mqppep_anova: mqppep_anova_script.Rmd annotate

annotate mqppep_anova_script.Rmd @ 0:d9b68bedbc91 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe

author	galaxyp
date	Mon, 11 Jul 2022 19:20:41 +0000
parents
children	2276e88d5a1f

rev	line source
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1 ---
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2 title: "MaxQuant Phosphoproteomic Enrichment Pipeline ANOVA/KSEA"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3 author:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	4 - "Nick Graham^[ORCiD 0000-0002-6811-1941, University of Southern California: Los Angeles, CA, US]"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	5 - "Larry Cheng^[ORCiD 0000-0002-6922-6433, Rutgers School of Graduate Studies: New Brunswick, NJ, US]"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	6 - "Art Eschenlauer^[ORCiD 0000-0002-2882-0508, University of Minnesota: Minneapolis, Minnesota, US]"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	7 date:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	8 - "May 28, 2018"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	9 - "; revised June 23, 2022"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	10 output:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	11 pdf_document:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	12 toc: true
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	13 toc_depth: 3
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	14 keep_tex: true
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	15 header-includes:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	16 - \usepackage{longtable}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	17 - \newcommand\T{\rule{0pt}{2.6ex}} % Top strut
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	18 - \newcommand\B{\rule[-1.2ex]{0pt}{0pt}} % Bottom strut
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	19 params:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	20 alphaFile: "test-data/alpha_levels.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	21 inputFile: "test-data/test_input_for_anova.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	22 preprocDb: "test-data/test_input_for_anova.sqlite"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	23 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	24 show_toc: true
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	25 firstDataColumn: "^Intensity[^_]"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	26 imputationMethod: !r c("group-median", "median", "mean", "random")[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	27 meanPercentile: 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	28 sdPercentile: 1.0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	29 regexSampleNames: "\\.\\d+[A-Z]$"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	30 regexSampleGrouping: "\\d+"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	31 imputedDataFilename: "test-data/limbo/imputedDataFilename.txt"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	32 imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	33 anovaKseaMetadata: "test-data/limbo/anovaKseaMetadata.txt"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	34 oneWayManyCategories: !r c("aov", "kruskal.test", "oneway.test")[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	35 oneWayTwoCategories: !r c("aov", "kruskal.test", "oneway.test")[3]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	36 kseaCutoffStatistic: !r c("p.value", "FDR")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	37 kseaCutoffThreshold: !r c( 0.1, 0.05)[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	38 kseaMinKinaseCount: 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	39 intensityHeatmapRows: 75
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	40 ---
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	41 <!--
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	42 kseaCutoffStatistic: !r c("p.value", "FDR")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	43 kseaCutoffThreshold: !r c(0.05, 0.1)[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	44
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	45 alphaFile: "test-data/alpha_levels.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	46 inputFile: "test-data/test_input_for_anova.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	47 preprocDb: "test-data/test_input_for_anova.sqlite"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	48 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	49
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	50 alphaFile: "test-data/alpha_levels.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	51 inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	52 preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	53 kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	54
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	55 alphaFile: "test-data/alpha_levels.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	56 inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	57 preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	58 kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	59
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	60 alphaFile: "test-data/alpha_levels.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	61 inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	62 preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	63 kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	64
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	65 inputFile: "test-data/density_failure.preproc_tab.tabular"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	66 kseaAppPrepDb: !r c(":memory:", "mqppep.sqlite")[2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	67 latex_document: default
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	68 -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	69 ```{r setup, include = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	70 #ref for debugging: https://yihui.org/tinytex/r/#debugging
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	71 options(tinytex.verbose = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	72
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	73 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	74 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	75 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	76
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	77 # freeze the random number generator so the same results will be produced
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	78 # from run to run
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	79 set.seed(28571)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	80
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	81 ### LIBRARIES
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	82 library(gplots)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	83 library(DBI)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	84 library(RSQLite)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	85 # Suppress "Warning: no DISPLAY variable so Tk is not available"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	86 suppressWarnings(suppressMessages(library(sqldf)))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	87
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	88 # required but not added to search list:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	89 # - DBI
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	90 # - RSQLite
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	91 # - ggplot2
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	92 # - knitr
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	93 # - latex2exp
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	94 # - preprocessCore
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	95 # - reshape2
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	96 # - vioplot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	97
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	98 ### CONSTANTS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	99
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	100 const_parfin <- par("fin")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	101 const_boxplot_fill <- "grey94"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	102 const_stripchart_cex <- 0.5
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	103 const_stripsmall_cex <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	104 sqrt(const_stripchart_cex * const_stripchart_cex / 2)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	105 const_stripchart_jitter <- 0.3
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	106 const_write_debug_files <- FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	107 const_table_anchor_bp <- "bp"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	108 const_table_anchor_ht <- "ht"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	109 const_table_anchor_p <- "p"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	110 const_table_anchor_tbp <- "tbp"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	111
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	112
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	113 const_ksea_astrsk_kinases <- 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	114 const_ksea_nonastrsk_kinases <- 2
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	115 const_ksea_all_kinases <- 3
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	116
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	117 const_log10_e <- log10(exp(1))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	118
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	119 ### FUNCTIONS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	120
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	121 # from `demo(error.catching)`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	122 ##' Catch and save both errors and warnings, and in the case of
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	123 ##' a warning, also keep the computed result.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	124 ##'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	125 ##' @title tryCatch both warnings (with value) and errors
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	126 ##' @param expr an \R expression to evaluate
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	127 ##' @return a list with 'value' and 'warning', where
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	128 ##' 'value' may be an error caught.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	129 ##' @author Martin Maechler;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	130 ##' Copyright (C) 2010-2012 The R Core Team
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	131 try_catch_w_e <- function(expr) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	132 wrn <- NULL
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	133 # warning handler
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	134 w_handler <- function(w) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	135 wrn <<- w
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	136 invokeRestart("muffleWarning")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	137 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	138 list(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	139 value = withCallingHandlers(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	140 tryCatch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	141 expr,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	142 error = function(e) e
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	143 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	144 warning = w_handler
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	145 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	146 warning = wrn
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	147 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	148 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	149
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	150
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	151 write_debug_file <- function(s) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	152 if (const_write_debug_files) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	153 s_path <- sprintf("test-data/%s.txt", deparse(substitute(s)))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	154 print(sprintf("DEBUG writing file %s", spath))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	155 write.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	156 s,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	157 file = s_path,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	158 sep = "\t",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	159 col.names = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	160 row.names = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	161 quote = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	162 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	163 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	164 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	165
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	166 # ref: http://adv-r.had.co.nz/Environments.html
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	167 # "When creating your own environment, note that you should set its parent
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	168 # environment to be the empty environment. This ensures you don't
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	169 # accidentally inherit objects from somewhere else."
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	170 # Caution: this prevents `with(my_env, expr)` from working when `expr`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	171 # contains anything from the global environment, even operators!
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	172 # Hence, `x <- 1; get("x", new_env())` fails by design.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	173 new_env <- function() {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	174 new.env(parent = emptyenv())
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	175 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	176
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	177 ### numerical/statistical helper functions
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	178
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	179 any_nan <- function(x) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	180 !any(x == "NaN")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	181 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	182
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	183 # determine standard deviation of quantile to impute
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	184 sd_finite <- function(x) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	185 ok <- is.finite(x)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	186 sd(x[ok])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	187 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	188
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	189 anova_func <- function(x, grouping_factor, one_way_f) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	190 subject <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	191 intensity = x
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	192 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	193 x_aov <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	194 one_way_f(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	195 formula = intensity ~ grouping_factor,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	196 data = subject
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	197 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	198 pvalue <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	199 if (identical(one_way_f, aov))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	200 summary(x_aov)[[1]][["Pr(>F)"]][1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	201 else
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	202 pvalue <- x_aov$p.value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	203 pvalue
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	204 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	205
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	206
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	207 ### LaTeX functions
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	208
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	209 latex_collapsed_vector <- function(collapse_string, v, underscore_whack = TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	210 v_sub <- if (underscore_whack) gsub("_", "\\\\_", v) else v
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	211 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	212 paste0(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	213 v_sub,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	214 collapse = collapse_string
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	215 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	216 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	217 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	218
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	219 latex_itemized_collapsed <- function(collapse_string, v, underscore_whack = TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	220 cat("\\begin{itemize}\n\\item ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	221 latex_collapsed_vector(collapse_string, v, underscore_whack)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	222 cat("\n\\end{itemize}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	223 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	224
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	225 latex_itemized_list <- function(v, underscore_whack = TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	226 latex_itemized_collapsed("\n\\item ", v, underscore_whack)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	227 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	228
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	229 latex_enumerated_collapsed <- function(collapse_string, v, underscore_whack = TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	230 cat("\\begin{enumerate}\n\\item ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	231 latex_collapsed_vector(collapse_string, v, underscore_whack)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	232 cat("\n\\end{enumerate}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	233 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	234
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	235 latex_enumerated_list <- function(v) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	236 latex_enumerated_collapsed("\n\\item ", v)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	237 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	238
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	239 latex_table_row <- function(v, extra = "", underscore_whack = TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	240 latex_collapsed_vector(" & ", v, underscore_whack)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	241 cat(extra)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	242 cat(" \\\\\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	243 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	244
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	245 # Use this like print.data.frame, from which it is adapted:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	246 data_frame_latex <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	247 function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	248 x,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	249 ...,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	250 # digits to pass to format.data.frame
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	251 digits = NULL,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	252 # TRUE -> right-justify columns; FALSE -> left-justify
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	253 right = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	254 # maximumn number of rows to print
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	255 max = NULL,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	256 # string with justification of each column
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	257 justification = NULL,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	258 # TRUE to center on page
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	259 centered = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	260 # optional caption
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	261 caption = NULL,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	262 # h(inline); b(bottom); t (top) or p (separate page)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	263 anchor = "h",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	264 # set underscore_whack to TRUE to escape underscores
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	265 underscore_whack = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	266 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	267 if (is.null(justification))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	268 justification <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	269 Reduce(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	270 f = paste,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	271 x = rep_len(if (right) "r" else "l", length(colnames(x)))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	272 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	273 n <- length(rownames(x))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	274 if (length(x) == 0L) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	275 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	276 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	277 # if n is one, use singular 'row', else use plural 'rows'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	278 ngettext(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	279 n,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	280 "data frame with 0 columns and %d row",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	281 "data frame with 0 columns and %d rows"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	282 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	283 n
