 FUN = function(i) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4822 pre <- strsplit(g$gene_name[i], "; ")[[1]] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4823 rslt <- paste(unique(pre), sep = "; ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4824 return(rslt) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4825 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4826 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4827 tmp <- unlist(tmp) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4828 tmp <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4829 make.names(tmp, unique = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4830 tmp <- sub( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4831 "No_Gene_Name", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4832 "not_found", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4833 tmp, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4834 fixed = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4835 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4836 ten_trunc_names <- trunc_ppep(rownames_m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4837 tmp <- sapply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4838 X = seq_len(nrow_m), |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4839 FUN = function(i) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4840 sprintf( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4841 "(%s) %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4842 tmp[i], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4843 ten_trunc_names[i] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4844 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4845 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4846 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4847 rownames(m) <- tmp |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4848 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4849 # draw the heading and heatmap |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4850 if (nrow_m > 0) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4851 number_of_peptides_found <- |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4852 ppep_heatmap( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4853 m = m, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4854 cutoff = cutoff, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4855 hm_heading_function = cat_hm_heading, |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4856 hm_main_title = |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4857 "log(intensities), row-scaled, unimputed, unnormalized", |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4858 suppress_row_dendrogram = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4859 master_cex = 0.35, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4860 sepcolor = "black", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4861 colsep = sample_colsep |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4862 ) |
|
26
bac8e9515863
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents:
25
diff
changeset
|
4863 if (number_of_peptides_found > 1) { |
|
bac8e9515863
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents:
25
diff
changeset
|
4864 cat("\\leavevmode\n") |
|
bac8e9515863
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents:
25
diff
changeset
|
4865 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4866 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4867 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4868 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4869 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4870 cat(filter_result_string) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
4871 cat("\\leavevmode\n") |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4872 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4873 if (!g_can_run_ksea) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4874 errmsg <- paste("Cannot proceed with KSEA analysis", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4875 "because too many values are missing.") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4876 if (FALSE) cat0( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4877 errmsg, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4878 "\\stepcounter{offset}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4879 "\\stepcounter{offset}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4880 "\\stepcounter{offset}\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4881 " in ", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4882 table_href(), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4883 ".\n\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4884 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4885 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4886 if (print_nb_messages) nbe(see_variable(p_value_data)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4887 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4888 if (print_nb_messages) nbe(see_variable(p_value_data)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4889 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4890 display_p_value_data <- p_value_data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4891 display_p_value_data$raw_anova_p <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4892 sprintf("%0.3g", display_p_value_data$raw_anova_p) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4893 display_p_value_data$fdr_adjusted_anova_p <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4894 sprintf("%0.3g", display_p_value_data$fdr_adjusted_anova_p) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4895 display_p_value_data$quality <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4896 sprintf("%0.3g", display_p_value_data$quality) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4897 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4898 headers_1st_line <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4899 c("", "Raw ANOVA", "FDR-adj.", "Missing", "Min. #", "", "") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4900 headers_2nd_line <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4901 c("Phosphopeptide", "p-value", "p-value", "values", "group-obs", "Quality", "Ranking") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4902 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4903 x = display_p_value_data, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4904 tabstops = c(2.75, 0.80, 0.80, 0.5, 0.6, 0.60), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4905 use_subsubsection_header = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4906 headings = c(headers_1st_line, headers_2nd_line), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4907 caption = "ANOVA results" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4908 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4909 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4910 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4911 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4912 x = save_sample_treatment_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4913 tabstops = c(1.25, 1.25), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4914 caption = "Sample classes", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4915 use_subsubsection_header = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4916 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4917 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4918 knitr::knit_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4919 return(invisible(-1)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4920 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4921 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4922 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4923 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4924 ```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4925 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4926 if (g_can_run_ksea && count_of_treatment_levels > 1) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4927 # Prepare two-way contrasts with adjusted p-values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4928 # Strategy: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4929 # - use imputed, log-transformed data: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4930 # - remember this when computing log2(fold-change) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4931 # - each contrast is between a combination of trt levels |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4932 # - for each contrast, compute samples that are members |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4933 # - compute one-way test: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4934 # - use `oneway.test` (Welch test) if numbers of samples |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4935 # are not equivalent between trt levels |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4936 # - otherwise, aov is fine but offers no advantage |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4937 # - adjust p-value, assuming that |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4938 # (# of pppeps)*(# of contrasts) tests were performed |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4939 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4940 # Each contrast is between a combination of trt levels |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4941 m2 <- combn( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4942 x = seq_len(length(levels(smpl_trt))), |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4943 m = 2, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4944 simplify = TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4945 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4946 contrast_count <- ncol(m2) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4947 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4948 # For each contrast, compute samples that are members |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4949 # - local function to construct a data.frame for each contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4950 # - the contrast in the first "column" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4951 f_m2 <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4952 function(cntrst, lvl1, lvl2) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4953 return( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4954 data.frame( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4955 contrast = cntrst, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4956 level = smpl_trt[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4957 smpl_trt %in% |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4958 levels(smpl_trt)[c(lvl1, lvl2)] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4959 ], |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4960 label = sample_name_matches[ |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4961 smpl_trt %in% |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
4962 levels(smpl_trt)[c(lvl1, lvl2)] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4963 ] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4964 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4965 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4966 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4967 # - compute a df for each contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4968 sample_level_dfs <- lapply( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4969 X = 1:contrast_count, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4970 FUN = function(i) f_m2(i, m2[1, i], m2[2, i]) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4971 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4972 # - compute a single df for all contrasts |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4973 combined_contrast_df <- Reduce(f = rbind, x = sample_level_dfs) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4974 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4975 # - dispose objects to free resources |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4976 rm(sample_level_dfs) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4977 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4978 # - write the df to a DB for later join-per-contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4979 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4980 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4981 RSQLite::dbWriteTable( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4982 conn = db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4983 name = "contrast", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4984 value = combined_contrast_df, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4985 overwrite = TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4986 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4987 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4988 # Create UK for insert |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4989 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4990 CREATE UNIQUE INDEX IF NOT EXISTS contrast__uk__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4991 ON contrast(contrast, label); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4992 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4993 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4994 # Create indexes for join |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4995 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4996 -- index for join in contrast_ppep_smpl_qnlt on a.label < b.label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4997 CREATE INDEX IF NOT EXISTS contrast__label__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4998 ON contrast(label); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
4999 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5000 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5001 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5002 -- index for joining two contrast_lvl_ppep_avg_quant on contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5003 CREATE INDEX IF NOT EXISTS contrast__contrast__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5004 ON contrast(contrast); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5005 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5006 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5007 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5008 -- index for joining two contrast_lvl_ppep_avg_quant on phophospep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5009 CREATE INDEX IF NOT EXISTS contrast__level__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5010 ON contrast(level); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5011 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5012 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5013 # - dispose objects to free resources |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5014 rm(combined_contrast_df) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5015 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5016 # Use imputed, log-transformed data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5017 # - remember that this was donoe when computing log2(fold-change) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5018 # - melt data matrix for use in later join-per-contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5019 casted <- cbind( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5020 data.frame(vrbl = rownames(quant_data_imp_qn_log)), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5021 quant_data_imp_qn_log |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5022 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5023 quant_data_imp_qn_log_melted <- reshape2::melt( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5024 casted, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5025 id.vars = "vrbl" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5026 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5027 colnames(quant_data_imp_qn_log_melted) <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5028 c("phosphopep", "sample", "quant") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5029 # - dispose objects to free resources |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5030 rm(casted) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5031 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5032 # - write the df to a DB for use in later join-per-contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5033 RSQLite::dbWriteTable( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5034 conn = db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5035 name = "ppep_smpl_qnlt", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5036 value = quant_data_imp_qn_log_melted, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5037 overwrite = TRUE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5038 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5039 # Create UK for insert |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5040 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5041 CREATE UNIQUE INDEX IF NOT EXISTS ppep_smpl_qnlt__uk__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5042 ON ppep_smpl_qnlt(phosphopep, sample); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5043 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5044 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5045 # Create index for join |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5046 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5047 -- index for join in contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5048 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__sample__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5049 ON ppep_smpl_qnlt(sample); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5050 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5051 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5052 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5053 -- index for joining two contrast_lvl_ppep_avg_quant on phopho.pep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5054 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__phosphopep__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5055 ON ppep_smpl_qnlt(phosphopep); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5056 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5057 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5058 # - dispose objects to free resources |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5059 rm(quant_data_imp_qn_log_melted) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5060 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5061 # - drop views if exist |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5062 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5063 -- drop view dependent on contrast_lvl_ppep_avg_quant |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5064 DROP VIEW IF EXISTS v_contrast_log2_fc; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5065 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5066 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5067 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5068 -- drop table dependent on contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5069 DROP TABLE IF EXISTS contrast_lvl_ppep_avg_quant; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5070 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5071 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5072 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5073 DROP TABLE IF EXISTS contrast_lvl_lvl_metadata; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5074 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5075 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5076 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5077 DROP VIEW IF EXISTS v_contrast_lvl_metadata; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5078 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5079 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5080 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5081 -- drop view dependent on contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5082 DROP VIEW IF EXISTS v_contrast_lvl_ppep_avg_quant; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5083 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5084 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5085 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5086 DROP VIEW IF EXISTS v_contrast_lvl_lvl; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5087 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5088 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5089 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5090 -- drop view upon which other views depend |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5091 DROP VIEW IF EXISTS contrast_ppep_smpl_qnlt; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5092 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5093 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5094 # - create view |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5095 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5096 -- view contrast_ppep_smpl_qnlt is used for each phopshopep to |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5097 -- compute p-value for test of trt effect for two trt levels |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5098 CREATE VIEW contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5099 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5100 SELECT contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5101 level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5102 phosphopep, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5103 sample, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5104 quant |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5105 FROM contrast AS c, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5106 ppep_smpl_qnlt AS q |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5107 WHERE q.sample = c.label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5108 ORDER BY contrast, level, phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5109 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5110 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5111 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5112 # - create simplification views |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5113 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5114 CREATE VIEW v_contrast_lvl_metadata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5115 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5116 SELECT contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5117 level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5118 group_concat(label, ';') AS samples |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5119 FROM contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5120 GROUP BY contrast, level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5121 /* view v_contrast_lvl_metadata is used |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5122 to simplify creation of table contrast_lvl_lvl_metadata */ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5123 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5124 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5125 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5126 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5127 CREATE VIEW v_contrast_lvl_ppep_avg_quant |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5128 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5129 SELECT contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5130 level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5131 phosphopep, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5132 avg(quant) AS avg_quant |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5133 FROM contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5134 GROUP BY contrast, level, phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5135 /* view v_contrast_lvl_ppep_avg_quant is used |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5136 to simplify view v_contrast_log2_fc */ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5137 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5138 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5139 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5140 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5141 # - create contrast-metadata table |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5142 if (print_nb_messages) nbe("CREATE TABLE contrast_lvl_lvl_metadata") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5143 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5144 CREATE TABLE contrast_lvl_lvl_metadata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5145 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5146 SELECT DISTINCT |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5147 a.contrast AS ab_contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5148 a.level AS a_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5149 b.level AS b_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5150 a.samples AS a_samples, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5151 b.samples AS b_samples, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5152 'log2(level_'||a.level||'/level_'||b.level||')' |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5153 AS fc_description |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5154 FROM v_contrast_lvl_metadata AS a, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5155 v_contrast_lvl_metadata AS b |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5156 WHERE a.contrast = b.contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5157 AND a.level > b.level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5158 /* view v_contrast_lvl_lvl is used |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5159 to simplify view v_contrast_log2_fc */ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5160 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5161 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5162 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5163 # - create pseudo-materialized view table |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5164 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5165 CREATE VIEW v_contrast_lvl_lvl |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5166 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5167 SELECT DISTINCT |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5168 a.contrast AS ab_contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5169 a.level AS a_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5170 b.level AS b_level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5171 FROM contrast AS a, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5172 contrast AS b |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5173 WHERE a.contrast = b.contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5174 AND a.level > b.level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5175 /* view v_contrast_lvl_lvl is used |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5176 to simplify view v_contrast_log2_fc */ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5177 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5178 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5179 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5180 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5181 # - create view to compute log2(fold-change) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5182 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5183 CREATE VIEW v_contrast_log2_fc |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5184 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5185 SELECT ab.ab_contrast AS contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5186 m.a_level AS a_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5187 c.avg_quant AS a_quant, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5188 m.a_samples AS a_samples, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5189 ab.b_level AS b_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5190 d.avg_quant AS b_quant, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5191 m.b_samples AS b_samples, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5192 m.fc_description AS fc_description, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5193 3.32193 * ( d.avg_quant - c.avg_quant) AS log2_fc, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5194 d.phosphopep AS phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5195 FROM contrast_lvl_lvl_metadata AS m, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5196 v_contrast_lvl_ppep_avg_quant AS d, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5197 v_contrast_lvl_lvl AS ab |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5198 INNER JOIN v_contrast_lvl_ppep_avg_quant AS c |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5199 ON c.contrast = ab.ab_contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5200 AND c.level = ab.a_level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5201 WHERE d.contrast = ab.ab_contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5202 AND m.ab_contrast = ab.ab_contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5203 AND d.level = ab.b_level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5204 AND d.phosphopep = c.phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5205 /* view to compute log2(fold-change) */ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5206 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5207 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5208 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5209 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5210 # For each contrast, compute samples that are members |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5211 # compute one-way test: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5212 # - use `oneway.test` (Welch test) if numbers of samples |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5213 # are not equivalent between trt levels |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5214 # - otherwise, aov is fine but offers no advantage |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5215 for (contrast in contrast_count:2) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5216 invisible(contrast) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5217 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5218 for (contrast in 1:contrast_count) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5219 contrast_df <- sqldf::sqldf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5220 x = paste0(" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5221 SELECT level, phosphopep, sample, quant |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5222 FROM contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5223 WHERE contrast = ", contrast, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5224 ORDER BY phosphopep, level, sample |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5225 "), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5226 connection = db |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5227 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5228 contrast_cast <- reshape2::dcast( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5229 data = contrast_df, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5230 formula = phosphopep ~ sample, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5231 value.var = "quant" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5232 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5233 contrast_cast_ncol <- ncol(contrast_cast) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5234 contrast_cast_data <- contrast_cast[, 2:contrast_cast_ncol] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5235 contrast_cast_samples <- colnames(contrast_cast_data) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5236 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5237 # - order grouping_factor by order of sample columns of contrast_cast_data |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5238 grouping_factor <- sqldf::sqldf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5239 x = paste0(" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5240 SELECT sample, level |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5241 FROM contrast_ppep_smpl_qnlt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5242 WHERE contrast = ", contrast, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5243 ORDER BY phosphopep, level, sample |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5244 LIMIT ", contrast_cast_ncol - 1 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5245 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5246 connection = db |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5247 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5248 rownames(grouping_factor) <- grouping_factor$sample |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5249 grouping_factor <- grouping_factor[, "level", drop = FALSE] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5250 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5251 # - run the two-level (one-way) test |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5252 p_value_data_contrast_ps <- |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5253 row_apply( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5254 x = contrast_cast_data, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5255 fun = anova_func, |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5256 grouping_factor = |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5257 as.factor(grouping_factor$level), # anova_func arg2 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5258 one_way_f = one_way_two_categories, # anova_func arg3 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5259 simplify = TRUE # TRUE is the default for simplify |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5260 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5261 contrast_data_adj_p_values <- p.adjust( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5262 p = p_value_data_contrast_ps, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5263 method = "fdr", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5264 n = length(p_value_data_contrast_ps) # this is the default, length(p) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5265 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5266 # - compute the fold-change |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5267 contrast_p_df <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5268 data.frame( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5269 contrast = contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5270 phosphopep = contrast_cast$phosphopep, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5271 p_value_raw = p_value_data_contrast_ps, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5272 p_value_adj = contrast_data_adj_p_values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5273 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5274 db_write_table_overwrite <- (contrast < 2) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5275 db_write_table_append <- !db_write_table_overwrite |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5276 RSQLite::dbWriteTable( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5277 conn = db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5278 name = "contrast_ppep_p_val", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5279 value = contrast_p_df, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5280 append = db_write_table_append |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5281 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5282 # Create UK for insert |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5283 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5284 CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5285 ON contrast_ppep_p_val(phosphopep, contrast); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5286 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5287 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5288 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5289 # Perhaps this could be done more elegantly using unique keys |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5290 # or creating the tables before saving data to them, but this |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5291 # is fast and, if the database exists on disk rather than in |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5292 # memory, it doesn't stress memory. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5293 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5294 CREATE TEMP table contrast_log2_fc |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5295 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5296 SELECT * |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5297 FROM v_contrast_log2_fc |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5298 ORDER BY contrast, phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5299 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5300 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5301 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5302 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5303 CREATE TEMP table ppep_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5304 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5305 SELECT p_value_raw, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5306 p_value_adj, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5307 contrast AS p_val_contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5308 phosphopep AS p_val_ppep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5309 FROM contrast_ppep_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5310 ORDER BY contrast, phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5311 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5312 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5313 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5314 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5315 DROP TABLE IF EXISTS contrast_log2_fc_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5316 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5317 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5318 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5319 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5320 CREATE TABLE contrast_log2_fc_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5321 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5322 SELECT a.*, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5323 b.p_value_raw, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5324 b.p_value_adj, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5325 b.p_val_contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5326 b.p_val_ppep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5327 FROM contrast_log2_fc a, ppep_p_val b |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5328 WHERE a.rowid = b.rowid |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5329 AND a.phosphopep = b.p_val_ppep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5330 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5331 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5332 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5333 # Create UK |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5334 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5335 CREATE UNIQUE INDEX IF NOT EXISTS contrast_log2_fc_p_val__uk__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5336 ON contrast_log2_fc_p_val(phosphopep, contrast); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5337 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5338 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5339 # Create indices for future queries |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5340 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5341 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__contrast__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5342 ON contrast_log2_fc_p_val(contrast); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5343 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5344 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5345 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5346 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__phosphopep__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5347 ON contrast_log2_fc_p_val(phosphopep); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5348 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5349 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5350 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5351 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_raw__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5352 ON contrast_log2_fc_p_val(p_value_raw); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5353 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5354 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5355 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5356 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_adj__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5357 ON contrast_log2_fc_p_val(p_value_adj); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5358 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5359 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5360 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5361 DROP VIEW IF EXISTS v_contrast_log2_fc_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5362 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5363 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5364 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5365 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5366 CREATE VIEW v_contrast_log2_fc_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5367 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5368 SELECT contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5369 a_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5370 a_samples, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5371 b_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5372 b_samples, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5373 a_quant, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5374 b_quant, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5375 fc_description, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5376 log2_fc, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5377 p_value_raw, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5378 p_value_adj, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5379 phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5380 FROM contrast_log2_fc_p_val |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5381 ORDER BY contrast, phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5382 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5383 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5384 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5385 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5386 DROP TABLE IF EXISTS kseaapp_metadata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5387 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5388 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5389 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5390 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5391 CREATE TABLE kseaapp_metadata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5392 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5393 WITH extended(deppep, ppep, gene_name, uniprot_id, phosphoresidue) AS ( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5394 SELECT DISTINCT |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5395 deppep.seq, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5396 ppep.seq, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5397 GeneName||';', |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5398 UniProtID||';', |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5399 PhosphoResidue||';' |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5400 FROM |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5401 ppep, deppep, mrgfltr_metadata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5402 WHERE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5403 mrgfltr_metadata.ppep_id = ppep.id |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5404 AND |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5405 ppep.deppep_id = deppep.id |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5406 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5407 SELECT |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5408 ppep AS `ppep`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5409 SUBSTR(uniprot_id, 1, INSTR(uniprot_id,';') - 1 ) AS `Protein`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5410 SUBSTR(gene_name, 1, INSTR(gene_name,';') - 1 ) AS `Gene`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5411 deppep AS `Peptide`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5412 REPLACE( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5413 REPLACE( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5414 SUBSTR(phosphoresidue, 1, INSTR(phosphoresidue,';') - 1 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5415 'p', |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5416 '' |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5417 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5418 ', ', |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5419 ';' |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5420 ) AS `Residue.Both` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5421 FROM extended |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5422 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5423 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5424 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5425 # Create indexes for join |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5426 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5427 CREATE INDEX IF NOT EXISTS kseaapp_metadata__ppep__idx |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5428 ON kseaapp_metadata(ppep); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5429 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5430 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5431 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5432 DROP VIEW IF EXISTS v_kseaapp_contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5433 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5434 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5435 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5436 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5437 CREATE VIEW v_kseaapp_contrast |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5438 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5439 SELECT a.*, b.Protein, b.Gene, b.Peptide, b.`Residue.Both` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5440 FROM v_contrast_log2_fc_p_val a, kseaapp_metadata b |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5441 WHERE b.ppep = a.phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5442 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5443 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5444 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5445 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5446 DROP VIEW IF EXISTS v_kseaapp_input |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5447 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5448 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5449 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5450 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5451 CREATE VIEW v_kseaapp_input |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5452 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5453 SELECT v.contrast, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5454 v.phosphopep, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5455 m.`Protein`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5456 m.`Gene`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5457 m.`Peptide`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5458 m.`Residue.Both`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5459 v.p_value_raw AS `p`, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5460 v.log2_fc AS `FC` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5461 FROM kseaapp_metadata AS m, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5462 v_contrast_log2_fc_p_val AS v |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5463 WHERE m.ppep = v.phosphopep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5464 AND NOT m.`Gene` = 'No_Gene_Name' |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5465 AND NOT v.log2_fc = 0 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5466 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5467 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
5468 ) |
|
27
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diff
changeset
|
5469 # We are done with DDL and insertion |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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|
5470 RSQLite::dbDisconnect(db) |
|
24
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|
5471 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5472 ``` |
|
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|