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	284 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	285 "\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	286 sep = ""
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	287 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	288 } else if (n == 0L) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	289 cat("0 rows for:\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	290 latex_itemized_list(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	291 v = names(x),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	292 underscore_whack = underscore_whack
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	293 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	294 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	295 if (is.null(max))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	296 max <- getOption("max.print", 99999L)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	297 if (!is.finite(max))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	298 stop("invalid 'max' / getOption(\"max.print\"): ",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	299 max)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	300 omit <- (n0 <- max %/% length(x)) < n
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	301 m <- as.matrix(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	302 format.data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	303 if (omit) x[seq_len(n0), , drop = FALSE] else x,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	304 digits = digits,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	305 na.encode = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	306 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	307 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	308 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	309 # h(inline); b(bottom); t (top) or p (separate page)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	310 paste0("\\begin{table}[", anchor, "]\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	311 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	312 if (!is.null(caption))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	313 cat(paste0(" \\caption{", caption, "}"))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	314 if (centered) cat("\\centering\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	315 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	316 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	317 " \\begin{tabular}{",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	318 justification,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	319 "}\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	320 sep = ""
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	321 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	322 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	323 # ref: https://tex.stackexchange.com/a/50353
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	324 # Describes use of \rule{0pt}{3ex}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	325 if (!is.null(caption))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	326 cat("\\B \\\\ \\hline\\hline\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	327 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	328 latex_table_row(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	329 v = colnames(m),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	330 extra = "\\T\\B",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	331 underscore_whack = underscore_whack
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	332 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	333 cat("\\hline\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	334 for (i in seq_len(length(m[, 1]))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	335 latex_table_row(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	336 v = m[i, ],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	337 underscore_whack = underscore_whack
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	338 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	339 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	340 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	341 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	342 " \\end{tabular}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	343 "\\end{table}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	344 sep = "\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	345 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	346 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	347 if (omit)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	348 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	349 n - n0, "rows ]\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	350 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	351 invisible(x)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	352 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	353
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	354 hypersub <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	355 function(s) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	356 hyper <- tolower(s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	357 hyper <- gsub("[^a-z0-9]+", "-", hyper)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	358 hyper <- gsub("[-]+", "-", hyper)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	359 hyper <- sub("^[-]", "", hyper)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	360 hyper <- sub("[-]$", "", hyper)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	361 return(hyper)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	362 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	363
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	364 subsection_header <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	365 function(s) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	366 hyper <- hypersub(s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	367 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	368 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	369 "\\hypertarget{%s}\n{\\subsection{%s}\\label{%s}}\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	370 hyper, s, hyper
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	371 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	372 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	373 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	374
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	375 subsubsection_header <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	376 function(s) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	377 hyper <- hypersub(s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	378 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	379 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	380 "\\hypertarget{%s}\n{\\subsubsection{%s}\\label{%s}}\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	381 hyper, s, hyper
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	382 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	383 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	384 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	385
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	386 ### SQLite functions
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	387
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	388 ddl_exec <- function(db, sql) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	389 discard <- DBI::dbExecute(conn = db, statement = sql)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	390 if (FALSE && discard != 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	391 need_newpage <- TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	392 if (need_newpage) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	393 need_newpage <<- FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	394 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	395 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	396 o_file <- stdout()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	397 cat("\n\\begin{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	398 cat(sql, file = o_file)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	399 cat(sprintf("\n%d rows affected by DDL\n", discard), file = o_file)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	400 cat("\n\\end{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	401 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	402 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	403
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	404 dml_no_rows_exec <- function(db, sql) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	405 discard <- DBI::dbExecute(conn = db, statement = sql)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	406 if (discard != 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	407 need_newpage <- TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	408 if (need_newpage) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	409 need_newpage <<- FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	410 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	411 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	412 cat("\n\\begin{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	413 o_file <- stdout()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	414 cat(sql, file = o_file)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	415 cat(sprintf("\n%d rows affected by DML\n", discard), file = o_file)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	416 cat("\n\\end{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	417 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	418 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	419
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	420 ### KSEA functions and helpers
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	421
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	422 # Adapted from KSEAapp::KSEA.Scores to allow retrieval of:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	423 # - maximum log2(FC)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	424 ksea_scores <- function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	425
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	426 # For human data, typically, ksdata = KSEAapp::ksdata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	427 ksdata,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	428
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	429 # Input data file having columns:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	430 # - Protein : abbreviated protein name
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	431 # - Gene : HUGO gene name
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	432 # - Peptide : peptide sequence without indications of phosphorylation
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	433 # - Reside.Both : position(s) of phosphorylation within Gene sequence
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	434 # - First letter designates AA that is modified
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	435 # - Numbers indicate position within Gene
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	436 # - Multiple values are separated by semicolons
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	437 # - p : p-value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	438 # - FC : fold-change
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	439 px,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	440
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	441 # A binary input of TRUE or FALSE, indicating whether or not to include
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	442 # NetworKIN predictions
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	443 networkin,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	444
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	445 # A numeric value between 1 and infinity setting the minimum NetworKIN
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	446 # score (can be left out if networkin = FALSE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	447 networkin_cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	448
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	449 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	450 if (length(grep(";", px$Residue.Both)) == 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	451 # There are no Residue.Both entries having semicolons, so new is
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	452 # simply px except two columns are renamed and a column is added
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	453 # for log2(abs(fold-change))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	454 new <- px
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	455 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	456 new$log2_fc <- log2(abs(as.numeric(as.character(new$FC))))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	457 new <- new[complete.cases(new$log2_fc), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	458 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	459 # Split each row having semicolons in Residue.Both into rows that are
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	460 # duplicated in all respects except that each row has a single
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	461 # member of the set "split-on-semicolon-Residue.Both"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	462 px_double <- px[grep(";", px$Residue.Both), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	463 residues <- as.character(px_double$Residue.Both)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	464 residues <- as.matrix(residues, ncol = 1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	465 split <- strsplit(residues, split = ";")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	466 # x gets count of residues in each row,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	467 # i.e., 1 + count of semicolons
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	468 x <- sapply(split, length)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	469 # Here is the set of split rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	470 px_single <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	471 Protein = rep(px_double$Protein, x),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	472 Gene = rep(px_double$Gene, x),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	473 Peptide = rep(px_double$Peptide, x),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	474 Residue.Both = unlist(split),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	475 p = rep(px_double$p, x),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	476 FC = rep(px_double$FC, x)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	477 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	478 # new first gets the split rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	479 new <- px[-grep(";", px$Residue.Both), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	480 # to new, append the rows that didn't need splitting in the first place
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	481 new <- rbind(new, px_single)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	482 # map Gene to SUB_GENE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	483 # map Residue.Both to SUB_MOD_RSD
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	484 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	485 # Eliminate any non-positive values to prevent introduction of
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	486 # infinite or NaN values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	487 new[(0 <= new$log2_fc), "log2_fc"] <- NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	488 # Because of preceding step, there is no need for abs in the next line
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	489 new$log2_fc <- log2(as.numeric(as.character(new$FC)))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	490 # Convert any illegal values from NaN to NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	491 new[is.nan(new$log2_fc), "log2_fc"] <- NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	492 # Eliminate rows having missing values (e.g., non-imputed data)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	493 new <- new[complete.cases(new$log2_fc), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	494 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	495 if (networkin == TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	496 # When NetworKIN is true, filter on NetworKIN.cutoff which includes
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	497 # PhosphoSitePlus data because its networkin_score is set to Inf
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	498 ksdata_filtered <- ksdata[grep("[a-z]", ksdata$Source), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	499 ksdata_filtered <- ksdata_filtered[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	500 (ksdata_filtered$networkin_score >= networkin_cutoff), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	501 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	502 # Otherwise, simply use PhosphSitePlus rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	503 ksdata_filtered <- ksdata[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	504 grep("PhosphoSitePlus", ksdata$Source), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	505 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	506 # Join the two data.frames on common columns SUB_GENE and SUB_MOD_RSD
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	507 # colnames of ksdata_filtered:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	508 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" "SUB_GENE_ID"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	509 # "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" "SITE_GRP_ID"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	510 # "SITE_...7_AA" "networkin_score" "Source"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	511 # colnames of new:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	512 # "Protein" "SUB_GENE" "Peptide" "SUB_MOD_RSD" "p" "FC" "log2_fc"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	513 # Equivalent to:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	514 # SELECT a.*. b.Protein, b.Peptide, b.p, b.FC, b.log2_fc
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	515 # FROM ksdata_filtered a
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	516 # INNER JOIN new b
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	517 # ON a.SUB_GENE = b.SUB_GENE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	518 # AND a.SUB_MOD_RSD = b.SUB_MOD_RSD
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	519 ksdata_dataset <- base::merge(ksdata_filtered, new)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	520 # colnames of ksdata_dataset:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	521 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	522 # "SUB_GENE_ID" "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	523 # "SITE_GRP_ID" "SITE_...7_AA" "networkin_score" "Source" "Protein"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	524 # "Peptide" "p" "FC" "log2_fc" (uniprot_no_isoform)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	525 # Re-order dataset; prior to accounting for isoforms
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	526 ksdata_dataset <- ksdata_dataset[order(ksdata_dataset$GENE), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	527 # Extract non-isoform accession in UniProtKB
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	528 ksdata_dataset$uniprot_no_isoform <- sapply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	529 ksdata_dataset$KIN_ACC_ID,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	530 function(x) unlist(strsplit(as.character(x), split = "-"))[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	531 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	532 # Discard previous results while selecting interesting columns ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	533 ksdata_dataset_abbrev <- ksdata_dataset[, c(5, 1, 2, 16:19, 14)]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	534 # Column names are now:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	535 # "GENE" "SUB_GENE" "SUB_MOD_RSD" "Peptide" "p"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	536 # "FC" "log2_fc" "Source"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	537 # Make column names human-readable
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	538 colnames(ksdata_dataset_abbrev) <- c(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	539 "Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	540 "FC", "log2FC", "Source"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	541 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	542 # SELECT * FROM ksdata_dataset_abbrev
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	543 # ORDER BY Kinase.Gene, Substrate.Gene, Substrate.Mod, p
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	544 ksdata_dataset_abbrev <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	545 ksdata_dataset_abbrev[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	546 order(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	547 ksdata_dataset_abbrev$Kinase.Gene,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	548 ksdata_dataset_abbrev$Substrate.Gene,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	549 ksdata_dataset_abbrev$Substrate.Mod,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	550 ksdata_dataset_abbrev$p),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	551 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	552 # First aggregation step to account for multiply phosphorylated peptides