5473 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
5474 ```{r echo = FALSE, results = 'asis'} |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5475 cat("\\newpage\n") |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5476 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5477 |
|
27
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|
5478 # KSEA Analysis Summaries |
|
24
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|
5479 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5480 Results of Kinase-Substrate Enrichment Analysis are presented here, if the substrates for any kinases are relatively enriched. Enrichments are found by the CRAN `KSEAapp` package: |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5481 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5482 - The package is available on CRAN, at https:/cran.r-project.org/package=KSEAapp |
|
657663e89728
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|
5483 - The method used is described in Casado et al. (2013) [doi:10.1126/scisignal.2003573](https:/doi.org/10.1126/scisignal.2003573) and Wiredja et al (2017) [doi:10.1093/bioinformatics/btx415](https:/doi.org/10.1093/bioinformatics/btx415). |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5484 - An online alternative (supporting only analysis of human data) is available at [https:/casecpb.shinyapps.io/ksea/](https:/casecpb.shinyapps.io/ksea/). |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5485 |
|
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|
5486 For each kinase, $i$, and each two-way contrast of treatments, $j$, an enrichment $z$-score is computed as: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5487 |
|
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|
5488 $$ |
|
27
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|
5489 \text{kinase enrichment }z\text{-score}_{j,i} = \frac{(\overline{`r sfc`}_{j,i} - \overline{`r pfc`}_j)\sqrt{m_{j,i}}}{\delta_j} |
|
24
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|
5490 $$ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5491 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5492 and fold-enrichment is computed as: |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5493 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5494 $$ |
|
27
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|
5495 \text{Enrichment}_{j,i} = \frac{\overline{`r sfc`}_{j,i}}{\overline{`r pfc`}_j} |
|
24
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|
5496 $$ |
|
657663e89728
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|
5497 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5498 where: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5499 |
|
27
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diff
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|
5500 - $\overline{`r sfc`}_{j,i}$ is the mean `r pfc_txt` in intensities of known substrates of the kinase $i$ in contrast $j$, |
|
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|
5501 - $\overline{`r pfc`}_j$ is the mean `r pfc_txt` of all phosphosites identified in contrast $j$, and |
|
24
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|
5502 - $m_{j,i}$ is the total number of phosphosite substrates of kinase $i$ identified in contrast $j$, |
|
27
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|
5503 - $\delta_j$ is the standard deviation of the $\log_2 (\text{fold-change})$ for contrast $j$ across all phosphosites in the dataset. |
|
24
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|
5504 - Note that the absolute value of fold-change is used so that both increased and decreased substrates of a kinase will contribute to its enrichment score. |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5505 |
|
27
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|
5506 $\text{FDR}_{j,i}$ is the False Discovery Rate corrected kinase enrichment score. |
|
24
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|
5507 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5508 Color intensity in heatmaps reflects magnitude of $z$-score for enrichment of respective kinase in respective contrast; hue reflects the sign of the $z$-score (blue, negative; red, positive). |
|
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|
5509 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5510 Asterisks in heatmaps reflect enrichments that are significant at `r ksea_cutoff_statistic` < `r ksea_cutoff_threshold`. |
|
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|
5511 |
|
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|
5512 - Kinase names are generally as presented at Phospho.ELM [http://phospho.elm.eu.org/kinases.html](http://phospho.elm.eu.org/kinases.html) (when available), although Phospho.ELM data are not yet incorporated into this analysis. |
|
657663e89728
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|
5513 - Kinase names having the suffix '(HPRD)' are as presented at [http://hprd.org/serine_motifs](http://hprd.org/serine_motifs) and [http://hprd.org/tyrosine_motifs](http://hprd.org/tyrosine_motifs) and are as originally reported in the Amanchy et al., 2007 (doi: [10.1038/nbt0307-285](https://doi.org/10.1038/nbt0307-285)). |
|
27
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|
5514 - Kinase-substrate data were also taken from [http://networkin.science/download.shtml](http://networkin.science/download.shtml) and from PhosphoSitePlus [https://www.phosphosite.org/staticDownloads](https://www.phosphosite.org/staticDownloads). |
|
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|
5515 |
|
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|
5516 For each enriched kinase, a heatmap showing the intensities is presented for up to `r g_intensity_hm_rows` substrates, i.e., those substrates having the highest"quality". |
|
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|
5517 |
|
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|
5518 Where possible, a heatmap of the correlations among these the selected substrates is also presented; if correlations cannot be computed (because of too many missing values), then the covariances are heatmapped for substrates having a variance greater than 1. |
|
29775869faba
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|
5519 |
|
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|
5520 ```{r ksea, echo = FALSE, fig.dim = c(12, 14.5), results = 'asis'} |
|
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|
5521 cat("\\clearpage\n") |
|
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5522 |
|
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|
5523 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db) |
|
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5524 |
|
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|
5525 # -- eliminate the table that's about to be defined |
|
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|
5526 ddl_exec(db, " |
|
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5527 DROP TABLE IF EXISTS site_metadata; |
|
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|
5528 ") |
|
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|
5529 |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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|
5530 # -- define the site_metadata table |
|
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|
5531 ddl_exec(db, " |
|
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|
5532 CREATE TABLE site_metadata( |
|
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|
5533 id INTEGER PRIMARY KEY |
|
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|
5534 , site_type_id INTEGER REFERENCES site_type(id) |
|
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|
5535 , full TEXT UNIQUE ON CONFLICT IGNORE |
|
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|
5536 , abbrev TEXT |
|
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|
5537 , pattern TEXT |
|
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|
5538 , motif TEXT |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5539 ); |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5540 ") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5541 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5542 # -- populate the table with initial values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5543 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5544 INSERT INTO site_metadata(full, abbrev, site_type_id) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5545 SELECT DISTINCT kinase_map, kinase_map, site_type_id |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5546 FROM ppep_gene_site |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5547 ORDER BY kinase_map; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5548 ") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5549 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5550 # -- drop bogus KSData view if exists |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5551 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5552 DROP VIEW IF EXISTS ks_data_v; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5553 ") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5554 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5555 # -- create view to serve as an impostor for KSEAapp::KSData |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5556 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5557 CREATE VIEW IF NOT EXISTS ks_data_v |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5558 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5559 SELECT |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5560 'NA' AS KINASE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5561 'NA' AS KIN_ACC_ID, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5562 kinase_map AS GENE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5563 'NA' AS KIN_ORGANISM, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5564 'NA' AS SUBSTRATE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5565 0 AS SUB_GENE_ID, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5566 'NA' AS SUB_ACC_ID, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5567 gene_names AS SUB_GENE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5568 'NA' AS SUB_ORGANISM, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5569 phospho_peptide AS SUB_MOD_RSD, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5570 0 AS SITE_GROUP_ID, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5571 'NA' AS 'SITE_7AA', |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5572 2 AS networkin_score, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5573 type_name AS Source |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5574 FROM ppep_gene_site_view; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5575 ") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5576 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5577 contrast_metadata_df <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5578 sqldf::sqldf("select * from contrast_lvl_lvl_metadata", connection = db) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5579 rslt <- new_env() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5580 rslt$score_list <- list() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5581 rslt$name_list <- list() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5582 rslt$longname_list <- list() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5583 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5584 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5585 DROP TABLE IF EXISTS contrast_ksea_scores; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5586 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5587 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5588 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5589 next_index <- 0 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5590 err_na_subscr_df_const <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5591 "missing values are not allowed in subscripted assignments of data frames" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5592 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5593 for (i_cntrst in seq_len(nrow(contrast_metadata_df))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5594 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5595 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5596 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5597 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5598 contrast_longlabel <- ( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5599 sprintf( |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5600 "Class %s -> Class %s", |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5601 contrast_metadata_df[i_cntrst, "b_level"], |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5602 contrast_metadata_df[i_cntrst, "a_level"] |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5603 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5604 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5605 kseaapp_input <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5606 sqldf::sqldf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5607 x = sprintf(" |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5608 SELECT `Protein`, `Gene`, `Peptide`, phosphopep AS `Residue.Both`, `p`, `FC` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5609 FROM v_kseaapp_input |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5610 WHERE contrast = %d |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5611 ", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5612 i_cntrst |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5613 ), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5614 connection = db |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5615 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5616 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5617 pseudo_ksdata <- dbReadTable(db, "ks_data_v") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5618 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5619 # This hack is because SQL table has the log2-transformed values |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5620 kseaapp_input[, "FC"] <- 2 ** kseaapp_input[, "FC", drop = TRUE] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5621 main_title <- ( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5622 sprintf( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5623 "Change from treatment %s to treatment %s", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5624 contrast_metadata_df[i_cntrst, "b_level"], |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5625 contrast_metadata_df[i_cntrst, "a_level"] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5626 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5627 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5628 sub_title <- contrast_longlabel |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5629 tryCatch( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5630 expr = { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5631 ksea_scores_rslt <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5632 ksea_scores( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5633 ksdata = pseudo_ksdata, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5634 px = kseaapp_input, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5635 networkin = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5636 networkin_cutoff = 2, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5637 minimum_substrate_count = ksea_min_substrate_count |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5638 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5639 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5640 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5641 ksea_scores_rslt <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5642 ksea_scores_rslt[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5643 ksea_scores_rslt$m >= ksea_min_substrate_count, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5644 , |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5645 drop = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5646 ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5647 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5648 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5649 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5650 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5651 x = ksea_scores_rslt, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5652 tabstops = c(0.8, 0.8, 0.8, 0.8, 0.8, 0.8), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5653 caption = paste("KSEA scores for contrast ", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5654 cntrst_b_level, "to", cntrst_a_level), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5655 use_subsubsection_header = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5656 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5657 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5658 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5659 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5660 if (print_nb_messages) nbe("Output contents of `ksea_scores_rslt` table\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5661 cat_variable(ksea_scores_rslt) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5662 cat("\n\\clearpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5663 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5664 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5665 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5666 next_index <- 1 + next_index |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5667 rslt$score_list[[next_index]] <- ksea_scores_rslt |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5668 rslt$name_list[[next_index]] <- contrast_label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5669 rslt$longname_list[[next_index]] <- contrast_longlabel |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5670 ksea_low_fdr_print( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5671 rslt = rslt, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5672 i_cntrst = i_cntrst, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5673 i = next_index, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5674 a_level = cntrst_a_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5675 b_level = cntrst_b_level, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5676 fold_change = cntrst_fold_change, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5677 caption = contrast_longlabel |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5678 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5679 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5680 }, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5681 error = function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5682 str(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5683 cat_margins() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5684 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5685 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5686 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5687 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5688 plotted_kinases <- NULL |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5689 if (g_can_run_ksea && length(rslt$score_list) > 1) { |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5690 for (i in seq_len(length(ksea_heatmap_titles))) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5691 hdr <- ksea_heatmap_titles[[i]] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5692 which_kinases <- i |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5693 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5694 cat("\\clearpage\n\\begin{center}\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5695 if (i == const_ksea_astrsk_kinases) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5696 cat(subsection_header(hdr)) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5697 } else { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5698 cat(subsection_header(hdr)) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5699 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5700 cat("\\end{center}\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5701 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5702 plotted_kinases <- ksea_heatmap( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5703 # the data frame outputs from the KSEA.Scores() function, in list format |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5704 score_list = rslt$score_list, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5705 # a character vector of all the sample names for heatmap annotation: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5706 # - the names must be in the same order as the data in score_list |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5707 # - please avoid long names, as they may get cropped in the final image |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5708 sample_labels = rslt$name_list, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5709 # character string of either "p.value" or "FDR" indicating the data column |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5710 # to use for marking statistically significant scores |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5711 stats = c("p.value", "FDR")[2], |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5712 # a numeric value between 0 and infinity indicating the min. number of |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5713 # substrates a kinase must have to be included in the heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5714 m_cutoff = 1, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5715 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5716 # for indicating significant kinases in the heatmap |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5717 p_cutoff = params$kseaCutoffThreshold, |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5718 # a binary input of TRUE or FALSE, indicating whether or not to perform |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5719 # hierarchical clustering of the sample columns |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5720 sample_cluster = TRUE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5721 # a binary input of TRUE or FALSE, indicating whether or not to export |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5722 # the heatmap as a .png image into the working directory |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5723 export = FALSE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5724 # additional arguments to gplots::heatmap.2, such as: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5725 # - main: main title of plot |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5726 # - xlab: x-axis label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5727 # - ylab: y-axis label |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5728 xlab = "Contrast", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5729 ylab = "Kinase", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5730 # print which kinases: |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5731 # - 1 : all kinases |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5732 # - 2 : significant kinases |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5733 # - 3 : non-significant kinases |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5734 which_kinases = which_kinases, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5735 margins = c(7, 15) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5736 ) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5737 if (!is.null(plotted_kinases)) { |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5738 cat("\\begin{center}\n") |
|
26
bac8e9515863
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents:
25
diff
changeset
|
5739 if (which_kinases != const_ksea_nonastrsk_kinases) |
|
bac8e9515863
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents:
25
diff
changeset
|
5740 cat("Asterisks reflect significance.\n") |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5741 cat("\\end{center}\n") |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
5742 } |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5743 } # end for (i in ... |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5744 } # end if (length ... |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5745 ``` |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5746 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5747 ```{r kseabar_calc, echo = FALSE, fig.dim = c(9.5, 6), results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5748 ksea_prints <- list() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5749 ksea_barplots <- list() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5750 for (i_cntrst in seq_len(length(rslt$score_list))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5751 next_index <- i_cntrst |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5752 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5753 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5754 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5755 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5756 contrast_longlabel <- ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5757 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5758 "Class %s -> Class %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5759 contrast_metadata_df[i_cntrst, "b_level"], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5760 contrast_metadata_df[i_cntrst, "a_level"] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5761 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5762 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5763 main_title <- ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5764 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5765 "Change from treatment %s to treatment %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5766 contrast_metadata_df[i_cntrst, "b_level"], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5767 contrast_metadata_df[i_cntrst, "a_level"] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5768 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5769 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5770 sub_title <- contrast_longlabel |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5771 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5772 expr = { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5773 ksea_scores_rslt <- rslt$score_list[[next_index]] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5774 if (print_nb_messages) nbe(see_variable(ksea_scores_rslt)) #ACE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5775 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5776 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5777 sink(deferred <- file()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5778 ksea_low_fdr_print( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5779 rslt = rslt, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5780 i_cntrst = i_cntrst, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5781 i = next_index, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5782 a_level = cntrst_a_level, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5783 b_level = cntrst_b_level, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5784 fold_change = cntrst_fold_change, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5785 caption = contrast_longlabel, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5786 write_db = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5787 anchor = const_table_anchor_t |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5788 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5789 cat("\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5790 sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5791 lines <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5792 paste( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5793 readLines(deferred, warn = FALSE), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5794 collapse = "\n" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5795 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5796 close(deferred) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5797 sq_put(ksea_prints, lines) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5798 sink(stderr()) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5799 cat("\n---\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5800 cat_variable(ksea_prints) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5801 barplot_closure <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5802 ksea_low_fdr_barplot_factory( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5803 rslt = rslt, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5804 i_cntrst = i_cntrst, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5805 i = next_index, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5806 a_level = cntrst_a_level, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5807 b_level = cntrst_b_level, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5808 fold_change = cntrst_fold_change, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5809 caption = contrast_longlabel |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5810 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5811 if (rlang::is_closure(barplot_closure)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5812 sq_put(ksea_barplots, barplot_closure) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5813 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5814 sq_put(ksea_barplots, no_op) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5815 str(ksea_barplots) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5816 cat("\n...\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5817 sink() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5818 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5819 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5820 error = function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5821 str(e) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5822 cat_margins() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5823 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5824 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5825 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5826 ``` |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5827 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5828 ```{r phosphoelm_kinase_upid_desc, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5829 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5830 have_kinase_descriptions <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5831 if (!is.null(bzip2df(kinase_uprt_desc_lut, kinase_uprt_desc_lut_bz2)) && |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5832 !is.null(bzip2df(kinase_name_uprt_lut, kinase_name_uprt_lut_bz2)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5833 ) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5834 rownames(kinase_uprt_desc_lut) <- kinase_uprt_desc_lut$UniProtID |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5835 kinase_name_to_desc_uprt <- function(s) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5836 rslt <- NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5837 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5838 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5839 which_rows <- eval(s == kinase_name_uprt_lut$kinase) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5840 kinase_uprtid <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5841 kinase_name_uprt_lut[which_rows, 2] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5842 # filter for first _HUMAN match if any |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5843 grepl_human <- grepl("_HUMAN$", kinase_uprtid) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5844 if (0 < sum(grepl_human)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5845 kinase_uprtid <- kinase_uprtid[grepl_human] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5846 # filter for first match if any |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5847 if (0 < length(kinase_uprtid)) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5848 kinase_uprtid <- kinase_uprtid[1] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5849 kinase_desc <- kinase_uprt_desc_lut[kinase_uprtid, 2] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5850 if (!is.na(kinase_desc)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5851 rslt <- c(kinase_desc, kinase_uprtid) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5852 else |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5853 rslt <- c(kinase_desc, "") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5854 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5855 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5856 warning = str |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5857 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5858 rslt |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5859 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5860 TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5861 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5862 kinase_name_to_desc_uprt <- function(s) NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5863 FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5864 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5865 ``` |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5866 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5867 ```{r write_params, echo = FALSE, results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5868 # perhaps this should be moved into the functions section, eventually ... |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5869 write_params <- function(db) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
5870 # write parameters to report |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5871 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5872 # write parameters to SQLite output |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5873 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5874 mqppep_anova_script_param_df <- data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5875 script = "mqppep_anova_script.Rmd", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5876 parameter = names(param_unlist), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5877 value = param_unlist |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5878 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5879 ddl_exec(db, " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5880 DROP TABLE IF EXISTS script_parameter; |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5881 " |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5882 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5883 ddl_exec(db, " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5884 CREATE TABLE IF NOT EXISTS script_parameter( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5885 script TEXT, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5886 parameter TEXT, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5887 value ANY, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5888 UNIQUE (script, parameter) ON CONFLICT REPLACE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5889 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5890 ; |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5891 " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5892 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5893 RSQLite::dbWriteTable( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5894 conn = db, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5895 name = "script_parameter", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5896 value = mqppep_anova_script_param_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5897 append = TRUE |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5898 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5899 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5900 loaded_packages_df <- sessioninfo::package_info("loaded") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5901 loaded_packages_df[, "library"] <- as.character(loaded_packages_df$library) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5902 loaded_packages_df <- data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5903 package = loaded_packages_df$package, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5904 version = loaded_packages_df$loadedversion, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5905 date = loaded_packages_df$date |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5906 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5907 #ACE cat("\\clearpage\n\\section{R package versions}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5908 #ACE data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5909 #ACE x = loaded_packages_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5910 #ACE tabstops = c(2.5, 1.25), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5911 #ACE caption = "R package versions" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5912 #ACE ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5913 cat("\\clearpage\n\\section{Input parameter settings}\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5914 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5915 x = param_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
5916 tabstops = c(1.75), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5917 underscore_whack = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5918 caption = "Input parameters", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5919 verbatim = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5920 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5921 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5922 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5923 if (!have_kinase_descriptions) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5924 write_params(db) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
5925 # We are done with output |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
5926 RSQLite::dbDisconnect(db) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
5927 param_df_exit() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
5928 knitr::knit_exit() |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
5929 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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changeset
|
5930 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
5931 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5932 ```{r kseabar, echo = FALSE, fig.dim = c(9.5, 12.3), results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5933 if (have_kinase_descriptions) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5934 my_section_header <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5935 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5936 "inases whose KSEA %s < %s\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5937 ksea_cutoff_statistic, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5938 signif(ksea_cutoff_threshold, 2) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5939 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5940 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5941 # Use enriched kinases to find enriched kinase-substrate pairs |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5942 enriched_kinases <- data.frame(kinase = ls(ksea_asterisk_hash)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5943 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5944 enriched_kinase_descs <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5945 Reduce( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5946 f = function(l, r) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5947 lkup <- kinase_name_to_desc_uprt(r) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5948 if (is.null(lkup)) l |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5949 else r2 <- rbind( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5950 l, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5951 data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5952 kinase = r, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5953 uniprot_id = lkup[2], |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5954 description = lkup[1] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5955 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5956 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5957 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5958 x = enriched_kinases$kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5959 init = NULL |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5960 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5961 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5962 if (length(enriched_kinase_descs) > 0 && nrow(enriched_kinase_descs) > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5963 cat("\n\\clearpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5964 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5965 x = enriched_kinase_descs, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5966 tabstops = c(0.9, 1.3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5967 headings = c("Kinase", "UniProt ID", "Description"), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5968 caption = paste0("Descriptions of k", my_section_header) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5969 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5970 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5971 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5972 if (FALSE) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5973 cat_variable(sqldf("SELECT kinase FROM enriched_kinases")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5974 cat_variable(sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5975 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5976 FROM pseudo_ksdata |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5977 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5978 ")) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5979 data_frame_table_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5980 x = sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5981 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5982 FROM pseudo_ksdata |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5983 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5984 "), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5985 justification = "l l l", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5986 centered = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5987 caption = "substrates of enriched kinases", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5988 anchor = c(const_table_anchor_p, const_table_anchor_t), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5989 underscore_whack = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5990 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5991 data_frame_table_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5992 x = sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5993 SELECT |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5994 gene AS kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5995 ppep, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5996 sub_gene, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5997 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5998 fdr_adjusted_anova_p, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
5999 quality, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6000 min_group_obs_count |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6001 FROM ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6002 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6003 FROM pseudo_ksdata |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6004 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6005 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6006 p_value_data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6007 WHERE ppep = phosphopeptide |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6008 GROUP BY kinase, ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6009 ORDER BY kinase, ppep, p_value_data.quality DESC |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6010 "), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6011 justification = "l l l l l l l", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6012 centered = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6013 caption = "labeled substrates of enriched kinases", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6014 anchor = c(const_table_anchor_p, const_table_anchor_t), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6015 underscore_whack = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6016 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6017 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6018 all_enriched_substrates <- sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6019 SELECT |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6020 gene AS kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6021 ppep, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6022 sub_gene, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6023 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6024 fdr_adjusted_anova_p, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6025 quality, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6026 min_group_obs_count |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6027 FROM ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6028 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6029 FROM pseudo_ksdata |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6030 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6031 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6032 p_value_data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6033 WHERE ppep = phosphopeptide |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6034 GROUP BY kinase, ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6035 ORDER BY kinase, ppep, p_value_data.quality DESC |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6036 ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6037 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6038 all_enriched_substrates <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6039 all_enriched_substrates[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6040 all_enriched_substrates$quality >= params$minQuality, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6041 , |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6042 drop = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6043 ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6044 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6045 all_enriched_substrates$sub_gene <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6046 sub( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6047 " ///.*", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6048 " ...", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6049 all_enriched_substrates$sub_gene |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6050 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6051 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6052 all_enriched_substrates$label <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6053 with( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6054 all_enriched_substrates, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6055 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6056 "(%s-%s) %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6057 kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6058 trunc_subgene(sub_gene), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6059 ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6060 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6061 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6062 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6063 # this global is set to TRUE by cat_enriched_heading immediately below |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6064 g_neednewpage <- FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6065 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6066 # helper used to label per-kinase substrate enrichment figure |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6067 cat_enriched_heading <- function(m, cut_args) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6068 cutoff <- cut_args$cutoff |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6069 kinase <- cut_args$kinase |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6070 if (g_neednewpage) cat("\\newpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6071 g_neednewpage <- TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6072 if (nrow(m) > g_intensity_hm_rows) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6073 cat(subsection_header( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6074 sprintf( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6075 "Highest-quality %d (of %d) enriched %s-substrates", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6076 g_intensity_hm_rows, |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6077 nrow(m), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6078 kinase |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6079 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6080 )) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6081 } else { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6082 if (nrow(m) == 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6083 return(FALSE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6084 