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	553 # and differing peptide sequences; the goal here is to combine results
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	554 # for all measurements of the same substrate.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	555 # SELECT `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	556 # `Source`, avg(log2FC) AS log2FC
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	557 # FROM ksdata_dataset_abbrev
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	558 # GROUP BY `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	559 # `Source`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	560 # ORDER BY `Kinase.Gene`;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	561 # in two steps:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	562 # (1) compute average log_2(fold-change)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	563 ksdata_dataset_abbrev <- aggregate(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	564 log2FC ~ Kinase.Gene + Substrate.Gene + Substrate.Mod + Source,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	565 data = ksdata_dataset_abbrev,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	566 FUN = mean
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	567 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	568 # (2) order by Kinase.Gene
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	569 ksdata_dataset_abbrev <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	570 ksdata_dataset_abbrev[order(ksdata_dataset_abbrev$Kinase.Gene), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	571 # SELECT `Kinase.Gene`, count(*)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	572 # FROM ksdata_dataset_abbrev
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	573 # GROUP BY `Kinase.Gene`;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	574 # in two steps:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	575 # (1) Extract the list of Kinase.Gene names
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	576 kinase_list <- as.vector(ksdata_dataset_abbrev$Kinase.Gene)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	577 # (2) Convert to a named list of counts of kinases in ksdata_dataset_abrev,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	578 # named by Kinase.Gene
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	579 kinase_list <- as.matrix(table(kinase_list))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	580 # Second aggregation step to account for all substrates per kinase
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	581 # CREATE TABLE mean_fc
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	582 # AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	583 # SELECT `Kinase.Gene`, avg(log2FC) AS log2FC
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	584 # FROM ksdata_dataset_abbrev
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	585 # GROUP BY `Kinase.Gene`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	586 mean_fc <- aggregate(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	587 log2FC ~ Kinase.Gene,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	588 data = ksdata_dataset_abbrev,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	589 FUN = mean
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	590 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	591 # mean_fc columns: "Kinase.Gene", "log2FC"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	592 if (FALSE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	593 # I need to re-think this; I was trying to find the most-represented
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	594 # peptide, but that horse has already left the barn
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	595 # SELECT `Kinase.Gene`, max(abs(log2FC)) AS log2FC
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	596 # FROM ksdata_dataset_abbrev
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	597 # GROUP BY `Kinase.Gene`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	598 max_fc <- aggregate(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	599 log2FC ~ Kinase.Gene,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	600 data = ksdata_dataset_abbrev,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	601 FUN = function(r) max(abs(r))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	602 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	603 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	604
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	605 # Create column 3: mS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	606 mean_fc$m_s <- mean_fc[, 2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	607 # Create column 4: Enrichment
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	608 mean_fc$enrichment <- mean_fc$m_s / abs(mean(new$log2_fc, na.rm = TRUE))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	609 # Create column 5: m, count of substrates
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	610 mean_fc$m <- kinase_list
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	611 # Create column 6: z-score
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	612 mean_fc$z_score <- (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	613 (mean_fc$m_s - mean(new$log2_fc, na.rm = TRUE)) *
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	614 sqrt(mean_fc$m)) / sd(new$log2_fc, na.rm = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	615 # Create column 7: p-value, deduced from z-score
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	616 mean_fc$p_value <- pnorm(-abs(mean_fc$z_score))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	617 # Create column 8: FDR, deduced by Benjamini-Hochberg adustment from p-value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	618 mean_fc$fdr <- p.adjust(mean_fc$p_value, method = "fdr")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	619
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	620 # Remove log2FC column, which is duplicated as mS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	621 mean_fc <- mean_fc[order(mean_fc$Kinase.Gene), -2]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	622 # Correct the column names which we had to hack because of the linter...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	623 colnames(mean_fc) <- c(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	624 "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	625 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	626 return(mean_fc)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	627 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	628
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	629 low_fdr_barplot <- function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	630 rslt,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	631 i_cntrst,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	632 i,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	633 a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	634 b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	635 fold_change,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	636 caption
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	637 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	638 rslt_score_list_i <- rslt$score_list[[i]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	639 if (!is.null(rslt_score_list_i)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	640 rslt_score_list_i_nrow <- nrow(rslt_score_list_i)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	641 k <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	642 contrast = as.integer(i_cntrst),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	643 a_level = rep.int(a_level, rslt_score_list_i_nrow),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	644 b_level = rep.int(b_level, rslt_score_list_i_nrow),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	645 kinase_gene = rslt_score_list_i$Kinase.Gene,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	646 mean_log2_fc = rslt_score_list_i$mS,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	647 enrichment = rslt_score_list_i$Enrichment,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	648 substrate_count = rslt_score_list_i$m,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	649 z_score = rslt_score_list_i$z.score,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	650 p_value = rslt_score_list_i$p.value,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	651 fdr = rslt_score_list_i$FDR
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	652 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	653 selector <- switch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	654 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	655 "FDR" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	656 k$fdr
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	657 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	658 "p.value" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	659 k$p_value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	660 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	661 stop(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	662 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	663 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	664 ksea_cutoff_statistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	665 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	666 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	667 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	668
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	669 k <- k[selector < ksea_cutoff_threshold, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	670
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	671 if (nrow(k) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	672 op <- par(mai = c(1, 1.5, 0.4, 0.4))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	673 numeric_z_score <- as.numeric(k$z_score)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	674 z_score_order <- order(numeric_z_score)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	675 kinase_name <- k$kinase_gene
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	676 long_caption <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	677 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	678 "Kinase z-score, %s < %s, %s",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	679 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	680 ksea_cutoff_threshold,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	681 caption
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	682 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	683 my_cex_caption <- 65.0 / max(65.0, nchar(long_caption))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	684 cat("\n\\clearpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	685 barplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	686 height = numeric_z_score[z_score_order],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	687 border = NA,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	688 xpd = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	689 cex.names = 1.0,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	690 cex.axis = 1.0,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	691 main = long_caption,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	692 cex.main = my_cex_caption,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	693 names.arg = kinase_name[z_score_order],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	694 horiz = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	695 srt = 45,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	696 las = 1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	697 par(op)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	698 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	699 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	700 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	701
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	702 # note that this adds elements to the global variable `ksea_asterisk_hash`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	703
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	704 low_fdr_print <- function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	705 rslt,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	706 i_cntrst,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	707 i,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	708 a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	709 b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	710 fold_change,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	711 caption
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	712 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	713 rslt_score_list_i <- rslt$score_list[[i]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	714 if (!is.null(rslt_score_list_i)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	715 rslt_score_list_i_nrow <- nrow(rslt_score_list_i)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	716 k <- contrast_ksea_scores <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	717 contrast = as.integer(i_cntrst),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	718 a_level = rep.int(a_level, rslt_score_list_i_nrow),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	719 b_level = rep.int(b_level, rslt_score_list_i_nrow),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	720 kinase_gene = rslt_score_list_i$Kinase.Gene,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	721 mean_log2_fc = rslt_score_list_i$mS,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	722 enrichment = rslt_score_list_i$Enrichment,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	723 substrate_count = rslt_score_list_i$m,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	724 z_score = rslt_score_list_i$z.score,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	725 p_value = rslt_score_list_i$p.value,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	726 fdr = rslt_score_list_i$FDR
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	727 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	728
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	729 selector <- switch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	730 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	731 "FDR" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	732 k$fdr
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	733 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	734 "p.value" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	735 k$p_value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	736 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	737 stop(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	738 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	739 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	740 ksea_cutoff_statistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	741 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	742 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	743 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	744
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	745 k <- k[selector < ksea_cutoff_threshold, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	746 # save kinase names to ksea_asterisk_hash
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	747 for (kinase_name in k$kinase_gene) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	748 ksea_asterisk_hash[[kinase_name]] <- 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	749 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	750
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	751 db_write_table_overwrite <- (i_cntrst < 2)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	752 db_write_table_append <- !db_write_table_overwrite
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	753 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	754 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	755 name = "contrast_ksea_scores",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	756 value = contrast_ksea_scores,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	757 append = db_write_table_append
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	758 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	759 selector <- switch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	760 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	761 "FDR" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	762 contrast_ksea_scores$fdr
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	763 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	764 "p.value" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	765 contrast_ksea_scores$p_value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	766 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	767 stop(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	768 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	769 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	770 ksea_cutoff_statistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	771 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	772 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	773 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	774 output_df <- contrast_ksea_scores[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	775 selector < ksea_cutoff_threshold,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	776 c("kinase_gene", "mean_log2_fc", "enrichment", "substrate_count",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	777 "z_score", "p_value", "fdr")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	778 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	779 output_order <- with(output_df, order(mean_log2_fc, kinase_gene))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	780 output_df <- output_df[output_order, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	781 colnames(output_df) <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	782 c(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	783 colnames(output_df)[1],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	784 colnames(output_df)[2],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	785 "enrichment",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	786 "m_s",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	787 "z_score",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	788 "p_value",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	789 "fdr"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	790 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	791 output_df$fdr <- sprintf("%0.4f", output_df$fdr)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	792 output_df$p_value <- sprintf("%0.2e", output_df$p_value)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	793 output_df$z_score <- sprintf("%0.2f", output_df$z_score)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	794 output_df$m_s <- sprintf("%d", output_df$m_s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	795 output_df$enrichment <- sprintf("%0.2f", output_df$enrichment)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	796 output_ncol <- ncol(output_df)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	797 colnames(output_df) <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	798 c(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	799 "Kinase",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	800 "\$\\overline{\\log_2 (\|\\text{fold-change}\|)}\$",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	801 "Enrichment",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	802 "Substrates",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	803 "z-score",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	804 "p-value",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	805 "FDR"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	806 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	807 selector <- switch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	808 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	809 "FDR" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	810 rslt$score_list[[i]]$FDR
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	811 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	812 "p.value" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	813 rslt$score_list[[i]]$p.value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	814 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	815 stop(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	816 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	817 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	818 ksea_cutoff_statistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	819 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	820 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	821 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	822 if (sum(selector < ksea_cutoff_threshold) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	823 math_caption <- gsub("{", "\\{", caption, fixed = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	824 math_caption <- gsub("}", "\\}", math_caption, fixed = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	825 data_frame_latex(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	826 x = output_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	827 justification = "l c c c c c c",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	828 centered = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	829 caption = sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	830 "\\text{%s}, %s < %s",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	831 math_caption,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	832 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	833 ksea_cutoff_threshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	834 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	835 anchor = const_table_anchor_p