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6085 nrow_m <- nrow(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6086 cat(subsection_header( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6087 sprintf( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6088 "%d enriched %s-substrate%s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6089 nrow_m, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6090 kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6091 if (nrow_m > 1) "s" else "" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6092 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6093 )) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6094 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6095 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6096 cat("\n\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6097 cat("\n\n\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6098 return(TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6099 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6100 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6101 # -------------------------------- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6102 # hack begin - show all substrates |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6103 enriched_substrates <- all_enriched_substrates |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6104 # add "FALSE &&" to prevent listing of substrates |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6105 if (show_enriched_substrates && nrow(enriched_substrates) > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6106 short_row_names <- sub( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6107 "$FAILED_MATCH_GENE_NAME", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6108 "not_found", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6109 enriched_substrates$sub_gene, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6110 fixed = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6111 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6112 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6113 if (print_nb_messages) nbe(see_variable(enriched_substrates)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6114 substrates_df <- with( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6115 enriched_substrates, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6116 data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6117 kinase = kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6118 substrate = sub(" ///*", "...", short_row_names), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6119 anova_p_value = signif(fdr_adjusted_anova_p, 2), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6120 min_group_obs_count = signif(min_group_obs_count, 0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6121 quality = signif(quality, 3), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6122 sequence = trunc_n(30)(ppep) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6123 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6124 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6125 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6126 substrates_df <- substrates_df[ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6127 with(substrates_df, order(kinase, -quality)), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6128 , |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6129 drop = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6130 ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6131 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6132 if (print_nb_messages) nbe(see_variable(substrates_df)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6133 if (nrow(substrates_df) < 1) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6134 substrates_df$sequence <- c() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6135 if (print_nb_messages) nbe(see_variable(substrates_df)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6136 names(substrates_df) <- headers_2nd_line <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6137 c("Kinase", "Substrate", "p-value", "per group)", "quality", "Sequence") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6138 headers_1st_line <- c("", "", "ANOVA", "min(values", "", "") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6139 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6140 x = substrates_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6141 tabstops = c(1.2, 0.8, 0.5, 0.65, 0.5), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6142 headings = c(headers_1st_line, headers_2nd_line), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6143 caption = "Details for all enriched substrates of enriched kinases" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6144 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6145 rm( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6146 enriched_substrates, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6147 substrates_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6148 short_row_names, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6149 headers_1st_line, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6150 headers_2nd_line |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6151 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6152 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6153 cat("\\clearpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6154 # hack end - show all substrates |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6155 # -------------------------------- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6156 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6157 # print deferred tables and graphs for kinases from contrasts |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6158 for (i_cntrst in seq_len(length(ksea_prints))) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6159 #latex_samepage({ |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6160 cat(ksea_prints[[i_cntrst]]) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6161 cat("\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6162 ksea_barplots[[i_cntrst]]() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6163 cat("\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6164 cat("\\clearpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6165 #}) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6166 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6167 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6168 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6169 ``` |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6170 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6171 ```{r enriched, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'} |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6172 if (g_can_run_ksea) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6173 g_did_enriched_header <- FALSE |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6174 for (kinase_name in sort(enriched_kinases$kinase)) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6175 enriched_substrates <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
6176 all_enriched_substrates[ |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6177 all_enriched_substrates$kinase == kinase_name, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6178 , |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6179 drop = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6180 ] |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
6181 ten_trunc_ppep <- trunc_enriched_substrate(enriched_substrates$ppep) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff
changeset
|
6182 enriched_substrates$label <- with( |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
24
diff
changeset
|
6183 enriched_substrates, |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents:
24
diff
changeset
|
6184 sprintf( |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6185 "(%s) %s", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
6186 make.names( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
6187 sub("$FAILED_MATCH_GENE_NAME", "not_found", sub_gene, fixed = TRUE), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6188 unique = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6189 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6190 ten_trunc_ppep |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
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diff
changeset
|
6191 ) |
|
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
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24
diff
changeset
|
6192 ) |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
6193 # Get the intensity values for the heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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parents:
diff
changeset
|
6194 enriched_intensities <- |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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diff
changeset
|
6195 as.matrix(unimputed_quant_data_log[enriched_substrates$ppep, , drop = FALSE]) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6196 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6197 # Remove rows having too many NA values to be relevant |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6198 good_rows <- (rowSums(enriched_intensities, na.rm = TRUE) != 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6199 #ACE nbe(see_variable(good_rows), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6200 enriched_substrates <- enriched_substrates[good_rows, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
6201 enriched_intensities <- enriched_intensities[good_rows, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6202 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
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diff
changeset
|
6203 # Rename the rows with the display-name for the heatmap |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6204 short_row_names <- sub( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
6205 "$FAILED_MATCH_GENE_NAME", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
6206 "not_found", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6207 enriched_substrates$sub_gene, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6208 fixed = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6209 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6210 short_row_names <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6211 make.names(short_row_names, unique = TRUE) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6212 long_row_names <- |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6213 sapply( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6214 X = rownames(enriched_intensities), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6215 FUN = function(rn) { |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6216 enriched_substrates[enriched_substrates$ppep == rn, "label"] |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6217 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6218 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6219 rownames(enriched_intensities) <- long_row_names |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6220 # Format as matrix for heatmap |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6221 m <- as.matrix(enriched_intensities) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6222 rownames(m) <- trunc_enriched_substrate(rownames(m)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6223 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6224 #ACE nb("m with bad rows: ", see_variable(m), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6225 #ACE good_rows <- (rowSums(m, na.rm = TRUE) != 0) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6226 #ACE nb(see_variable(good_rows), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6227 #ACE m <- m[good_rows, , drop = FALSE] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6228 #ACE nb("m without(?) bad rows: ", see_variable(m), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6229 #ACE nb(see_variable(short_row_names), "\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
6230 #ACE local_short_row_names <- short_row_names[good_rows] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
6231 #ACE local_long_row_names <- long_row_names[good_rows] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6232 #ACE local_enriched_intensities <- enriched_intensities[local_long_row_names, ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6233 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6234 # Draw the heading and heatmap |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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26
diff
changeset
|
6235 nrow_m <- nrow(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6236 if (nrow_m > 0) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
26
diff
changeset
|
6237 if (!g_did_enriched_header) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
6238 cat("\n\\clearpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff
changeset
|
6239 cat(section_header(paste0("K", my_section_header))) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents:
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diff
changeset
|
6240 g_did_enriched_header <- TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6241 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
6242 is_na_m <- is.na(m) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6243 cellnote_m <- is_na_m |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
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diff
changeset
|
6244 cellnote_m[!is_na_m] <- "" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6245 cellnote_m[is_na_m] <- "NA" |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6246 cut_args <- new_env() |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6247 cut_args$cutoff <- cutoff |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6248 cut_args$kinase <- kinase_name |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6249 cut_args$statistic <- ksea_cutoff_statistic |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6250 cut_args$threshold <- ksea_cutoff_threshold |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6251 number_of_peptides_found <- |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6252 ppep_heatmap( |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6253 m = m, |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6254 cellnote = cellnote_m, |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6255 cutoff = cut_args, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6256 hm_heading_function = cat_enriched_heading, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6257 hm_main_title |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6258 = "Unnormalized (zero-imputed) intensities of enriched kinase-substrates", |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6259 suppress_row_dendrogram = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6260 master_cex = 0.35, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6261 sepcolor = "black", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6262 colsep = sample_colsep |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6263 ) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
6264 if (number_of_peptides_found > 1) { |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6265 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6266 tryCatch( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6267 { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6268 rownames(m) <- short_row_names |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6269 cov_heatmap(m, nrow_m > g_intensity_hm_rows) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6270 }, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6271 error = function(e) { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6272 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6273 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6274 "ERROR: %s\n\\newline\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6275 mget("e") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6276 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6277 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6278 cat( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6279 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6280 "message: %s\n\\newline\n", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6281 e$message |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6282 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6283 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6284 cat_margins() |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6285 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6286 ) |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