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	836 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	837 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	838 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	839 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	840 "\\break
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	841 No kinases had
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	842 \$\\text{%s}_\\text{enrichment} < %s\$
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	843 for contrast %s\\hfill\\break\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	844 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	845 ksea_cutoff_threshold,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	846 caption
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	847 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	848 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	849 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	850 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	851 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	852
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	853 # create_breaks is a helper for ksea_heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	854 create_breaks <- function(merged_scores) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	855 if (min(merged_scores, na.rm = TRUE) < -1.6) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	856 breaks_neg <- seq(-1.6, 0, length.out = 30)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	857 breaks_neg <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	858 append(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	859 seq(min(merged_scores, na.rm = TRUE), -1.6, length.out = 10),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	860 breaks_neg
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	861 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	862 breaks_neg <- sort(unique(breaks_neg))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	863 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	864 breaks_neg <- seq(-1.6, 0, length.out = 30)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	865 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	866 if (max(merged_scores, na.rm = TRUE) > 1.6) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	867 breaks_pos <- seq(0, 1.6, length.out = 30)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	868 breaks_pos <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	869 append(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	870 breaks_pos,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	871 seq(1.6, max(merged_scores, na.rm = TRUE),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	872 length.out = 10)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	873 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	874 breaks_pos <- sort(unique(breaks_pos))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	875 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	876 breaks_pos <- seq(0, 1.6, length.out = 30)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	877 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	878 breaks_all <- unique(append(breaks_neg, breaks_pos))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	879 mycol_neg <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	880 gplots::colorpanel(n = length(breaks_neg),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	881 low = "blue",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	882 high = "white")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	883 mycol_pos <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	884 gplots::colorpanel(n = length(breaks_pos) - 1,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	885 low = "white",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	886 high = "red")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	887 mycol <- unique(append(mycol_neg, mycol_pos))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	888 color_breaks <- list(breaks_all, mycol)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	889 return(color_breaks)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	890 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	891
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	892 # draw_kseaapp_summary_heatmap is a helper function for ksea_heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	893 draw_kseaapp_summary_heatmap <- function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	894 x,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	895 sample_cluster,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	896 merged_asterisk,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	897 my_cex_row,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	898 color_breaks,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	899 margins,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	900 ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	901 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	902 merged_scores <- x
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	903 if (!is.matrix(x)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	904 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	905 paste0(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	906 "No plot because \\texttt{typeof(x)} is '",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	907 typeof(x),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	908 "' rather than 'matrix'.\n\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	909 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	910 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	911 } else if (nrow(x) < 2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	912 cat("No plot because matrix x has ", nrow(x), " rows.\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	913 cat("\\begin{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	914 str(x)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	915 cat("\\end{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	916 } else if (ncol(x) < 2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	917 cat("No plot because matrix x has ", ncol(x), " columns.\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	918 cat("\\begin{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	919 str(x)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	920 cat("\\end{verbatim}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	921 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	922 gplots::heatmap.2(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	923 x = merged_scores,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	924 Colv = sample_cluster,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	925 scale = "none",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	926 cellnote = merged_asterisk,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	927 notecol = "white",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	928 cexCol = 0.9,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	929 # Heuristically assign size of row labels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	930 cexRow = min(1.0, ((3 * my_cex_row) ^ 1.7) / 2.25),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	931 srtCol = 45,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	932 srtRow = 45,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	933 notecex = 3 * my_cex_row,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	934 col = color_breaks[[2]],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	935 density.info = "none",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	936 trace = "none",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	937 breaks = color_breaks[[1]],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	938 lmat = rbind(c(0, 3), c(2, 1), c(0, 4)),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	939 lhei = c(0.4, 8.0, 1.1),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	940 lwid = c(0.5, 3),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	941 key = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	942 margins = margins,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	943 ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	944 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	945 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	946 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	947
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	948 # Adapted from KSEAapp::KSEA.Heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	949 ksea_heatmap <- function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	950 # the data frame outputs from the KSEA.Scores() function, in list format
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	951 score_list,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	952 # a character vector of all the sample names for heatmap annotation:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	953 # - the names must be in the same order as the data in score_list
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	954 # - please avoid long names, as they may get cropped in the final image
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	955 sample_labels,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	956 # character string of either "p.value" or "FDR" indicating the data column
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	957 # to use for marking statistically significant scores
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	958 stats,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	959 # a numeric value between 0 and infinity indicating the min. number of
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	960 # substrates a kinase must have to be included in the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	961 m_cutoff,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	962 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	963 # for indicating significant kinases in the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	964 p_cutoff =
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	965 stop("argument 'p_cutoff' is required for function 'ksea_heatmap'"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	966 # a binary input of TRUE or FALSE, indicating whether or not to perform
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	967 # hierarchical clustering of the sample columns
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	968 sample_cluster,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	969 # a binary input of TRUE or FALSE, indicating whether or not to export
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	970 # the heatmap as a .png image into the working directory
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	971 export = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	972 # bottom and right margins; adjust as needed if contrast names are too long
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	973 margins = c(6, 20),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	974 # print which kinases?
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	975 # - Mandatory argument, must be one of const_ksea_.*_kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	976 which_kinases,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	977 # additional arguments to gplots::heatmap.2, such as:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	978 # - main: main title of plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	979 # - xlab: x-axis label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	980 # - ylab: y-axis label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	981 ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	982 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	983 filter_m <- function(dataset, m_cutoff) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	984 filtered <- dataset[(dataset$m >= m_cutoff), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	985 return(filtered)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	986 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	987 score_list_m <- lapply(score_list, function(...) filter_m(..., m_cutoff))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	988 for (i in seq_len(length(score_list_m))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	989 names <- colnames(score_list_m[[i]])[c(2:7)]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	990 colnames(score_list_m[[i]])[c(2:7)] <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	991 paste(names, i, sep = ".")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	992 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	993 master <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	994 Reduce(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	995 f = function(...) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	996 base::merge(..., by = "Kinase.Gene", all = FALSE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	997 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	998 x = score_list_m
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	999 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1000
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1001 row.names(master) <- master$Kinase.Gene
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1002 columns <- as.character(colnames(master))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1003 merged_scores <- as.matrix(master[, grep("z.score", columns), drop = FALSE])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1004 colnames(merged_scores) <- sample_labels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1005 merged_stats <- as.matrix(master[, grep(stats, columns)])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1006 asterisk <- function(mtrx, p_cutoff) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1007 new <- data.frame()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1008 for (i in seq_len(nrow(mtrx))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1009 for (j in seq_len(ncol(mtrx))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1010 my_value <- mtrx[i, j]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1011 if (!is.na(my_value) && my_value < p_cutoff) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1012 new[i, j] <- "*"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1013 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1014 new[i, j] <- ""
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1015 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1016 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1017 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1018 return(new)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1019 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1020 merged_asterisk <- as.matrix(asterisk(merged_stats, p_cutoff))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1021
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1022 # begin hack to print only significant rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1023 asterisk_rows <- rowSums(merged_asterisk == "*") > 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1024 all_rows <- rownames(merged_stats)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1025 names(asterisk_rows) <- all_rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1026 non_asterisk_rows <- names(asterisk_rows[asterisk_rows == FALSE])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1027 asterisk_rows <- names(asterisk_rows[asterisk_rows == TRUE])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1028 merged_scores_asterisk <- merged_scores[names(asterisk_rows), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1029 merged_scores_non_asterisk <- merged_scores[names(non_asterisk_rows), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1030 # end hack to print only significant rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1031
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1032 row_list <- list()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1033 row_list[[const_ksea_astrsk_kinases]] <- asterisk_rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1034 row_list[[const_ksea_all_kinases]] <- all_rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1035 row_list[[const_ksea_nonastrsk_kinases]] <- non_asterisk_rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1036
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1037 i <- which_kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1038 my_row_names <- row_list[[i]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1039 scrs <- merged_scores[my_row_names, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1040 stts <- merged_stats[my_row_names, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1041 merged_asterisk <- as.matrix(asterisk(stts, p_cutoff))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1042
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1043 color_breaks <- create_breaks(scrs)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1044 plot_height <- nrow(scrs) ^ 0.55
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1045 plot_width <- ncol(scrs) ^ 0.7
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1046 my_cex_row <- 0.25 * 16 / plot_height
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1047 if (export == "TRUE") {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1048 png(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1049 "KSEA.Merged.Heatmap.png",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1050 width = plot_width * 300,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1051 height = 2 * plot_height * 300,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1052 res = 300,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1053 pointsize = 14
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1054 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1055 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1056 draw_kseaapp_summary_heatmap(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1057 x = scrs,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1058 sample_cluster = sample_cluster,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1059 merged_asterisk = merged_asterisk,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1060 my_cex_row = my_cex_row,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1061 color_breaks = color_breaks,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1062 margins = margins
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1063 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1064 if (export == "TRUE") {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1065 dev.off()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1066 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1067 return(my_row_names)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1068 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1069
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1070 # helper for heatmaps of phosphopeptide intensities
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1071
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1072 draw_intensity_heatmap <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1073 function(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1074 m, # matrix with rownames already formatted
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1075 cutoff, # cutoff used by hm_heading_function
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1076 hm_heading_function, # construct and cat heading from m and cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1077 hm_main_title, # main title for plot (drawn below heading)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1078 suppress_row_dendrogram = TRUE, # set to false to show dendrogram
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1079 max_peptide_count # experimental:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1080 = intensity_hm_rows, # values of 50 and 75 worked well
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1081 ... # passthru parameters for heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1082 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1083 peptide_count <- 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1084 # emit the heading for the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1085 if (hm_heading_function(m, cutoff)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1086 peptide_count <- min(max_peptide_count, nrow(m))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1087 if (nrow(m) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1088 m_margin <- m[peptide_count:1, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1089 # Margin setting was heuristically derived
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1090 margins <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1091 c(0.5, # col
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1092 max(80, sqrt(nchar(rownames(m_margin)))) * 5 / 16 # row
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1093 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1094 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1095 if (nrow(m) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1096 tryCatch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1097 {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1098 old_oma <- par("oma")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1099 par(cex.main = 0.6)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1100 # Heuristically determined character size adjustment formula
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1101 char_contractor <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1102 250000 / (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1103 max(4500, (nchar(rownames(m_margin)))^2) * intensity_hm_rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1104 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1105 heatmap(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1106 m[peptide_count:1, ],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1107 Rowv = if (suppress_row_dendrogram) NA else NULL,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1108 Colv = NA,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1109 cexRow = char_contractor,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1110 cexCol = char_contractor * 50 / max_peptide_count,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1111 scale = "row",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1112 margins = margins,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1113 main =
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1114 "Unimputed, unnormalized log(intensities)",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1115 xlab = "",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1116 las = 1,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1117 ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1118 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1119 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1120 error = function(e) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1121 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1122 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1123 "\nCould not draw heatmap, possibly because of too many missing values. Internal message: %s\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1124 e$message
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1125 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1126 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1127 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1128 finally = par(old_oma)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1129 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1130 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1131 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1132 return(peptide_count)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1133 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1134 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1135
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1136 ```{r, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1137 cat("\\listoftables\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1138 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1139 # Purpose
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1140
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1141 To perform for phosphopeptides:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1142
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1143 - imputation of missing values,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1144 - quantile normalization,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1145 - ANOVA (using the R stats::`r params$oneWayManyCategories` function), and
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1146 - KSEA (Kinase-Substrate Enrichment Analysis) using code adapted from the CRAN `KSEAapp` package to search for kinase substrates from the following databases:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1147 - PhosphoSitesPlus [https://www.phosphosite.org](https://www.phosphosite.org)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1148 - The Human Proteome Database [http://hprd.org](http://hprd.org)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1149 - NetworKIN [http://networkin.science/](http://networkin.science/)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1150 - Phosida [http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx](http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1151
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1152 ```{r include = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1153
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1154 ### GLOBAL VARIABLES
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1155
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1156 # parameters for KSEA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1157
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1158 ksea_cutoff_statistic <- params$kseaCutoffStatistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1159 ksea_cutoff_threshold <- params$kseaCutoffThreshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1160 ksea_min_kinase_count <- params$kseaMinKinaseCount
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1161
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1162 ksea_heatmap_titles <- list()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1163 ksea_heatmap_titles[[const_ksea_astrsk_kinases]] <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1164 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1165 "Summary for all kinases enriched in one or more contrasts at %s < %s",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1166 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1167 ksea_cutoff_threshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1168 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1169 ksea_heatmap_titles[[const_ksea_all_kinases]] <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1170 "Summary figure for all contrasts and all kinases"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1171 ksea_heatmap_titles[[const_ksea_nonastrsk_kinases]] <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1172 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1173 "Summary for all kinases not enriched at %s < %s in any contrast",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1174 ksea_cutoff_statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1175 ksea_cutoff_threshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1176 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1177 # hash to hold names of significantly enriched kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1178 ksea_asterisk_hash <- new_env()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1179
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1180 # READ PARAMETERS (mostly)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1181
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1182 intensity_hm_rows <- params$intensityHeatmapRows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1183 # Input Filename
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1184 input_file <- params$inputFile
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1185
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1186 # First data column - ideally, this could be detected via regexSampleNames,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1187 # but for now leave it as is.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1188 first_data_column <- params$firstDataColumn
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1189 fdc_is_integer <- is.integer(first_data_column)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1190 if (fdc_is_integer) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1191 first_data_column <- as.integer(params$firstDataColumn)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1192 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1193
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1194 # False discovery rate adjustment for ANOVA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1195 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1196 val_fdr <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1197 read.table(file = params$alphaFile, sep = "\t", header = FALSE, quote = "")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1198
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1199 if (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1200 ncol(val_fdr) != 1 \|\|
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1201 sum(!is.numeric(val_fdr[, 1])) \|\|
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1202 sum(val_fdr[, 1] < 0) \|\|
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1203 sum(val_fdr[, 1] > 1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1204 ) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1205 stop("alphaFile should be one column of numbers within the range [0.0,1.0]")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1206 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1207 val_fdr <- val_fdr[, 1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1208
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1209 #Imputed Data filename
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1210 imputed_data_filename <- params$imputedDataFilename
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1211 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1212 anova_ksea_mtdt_file <- params$anovaKseaMetadata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1213
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1214 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1215
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1216 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1217 # Imputation method, should be one of
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1218 # "random", "group-median", "median", or "mean"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1219 imputation_method <- params$imputationMethod
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1220
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1221 # Selection of percentile of logvalue data to set the mean for random number
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1222 # generation when using random imputation
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1223 mean_percentile <- params$meanPercentile / 100.0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1224
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1225 # deviation adjustment-factor for random values; real number.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1226 sd_percentile <- params$sdPercentile
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1227
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1228 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1229 regex_sample_names <- params$regexSampleNames
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1230
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1231 # Regular expression to extract Sample Grouping from Sample Name;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1232 # if error occurs, compare sample_treatment_levels vs. sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1233 # to see if groupings/pairs line up
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1234 # e.g., "(\\d+)"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1235 regex_sample_grouping <- params$regexSampleGrouping
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1236
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1237 one_way_all_categories_fname <- params$oneWayManyCategories
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1238 one_way_all_categories <- try_catch_w_e(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1239 match.fun(one_way_all_categories_fname))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1240 if (!is.function(one_way_all_categories$value)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1241 write("fatal error for parameter oneWayManyCategories:", stderr())
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1242 write(one_way_all_categories$value$message, stderr())
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1243 if (sys.nframe() > 0) quit(save = "no", status = 1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1244 stop("Cannot continue. Goodbye.")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1245 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1246 one_way_all_categories <- one_way_all_categories$value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1247
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1248 one_way_two_categories_fname <- params$oneWayManyCategories
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1249 one_way_two_categories <- try_catch_w_e(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1250 match.fun(one_way_two_categories_fname))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1251 if (!is.function(one_way_two_categories$value)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1252 cat("fatal error for parameter oneWayTwoCategories: \n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1253 cat(one_way_two_categories$value$message, fill = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1254 if (sys.nframe() > 0) quit(save = "no", status = 1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1255 stop("Cannot continue. Goodbye.")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1256 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1257 one_way_two_categories <- one_way_two_categories$value
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1258
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1259 preproc_db <- params$preprocDb
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1260 ksea_app_prep_db <- params$kseaAppPrepDb
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1261 result <- file.copy(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1262 from = preproc_db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1263 to = ksea_app_prep_db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1264 overwrite = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1265 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1266 if (!result) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1267 write(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1268 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1269 "fatal error copying initial database '%s' to output '%s'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1270 preproc_db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1271 ksea_app_prep_db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1272 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1273 stderr()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1274 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1275 if (sys.nframe() > 0) quit(save = "no", status = 1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1276 stop("Cannot continue. Goodbye.")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1277 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1278 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1279
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1280 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1281 ### READ DATA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1282
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1283 # read.table reads a file in table format and creates a data frame from it.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1284 # - note that `quote = ""` means that quotation marks are treated literally.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1285 full_data <- read.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1286 file = input_file,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1287 sep = "\t",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1288 header = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1289 quote = "",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1290 check.names = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1291 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1292 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1293
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1294 # Extract Sample Names and Treatment Levels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1295
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1296 Column names parsed from input file are shown in Table 1; sample names and treatment levels, in Table 2.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1297
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1298 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1299
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1300 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1301
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1302 if (!fdc_is_integer) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1303 if (length(data_column_indices) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1304 first_data_column <- data_column_indices[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1305 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1306 stop(paste("failed to convert firstDataColumn:", first_data_column))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1307 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1308 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1309
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1310 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1311 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1312 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1313 "\n\nThe input data file has peptide-intensity data for each sample",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1314 "in one of columns %d through %d.\n\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1315 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1316 min(data_column_indices),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1317 max(data_column_indices)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1318 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1319 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1320
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1321 # Write column names as a LaTeX enumerated list.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1322 column_name_df <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1323 column = seq_len(length(colnames(full_data))),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1324 name = paste0("\\verb@", colnames(full_data), "@")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1325 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1326 data_frame_latex(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1327 x = column_name_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1328 justification = "l l",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1329 centered = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1330 caption = "Input data column names",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1331 anchor = const_table_anchor_bp,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1332 underscore_whack = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1333 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1334
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1335 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1336
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1337 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1338 quant_data <- full_data[first_data_column:length(full_data)]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1339 quant_data[quant_data == 0] <- NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1340 rownames(quant_data) <- rownames(full_data) <- full_data$Phosphopeptide
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1341 # Extract factors and trt-replicates using regular expressions.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1342 # Typically:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1343 # regex_sample_names is "\\.\\d+[A-Z]$"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1344 # regex_sample_grouping is "\\d+"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1345 # This would distinguish trt-replicates by terminal letter [A-Z]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1346 # in sample names and group them into trts by the preceding digits.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1347 # e.g.:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1348 # group .1A .1B .1C into group 1;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1349 # group .2A .2B .2C, into group 2;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1350 # etc.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1351 m <- regexpr(regex_sample_names, colnames(quant_data), perl = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1352 sample_name_matches <- regmatches(names(quant_data), m)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1353 colnames(quant_data) <- sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1354
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1355 write_debug_file(quant_data)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1356
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1357 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1358 sample_treatment_levels <- as.factor(regmatches(sample_name_matches, rx_match))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1359 number_of_samples <- length(sample_name_matches)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1360 sample_treatment_df <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1361 level = sample_treatment_levels,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1362 sample = sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1363 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1364 data_frame_latex(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1365 x = sample_treatment_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1366 justification = "rp{0.2\\linewidth} lp{0.3\\linewidth}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1367 centered = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1368 caption = "Treatment levels",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1369 anchor = const_table_anchor_tbp,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1370 underscore_whack = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1371 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1372 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1373
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1374 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1375 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1376 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1377
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1378 ## Are the log-transformed sample distributions similar?