6287 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6288 substrates_df <- with( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6289 enriched_substrates, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6290 data.frame( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6291 substrate = sub(" ///*", "...", short_row_names), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6292 sequence = trunc_long_ppep(ppep), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6293 anova_p_value = signif(fdr_adjusted_anova_p, 2), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6294 min_group_obs_count = signif(min_group_obs_count, 0), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6295 quality = signif(quality, 3) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6296 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6297 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6298 excess_substrates <- nrow(substrates_df) > g_intensity_hm_rows |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6299 if (excess_substrates) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6300 substrates_df <- substrates_df[1:g_intensity_hm_rows, ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6301 names(substrates_df) <- headers_2nd_line <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6302 c("Substrate", "Sequence", "p-value", "per group)", "quality") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6303 headers_1st_line <- c("", "", "ANOVA", "min(values", "") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6304 if (1 < nrow(enriched_substrates)) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6305 cat("\n\\newpage\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6306 cat(subsubsection_header( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6307 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6308 "Details for %s%s-substrates", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6309 if (excess_substrates) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6310 sprintf( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6311 "%s \"highest quality\" ", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6312 g_intensity_hm_rows |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
6313 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6314 else "", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6315 kinase_name |
|
25
a5f69695516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents:
24
diff
changeset
|
6316 ) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6317 )) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6318 substrates_df <- substrates_df[order(-substrates_df$quality), ] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6319 data_frame_tabbing_latex( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6320 x = substrates_df, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6321 tabstops = c(0.8, 3.8, 0.6, 0.8), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6322 headings = c(headers_1st_line, headers_2nd_line) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6323 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6324 } else { |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6325 if (print_nb_messages) nbe(see_variable(nrow_m > 0), "\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6326 } |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6327 if (print_nb_messages) nb("end kinase ", kinase_name, "\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6328 } |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6329 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6330 # Write output tabular files |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6331 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6332 # get kinase, ppep, concat(kinase) tuples for enriched kinases |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6333 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6334 if (print_nb_messages) nb("kinase_ppep_label <- ...\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6335 if (print_nb_messages) nbe("kinase_ppep_label <- ...\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6336 kinase_ppep_label <- sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6337 WITH |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6338 t(ppep, label) AS |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6339 ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6340 SELECT DISTINCT |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6341 SUB_MOD_RSD AS ppep, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6342 group_concat(gene, '; ') AS label |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6343 FROM pseudo_ksdata |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6344 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6345 GROUP BY ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6346 ), |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6347 k(kinase, ppep_join) AS |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6348 ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6349 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep_join |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6350 FROM pseudo_ksdata |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6351 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6352 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6353 SELECT k.kinase, t.ppep, t.label |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6354 FROM t, k |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6355 WHERE t.ppep = k.ppep_join |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6356 ORDER BY k.kinase, t.ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6357 ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6358 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6359 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6360 # extract what we need from full_data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6361 impish <- cbind(rownames(quant_data_imp), quant_data_imp) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6362 colnames(impish)[1] <- "Phosphopeptide" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6363 data_table_imputed_sql <- " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6364 SELECT |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6365 f.*, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6366 k.label AS KSEA_enrichments, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6367 q.* |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6368 FROM |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6369 metadata_plus_p f |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6370 LEFT JOIN kinase_ppep_label k |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6371 ON f.Phosphopeptide = k.ppep, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6372 impish q |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6373 WHERE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6374 f.Phosphopeptide = q.Phosphopeptide |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6375 " |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6376 data_table_imputed <- sqldf(data_table_imputed_sql) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6377 # Zap the duplicated 'Phosphopeptide' column named 'ppep' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6378 data_table_imputed <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6379 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6380 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6381 # Output imputed, un-normalized data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6382 if (print_nb_messages) nb("Output imputed, un-normalized data tabular file\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6383 if (print_nb_messages) nbe("Output imputed, un-normalized data tabular file\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6384 write.table( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6385 data_table_imputed |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6386 , file = imputed_data_filename |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6387 , sep = "\t" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6388 , col.names = TRUE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6389 , row.names = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6390 , quote = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6391 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6392 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6393 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6394 #output quantile normalized data |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6395 impish <- cbind(rownames(quant_data_imp_qn_log), quant_data_imp_qn_log) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6396 colnames(impish)[1] <- "Phosphopeptide" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6397 data_table_imputed <- sqldf(data_table_imputed_sql) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6398 # Zap the duplicated 'Phosphopeptide' column named 'ppep' |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6399 data_table_imputed <- |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6400 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))] |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6401 if (print_nb_messages) nb("Output quantile normalized data tabular file\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6402 if (print_nb_messages) nbe("Output quantile normalized data tabular file\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6403 write.table( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6404 data_table_imputed, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6405 file = imp_qn_lt_data_filenm, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6406 sep = "\t", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6407 col.names = TRUE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6408 row.names = FALSE, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6409 quote = FALSE |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6410 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6411 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6412 ppep_kinase <- sqldf(" |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6413 SELECT DISTINCT k.ppep, k.kinase |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6414 FROM ( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6415 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6416 FROM pseudo_ksdata |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6417 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6418 ) k |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6419 ORDER BY k.ppep, k.kinase |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6420 ") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6421 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6422 RSQLite::dbWriteTable( |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6423 conn = db, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6424 name = "ksea_enriched_ks", |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6425 value = ppep_kinase, |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6426 append = FALSE |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6427 ) |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6428 } |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6429 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6430 if (print_nb_messages) nb("RSQLite::dbWriteTable anova_signif\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6431 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6432 RSQLite::dbWriteTable( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6433 conn = db, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6434 name = "anova_signif", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6435 value = p_value_data, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6436 append = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6437 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6438 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6439 ddl_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6440 DROP VIEW IF EXISTS stats_metadata_v; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6441 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6442 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6443 dml_no_rows_exec(db, " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6444 CREATE VIEW stats_metadata_v |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6445 AS |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6446 SELECT DISTINCT m.*, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6447 p.raw_anova_p, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6448 p.fdr_adjusted_anova_p, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6449 kek.kinase AS ksea_enrichments |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6450 FROM |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6451 mrgfltr_metadata_view m |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6452 LEFT JOIN anova_signif p |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6453 ON m.phospho_peptide = p.phosphopeptide |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6454 LEFT JOIN ksea_enriched_ks kek |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6455 ON m.phospho_peptide = kek.ppep |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6456 ; |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6457 " |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6458 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6459 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6460 if (print_nb_messages) nb("Output contents of `stats_metadata_v` table to tabular file\n") |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6461 if (print_nb_messages) nbe("Output contents of `stats_metadata_v` table to tabular file\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6462 write.table( |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6463 dbReadTable(db, "stats_metadata_v"), |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6464 file = anova_ksea_mtdt_file, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6465 sep = "\t", |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6466 col.names = TRUE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6467 row.names = FALSE, |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6468 quote = FALSE |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6469 ) |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6470 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6471 cat("\n\\clearpage\n") |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6472 |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6473 ``` |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6474 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6475 # Data-processing summary flowchart |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6476 |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6477  |
|
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents:
26
diff
changeset
|
6478 |
|
24
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6479 ```{r parmlist, echo = FALSE, fig.dim = c(9, 10), results = 'asis'} |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6480 cat("\\leavevmode\n\n\n") |
|
657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
eschen42
parents:
diff
changeset
|
6481 |
|
27
29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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6482 write_params(db) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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6483 # We are done with output |
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657663e89728
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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6484 RSQLite::dbDisconnect(db) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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6485 |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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6486 cat("\\clearpage\n\\section{R package versions}\n") |
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29775869faba
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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6487 utils::toLatex(utils::sessionInfo()) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47
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6488 ``` |