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1379
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1380 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1381
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1382 quant_data[quant_data == 0] <- NA #replace 0 with NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1383 quant_data_log <- log10(quant_data)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1384
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1385 rownames(quant_data_log) <- rownames(quant_data)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1386 colnames(quant_data_log) <- sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1387
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1388 write_debug_file(quant_data_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1389
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1390 # data visualization
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1391 old_par <- par(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1392 mai = par("mai") + c(0.5, 0, 0, 0)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1393 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1394 # ref: https://r-charts.com/distribution/add-points-boxplot/
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1395 # Vertical plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1396 boxplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1397 quant_data_log
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1398 , las = 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1399 , col = const_boxplot_fill
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1400 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1401 , xlab = "Sample"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1402 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1403 par(old_par)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1404
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1405
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1406
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1407 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1408 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1409
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1410 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1411
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1412 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1413 if (nrow(quant_data_log) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1414 quant_data_log_stack <- stack(quant_data_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1415 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) +
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1416 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) +
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1417 ggplot2::ylab("Probability density") +
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1418 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1419 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1420 cat("No density plot because there are too few peptides.\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1421 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1422 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1423
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1424 ## Globally, are peptide intensities are approximately unimodal?
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1425
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1426 <!--
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1427 # bquote could be used as an alternative to latex2exp::TeX below particularly
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1428 # and when plotting math expressions generally, at the expense of mastering
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1429 # another syntax, which hardly seems worthwhile when I need to use TeX
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1430 # elsewhere; here's an introduction to bquote:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1431 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1432 -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1433 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1434
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1435 # identify the location of missing values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1436 fin <- is.finite(as.numeric(as.matrix(quant_data_log)))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1437
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1438 logvalues <- as.numeric(as.matrix(quant_data_log))[fin]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1439 logvalues_density <- density(logvalues)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1440 plot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1441 x = logvalues_density,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1442 main = latex2exp::TeX(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1443 "Smoothed estimated probability density vs. $log_{10}$(peptide intensity)"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1444 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1445 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1446 ylab = "Probability density"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1447 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1448 hist(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1449 x = as.numeric(as.matrix(quant_data_log)),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1450 xlim = c(min(logvalues_density$x), max(logvalues_density$x)),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1451 breaks = 100,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1452 main = latex2exp::TeX("Frequency vs. $log_{10}$(peptide intensity)"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1453 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1454 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1455 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1456
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1457 ## Distribution of standard deviations of $log_{10}(\text{intensity})$, ignoring missing values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1458
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1459 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1460 # determine quantile
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1461 q1 <- quantile(logvalues, probs = mean_percentile)[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1462
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1463 # 1 = row of matrix (ie, phosphopeptide)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1464 sds <- apply(quant_data_log, 1, sd_finite)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1465 if (sum(!is.na(sds)) > 2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1466 plot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1467 density(sds, na.rm = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1468 , main = "Smoothed estimated probability density vs. std. deviation"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1469 , sub = "(probability estimation made with Gaussian smoothing)"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1470 , ylab = "Probability density"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1471 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1472 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1473 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1474 "At least two non-missing values are required to plot",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1475 "probability density.\n\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1476 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1477 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1478
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1479 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1480
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1481 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1482 # Determine number of cells to impute
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1483 temp <- quant_data[is.na(quant_data)]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1484
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1485 # Determine number of values to impute
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1486 number_to_impute <- length(temp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1487
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1488 # Determine percent of missing values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1489 pct_missing_values <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1490 round(length(temp) / (length(logvalues) + length(temp)) * 100)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1491 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1492
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1493 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1494
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1495 # prep for trt-median based imputation
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1496
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1497 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1498 # Impute Missing Values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1499
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1500 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1501
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1502 imp_smry_pot_peptides_before <- nrow(quant_data_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1503 imp_smry_missing_values_before <- number_to_impute
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1504 imp_smry_pct_missing <- pct_missing_values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1505
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1506 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1507
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1508 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1509 #Determine number of cells to impute
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1510
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1511 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1512 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1513
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1514 # Identify which values are missing and need to be imputed
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1515 ind <- which(is.na(quant_data), arr.ind = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1516
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1517 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1518 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1519
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1520 # Apply imputation
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1521 switch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1522 imputation_method
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1523 , "group-median" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1524 quant_data_imp <- quant_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1525 imputation_method_description <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1526 paste("Substitute missing value with",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1527 "median peptide-intensity for sample group.\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1528 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1529 sample_level_integers <- as.integer(sample_treatment_levels)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1530 # Take the accurate ln(x+1) because the data are log-normally distributed
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1531 # and because median can involve an average of two measurements.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1532 quant_data_imp <- log1p(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1533 for (i in seq_len(length(levels(sample_treatment_levels)))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1534 # Determine the columns for this factor-level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1535 level_cols <- i == sample_level_integers
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1536 # Extract those columns
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1537 lvlsbst <- quant_data_imp[, level_cols, drop = FALSE]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1538 # assign to ind the row-column pairs corresponding to each NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1539 ind <- which(is.na(lvlsbst), arr.ind = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1540 # No group-median exists if there is only one sample
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1541 # a given ppep has no measurement; otherwise, proceed.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1542 if (ncol(lvlsbst) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1543 the_centers <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1544 apply(lvlsbst, 1, median, na.rm = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1545 for (j in seq_len(nrow(lvlsbst))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1546 for (k in seq_len(ncol(lvlsbst))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1547 if (is.na(lvlsbst[j, k])) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1548 lvlsbst[j, k] <- the_centers[j]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1549 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1550 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1551 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1552 quant_data_imp[, level_cols] <- lvlsbst
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1553 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1554 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1555 # Take the accurate e^x - 1 to match scaling of original input.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1556 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1557 good_rows <- !is.na(rowMeans(quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1558 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1559 , "median" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1560 quant_data_imp <- quant_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1561 imputation_method_description <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1562 paste("Substitute missing value with",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1563 "median peptide-intensity across all sample classes.\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1564 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1565 # Take the accurate ln(x+1) because the data are log-normally distributed
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1566 # and because median can involve an average of two measurements.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1567 quant_data_imp <- log1p(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1568 quant_data_imp[ind] <- apply(quant_data_imp, 1, median, na.rm = TRUE)[ind[, 1]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1569 # Take the accurate e^x - 1 to match scaling of original input.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1570 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1571 good_rows <- !is.nan(rowMeans(quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1572 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1573 , "mean" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1574 quant_data_imp <- quant_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1575 imputation_method_description <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1576 paste("Substitute missing value with",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1577 "geometric-mean peptide intensity across all sample classes.\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1578 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1579 # Take the accurate ln(x+1) because the data are log-normally distributed,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1580 # so arguments to mean should be previously transformed.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1581 # this will have to be
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1582 quant_data_imp <- log1p(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1583 # Assign to NA cells the mean for the row
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1584 quant_data_imp[ind] <- apply(quant_data_imp, 1, mean, na.rm = TRUE)[ind[, 1]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1585 # Take the accurate e^x - 1 to match scaling of original input.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1586 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1587 good_rows <- !is.nan(rowMeans(quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1588 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1589 , "random" = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1590 quant_data_imp <- quant_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1591 m1 <- median(sds, na.rm = TRUE) * sd_percentile #sd to be used is the median sd
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1592 # If you want results to be reproducible, you will want to call
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1593 # base::set.seed before calling stats::rnorm
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1594 imputation_method_description <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1595 paste("Substitute each missing value with random intensity",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1596 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1597 "random intensity $N \\sim (%0.2f, %0.2f)$.\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1598 q1, m1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1599 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1600 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1601 cat(sprintf("mean_percentile (from input parameter) is %2.0f\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1602 100 * mean_percentile))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1603 cat(sprintf("sd_percentile (from input parameter) is %0.2f\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1604 sd_percentile))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1605 quant_data_imp[ind] <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1606 10 ^ rnorm(number_to_impute, mean = q1, sd = m1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1607 quant_data_imp_ln <- log1p(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1608 good_rows <- !is.nan(rowMeans(quant_data_imp))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1609 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1610 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1611 quant_data_imp_log10 <- quant_data_imp_ln * const_log10_e
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1612
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1613 if (length(good_rows) < 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1614 print("ERROR: Cannot impute data; there are no good rows!")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1615 return(-1)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1616 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1617 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1618
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1619 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1620 cat("\\quad\n\nImputation method:\n\n\n", imputation_method_description)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1621 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1622
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1623 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1624
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1625 imp_smry_pot_peptides_after <- sum(good_rows)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1626 imp_smry_rejected_after <- sum(!good_rows)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1627 imp_smry_missing_values_after <- sum(is.na(quant_data_imp[good_rows, ]))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1628 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1629 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1630 # ref: http://www1.maths.leeds.ac.uk/latex/TableHelp1.pdf
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1631 tabular_lines_fmt <- paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1632 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1633 " \\caption{Imputation Results}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1634 " \\centering", # \centering centers the table on the page
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1635 " \\begin{tabular}{l c c c}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1636 " \\hline\\hline",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1637 " \\ & potential peptides & missing values & rejected",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1638 " peptides \\\\ [0.5ex]",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1639 " \\hline",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1640 " before imputation & %d & %d (%d\\%s) & \\\\",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1641 " after imputation & %d & %d & %d \\\\ [1ex]",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1642 " \\hline",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1643 " \\end{tabular}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1644 #" \\label{table:nonlin}", # may be used to refer this table in the text
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1645 "\\end{table}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1646 sep = "\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1647 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1648 tabular_lines <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1649 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1650 tabular_lines_fmt,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1651 imp_smry_pot_peptides_before,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1652 imp_smry_missing_values_before,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1653 imp_smry_pct_missing,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1654 "%",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1655 imp_smry_pot_peptides_after,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1656 imp_smry_missing_values_after,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1657 imp_smry_rejected_after
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1658 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1659 cat(tabular_lines)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1660 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1661 ```{r echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1662
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1663
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1664 # Zap rows where imputation was ineffective
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1665 full_data <- full_data [good_rows, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1666 quant_data <- quant_data [good_rows, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1667
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1668 quant_data_imp <- quant_data_imp[good_rows, ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1669 write_debug_file(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1670 quant_data_imp_good_rows <- quant_data_imp
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1671
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1672 write_debug_file(quant_data_imp_good_rows)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1673 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1674
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1675 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1676
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1677 can_plot_before_after_imp <- TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1678 d_combined <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1679 as.numeric(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1680 as.matrix(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1681 log10(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1682 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1683 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1684 d_original <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1685 as.numeric(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1686 as.matrix(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1687 log10(quant_data_imp[!is.na(quant_data)])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1688 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1689 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1690
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1691 if (sum(!is.na(d_original)) > 2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1692 d_original <- density(d_original)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1693 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1694 can_plot_before_after_imp <- FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1695 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1696 if (can_plot_before_after_imp && sum(is.na(d_combined)) < 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1697 d_combined <- density(d_combined)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1698 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1699 can_plot_before_after_imp <- FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1700 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1701
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1702 if (sum(is.na(quant_data)) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1703 # There ARE missing values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1704 d_imputed <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1705 as.numeric(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1706 as.matrix(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1707 log10(quant_data_imp[is.na(quant_data)])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1708 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1709 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1710 if (can_plot_before_after_imp && sum(is.na(d_imputed)) < 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1711 d_imputed <- (density(d_imputed))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1712 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1713 can_plot_before_after_imp <- FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1714 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1715 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1716 # There are NO missing values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1717 d_imputed <- d_combined
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1718 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1719
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1720 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1721
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1722 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1723 zero_sd_rownames <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1724 rownames(quant_data_imp)[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1725 is.na((apply(quant_data_imp, 1, sd, na.rm = TRUE)) == 0)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1726 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1727
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1728 if (length(zero_sd_rownames) >= nrow(quant_data_imp)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1729 stop("All peptides have zero standard deviation. Cannot continue.")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1730 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1731 if (length(zero_sd_rownames) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1732 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1733 sprintf("%d peptides with zero variance were removed from statistical consideration",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1734 length(zero_sd_rownames)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1735 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1736 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1737 zap_named_rows <- function(df, nms) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1738 return(df[!(row.names(df) %in% nms), ])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1739 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1740 quant_data_imp <- zap_named_rows(quant_data_imp, zero_sd_rownames)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1741 quant_data <- zap_named_rows(quant_data, zero_sd_rownames)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1742 full_data <- zap_named_rows(full_data, zero_sd_rownames)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1743 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1744
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1745 if (sum(is.na(quant_data)) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1746 cat("\\leavevmode\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1747 # data visualization
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1748 old_par <- par(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1749 mai = par("mai") + c(0.5, 0, 0, 0)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1750 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1751 # Copy quant data to x
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1752 x <- quant_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1753 # x gets to have values of:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1754 # - NA for observed values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1755 # - 1 for missing values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1756 x[is.na(x)] <- 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1757 x[x > 1] <- NA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1758 x[x == 0] <- 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1759 # Log-transform imputed data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1760 # update variable because rows may have been eliminated from quant_data_imp
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1761 quant_data_imp_log10 <- log10(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1762
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1763 write_debug_file(quant_data_imp_log10)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1764
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1765 # Set blue_dots to log of quant data or NA for NA quant data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1766 blue_dots <- log10(quant_data)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1767 # Set red_dots to log of imputed data or NA for observed quant data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1768 red_dots <- quant_data_imp_log10 * x
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1769
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1770 count_red <- sum(!is.na(red_dots))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1771 count_blue <- sum(!is.na(blue_dots))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1772 ylim_save <- ylim <- c(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1773 min(red_dots, blue_dots, na.rm = TRUE),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1774 max(red_dots, blue_dots, na.rm = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1775 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1776 show_stripchart <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1777 50 > (count_red + count_blue) / length(sample_name_matches)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1778 if (show_stripchart) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1779 boxplot_sub <- "Light blue = data before imputation; Red = imputed data"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1780 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1781 boxplot_sub <- ""
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1782 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1783
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1784 # Vertical plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1785 colnames(blue_dots) <- sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1786 boxplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1787 blue_dots
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1788 , las = 1 # "always horizontal"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1789 , col = const_boxplot_fill
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1790 , ylim = ylim
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1791 , main = "Peptide intensities after eliminating unusable peptides"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1792 , sub = boxplot_sub
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1793 , xlab = "Sample"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1794 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1795 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1796
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1797 if (show_stripchart) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1798 # Points
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1799 # ref: https://r-charts.com/distribution/add-points-boxplot/
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1800 # NA values are not plotted
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1801 stripchart(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1802 blue_dots, # Data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1803 method = "jitter", # Random noise
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1804 jitter = const_stripchart_jitter,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1805 pch = 19, # Pch symbols
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1806 cex = const_stripsmall_cex, # Size of symbols reduced
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1807 col = "lightblue", # Color of the symbol
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1808 vertical = TRUE, # Vertical mode
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1809 add = TRUE # Add it over
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1810 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1811 stripchart(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1812 red_dots, # Data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1813 method = "jitter", # Random noise
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1814 jitter = const_stripchart_jitter,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1815 pch = 19, # Pch symbols
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1816 cex = const_stripsmall_cex, # Size of symbols reduced
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1817 col = "red", # Color of the symbol
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1818 vertical = TRUE, # Vertical mode
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1819 add = TRUE # Add it over
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1820 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1821
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1822 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1823 if (TRUE) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1824 # show measured values in blue on left half-violin plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1825 cat("\\leavevmode\n\\quad\n\n\\quad\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1826 vioplot::vioplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1827 x = lapply(blue_dots, function(x) x[!is.na(x)]),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1828 col = "lightblue1",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1829 side = "left",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1830 plotCentre = "line",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1831 ylim = ylim_save,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1832 main = "Distributions of observed and imputed data",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1833 sub = "Light blue = observed data; Pink = imputed data",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1834 xlab = "Sample",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1835 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1836 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1837 red_violins <- lapply(red_dots, function(x) x[!is.na(x)])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1838 cols_to_delete <- c()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1839 for (ix in seq_len(length(red_violins))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1840 if (length(red_violins[[ix]]) < 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1841 cols_to_delete <- c(cols_to_delete, ix)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1842 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1843 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1844 # destroy any unimputable columns
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1845 if (!is.null(cols_to_delete)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1846 red_violins <- red_violins[-cols_to_delete]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1847 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1848 # plot imputed values in red on right half-violin plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1849 vioplot::vioplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1850 x = red_violins,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1851 col = "lightpink1",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1852 side = "right",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1853 plotCentre = "line",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1854 add = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1855 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1856 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1857
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1858 par(old_par)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1859
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1860 # density plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1861 cat("\\leavevmode\n\n\n\n\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1862 if (can_plot_before_after_imp) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1863 ylim <- c(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1864 0,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1865 max(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1866 if (is.list(d_combined)) d_combined$y else d_combined,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1867 if (is.list(d_original)) d_original$y else d_original,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1868 if (is.list(d_imputed)) d_imputed$y else d_imputed,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1869 na.rm = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1870 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1871 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1872 plot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1873 d_combined,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1874 ylim = ylim,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1875 sub =
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1876 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1877 "Blue = data before imputation; Red = imputed data;",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1878 "Black = combined"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1879 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1880 main = "Density of peptide intensity before and after imputation",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1881 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1882 ylab = "Probability density"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1883 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1884 lines(d_original, col = "blue")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1885 lines(d_imputed, col = "red")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1886 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1887 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1888 "There are too few points to plot the density of peptide intensity",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1889 "before and after imputation."
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1890 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1891 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1892 cat("\\leavevmode\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1893 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1894 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1895
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1896 # Perform Quantile Normalization
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1897
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1898 The excellent `normalize.quantiles` function from
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1899 [the `preprocessCore` Bioconductor package](http://bioconductor.org/packages/release/bioc/html/preprocessCore.html)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1900 performs "quantile normalization" as described Bolstad et al. (2003),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1901 DOI [10.1093/bioinformatics/19.2.185](https://doi.org/10.1093%2Fbioinformatics%2F19.2.185)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1902 and its supplementary material [http://bmbolstad.com/misc/normalize/normalize.html](http://bmbolstad.com/misc/normalize/normalize.html),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1903 i.e., it assumes that the goal is to detect
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1904 subtle differences among grossly similar samples (having similar distributions)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1905 by equailzing intra-quantile quantitations.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1906 Unfortunately, one software library upon which it depends
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1907 [suffers from a concurrency defect](https://support.bioconductor.org/p/122925/#9135989)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1908 that requires that a specific, non-concurrent version of the library be
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1909 installed. The installation command equivalent to what was used to install the library to produce the results presented here is:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1910 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1911 conda install bioconductor-preprocesscore openblas=0.3.3
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1912 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1913
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1914
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1915 <!--
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1916 # Apply quantile normalization using preprocessCore::normalize.quantiles
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1917 # ---
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1918 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1919 # except this: https://support.bioconductor.org/p/122925/#9135989
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1920 # says to install it like this:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1921 # ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1922 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1923 # ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1924 # conda installation (necessary because of a bug in recent openblas):
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1925 # conda install bioconductor-preprocesscore openblas=0.3.3
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1926 # ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1927 # ---
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1928 # normalize.quantiles {preprocessCore} -- Quantile Normalization
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1929 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1930 # Description:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1931 # Using a normalization based upon quantiles, this function normalizes a
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1932 # matrix of probe level intensities.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1933 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1934 # THIS FUNCTIONS WILL HANDLE MISSING DATA (ie NA values), based on the
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1935 # assumption that the data is missing at random.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1936 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1937 # Usage:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1938 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1939 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1940 # Arguments:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1941 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1942 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1943 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1944 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1945 # but in certain situations not making a copy of the matrix, but instead normalizing
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1946 # it in place will be more memory friendly.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1947 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1948 # - keep.names: Boolean option to preserve matrix row and column names in output.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1949 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1950 # Details:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1951 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1952 # No special allowances are made for outliers. If you make use of quantile normalization
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1953 # please cite Bolstad et al, Bioinformatics (2003).
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1954 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1955 # This functions will handle missing data (ie NA values), based on
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1956 # the assumption that the data is missing at random.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1957 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1958 # Note that the current implementation optimizes for better memory usage
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1959 # at the cost of some additional run-time.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1960 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1961 # Value: A normalized matrix.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1962 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1963 # Author: Ben Bolstad, bmbolstad.com
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1964 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1965 # References
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1966 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1967 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1968 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1969 #
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1970 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1971 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1972 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1973 # http://bmbolstad.com/misc/normalize/normalize.html
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1974 # ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1975 -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1976 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1977
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1978 if (nrow(quant_data_imp) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1979 quant_data_imp_qn <- preprocessCore::normalize.quantiles(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1980 as.matrix(quant_data_imp), keep.names = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1981 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1982 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1983 quant_data_imp_qn <- as.matrix(quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1984 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1985
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1986 quant_data_imp_qn <- as.data.frame(quant_data_imp_qn)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1987
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1988 write_debug_file(quant_data_imp_qn)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1989
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1990 quant_data_imp_qn_log <- log10(quant_data_imp_qn)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1991
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1992 write_debug_file(quant_data_imp_qn_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1993
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1994 quant_data_imp_qn_ls <- t(scale(t(log10(quant_data_imp_qn))))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1995
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1996 sel <- apply(quant_data_imp_qn_ls, 1, any_nan)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1997 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1998
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1999 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls2[which(sel), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2000 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2001
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2002 quant_data_imp_qn_ls <- as.data.frame(quant_data_imp_qn_ls)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2003
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2004 write_debug_file(quant_data_imp_qn_ls)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2005 write_debug_file(quant_data_imp_qn_ls2)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2006
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2007 # Create data.frame used by ANOVA analysis
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2008 data_table_imp_qn_lt <- cbind(full_data[1:9], quant_data_imp_qn_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2009 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2010
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2011 <!-- ACE insertion begin -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2012 ## Are normalized, imputed, log-transformed sample distributions similar?
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2013
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2014 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2015
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2016 # Save unimputed quant_data_log for plotting below
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2017 unimputed_quant_data_log <- quant_data_log
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2018
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2019 # log10 transform (after preparing for zero values,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2020 # which should never happen...)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2021 quant_data_imp_qn[quant_data_imp_qn == 0] <- .000000001
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2022 quant_data_log <- log10(quant_data_imp_qn)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2023
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2024 how_many_peptides <- nrow(quant_data_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2025
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2026 if ((how_many_peptides) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2027 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2028 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2029 "Intensities for %d peptides:\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2030 how_many_peptides
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2031 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2032 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2033 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2034
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2035
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2036 # data visualization
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2037 old_par <- par(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2038 mai = par("mai") + c(0.5, 0, 0, 0)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2039 , oma = par("oma") + c(0.5, 0, 0, 0)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2040 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2041 # ref: https://r-charts.com/distribution/add-points-boxplot/
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2042 # Vertical plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2043 colnames(quant_data_log) <- sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2044 boxplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2045 quant_data_log
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2046 , las = 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2047 , col = const_boxplot_fill
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2048 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2049 , xlab = "Sample"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2050 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2051 par(old_par)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2052 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2053 cat("There are no peptides to plot\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2054 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2055
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2056 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2057
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2058 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2059
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2060 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2061 if (nrow(quant_data_log) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2062 quant_data_log_stack <- stack(quant_data_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2063 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) +
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2064 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) +
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2065 ggplot2::ylab("Probability density") +
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2066 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2067 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2068 cat("No density plot because there are fewer than two peptides to plot.\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2069 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2070 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2071 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2072 cat("\\leavevmode\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2073 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2074
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2075 # ANOVA Analysis
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2076
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2077 ```{r, echo = FALSE}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2078 # Make new data frame containing only Phosphopeptides
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2079 # to connect preANOVA to ANOVA (connect_df)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2080 connect_df <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2081 data_table_imp_qn_lt$Phosphopeptide
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2082 , data_table_imp_qn_lt[, first_data_column]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2083 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2084 colnames(connect_df) <- c("Phosphopeptide", "Intensity")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2085 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2086
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2087 ```{r echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2088 count_of_treatment_levels <- length(levels(sample_treatment_levels))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2089 if (count_of_treatment_levels < 2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2090 nuke_control_sequences <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2091 function(s) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2092 s <- gsub("[\\]", "xyzzy_plugh", s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2093 s <- gsub("[$]", "\\\\$", s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2094 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2095 return(s)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2096 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2097 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2098 "ERROR!!!! Cannot perform ANOVA analysis",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2099 "(see next page)\\newpage\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2100 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2101 cat(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2102 "ERROR: ANOVA analysis",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2103 "requires two or more factor levels!\n\n\n"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2104 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2105
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2106 cat("\n\n\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2107 cat("Unparsed sample names are:\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2108 "\\begin{quote}\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2109 paste(names(quant_data_imp_qn_log), collapse = "\n\n\n"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2110 "\n\\end{quote}\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2111
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2112 regex_sample_names <- nuke_control_sequences(regex_sample_names)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2113
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2114 cat("\\leavevmode\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2115 cat("Parsing rule for SampleNames is",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2116 "\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2117 "\\text{'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2118 regex_sample_names,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2119 "'}\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2120 sep = ""
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2121 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2122
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2123 cat("\nParsed sample names are:\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2124 "\\begin{quote}\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2125 paste(sample_name_matches, collapse = "\n\n\n"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2126 "\n\\end{quote}\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2127
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2128 regex_sample_grouping <- nuke_control_sequences(regex_sample_grouping)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2129
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2130 cat("\\leavevmode\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2131 cat("Parsing rule for SampleGrouping is",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2132 "\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2133 "\\text{'",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2134 regex_sample_grouping,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2135 "'}\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2136 sep = ""
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2137 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2138
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2139 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2140 cat("Sample group assignments are:\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2141 "\\begin{quote}\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2142 paste(regmatches(sample_name_matches, rx_match), collapse = "\n\n\n"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2143 "\n\\end{quote}\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2144
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2145 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2146
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2147 p_value_data_anova_ps <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2148 apply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2149 quant_data_imp_qn_log,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2150 1,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2151 anova_func,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2152 grouping_factor = sample_treatment_levels,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2153 one_way_f = one_way_all_categories
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2154 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2155
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2156 p_value_data_anova_ps_fdr <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2157 p.adjust(p_value_data_anova_ps, method = "fdr")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2158 p_value_data <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2159 phosphopeptide = full_data[, 1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2160 ,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2161 raw_anova_p = p_value_data_anova_ps
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2162 ,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2163 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2164 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2165
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2166 # output ANOVA file to constructed filename,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2167 # e.g. "Outputfile_pST_ANOVA_STEP5.txt"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2168 # becomes "Outpufile_pST_ANOVA_STEP5_FDR0.05.txt"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2169
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2170 # Re-output datasets to include p-values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2171 metadata_plus_p <- cbind(full_data[1:9], p_value_data[, 2:3])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2172 write.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2173 cbind(metadata_plus_p, quant_data_imp),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2174 file = imputed_data_filename,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2175 sep = "\t",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2176 col.names = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2177 row.names = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2178 quote = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2179 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2180
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2181 write.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2182 cbind(metadata_plus_p, quant_data_imp_qn_log),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2183 file = imp_qn_lt_data_filenm,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2184 sep = "\t",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2185 col.names = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2186 row.names = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2187 quote = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2188 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2189
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2190
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2191 p_value_data <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2192 p_value_data[order(p_value_data$fdr_adjusted_anova_p), ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2193
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2194 first_page_suppress <- 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2195 number_of_peptides_found <- 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2196 cutoff <- val_fdr[1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2197 for (cutoff in val_fdr) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2198 if (number_of_peptides_found > 49) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2199 cat("\\leavevmode\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2200 break
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2201 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2202
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2203 #loop through FDR cutoffs
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2204
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2205 filtered_p <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2206 p_value_data[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2207 which(p_value_data$fdr_adjusted_anova_p < cutoff),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2208 , drop = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2209 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2210 filtered_data_filtered <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2211 quant_data_imp_qn_log[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2212 rownames(filtered_p),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2213 , drop = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2214 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2215 filtered_data_filtered <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2216 filtered_data_filtered[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2217 order(filtered_p$fdr_adjusted_anova_p),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2218 , drop = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2219 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2220
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2221 # <!-- ACE insertion start -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2222
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2223 if (nrow(filtered_p) && nrow(filtered_data_filtered) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2224 if (first_page_suppress == 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2225 first_page_suppress <- 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2226 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2227 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2228 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2229 if (nrow(filtered_data_filtered) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2230 subsection_header(sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2231 "Intensity distributions for %d phosphopeptides whose adjusted p-value < %0.2f\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2232 nrow(filtered_data_filtered),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2233 cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2234 ))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2235 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2236 subsection_header(sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2237 "Intensity distribution for one phosphopeptide (%s) whose adjusted p-value < %0.2f\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2238 rownames(filtered_data_filtered)[1],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2239 cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2240 ))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2241 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2242 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2243 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2244
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2245 old_oma <- par("oma")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2246 old_par <- par(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2247 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2248 oma = old_oma * c(1, 1, 0.3, 1),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2249 cex.main = 0.9,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2250 cex.axis = 0.7,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2251 fin = c(9, 7.25)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2252 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2253 # ref: https://r-charts.com/distribution/add-points-boxplot/
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2254 # Vertical plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2255 colnames(filtered_data_filtered) <- sample_name_matches
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2256 tryCatch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2257 boxplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2258 filtered_data_filtered,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2259 main = "Imputed, normalized intensities", # no line plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2260 las = 1,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2261 col = const_boxplot_fill,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2262 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2263 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2264 error = function(e) print(e)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2265 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2266 par(old_par)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2267 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2268 cat(sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2269 "%s < %0.2f\n\n\n\n\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2270 "No peptides were found to have cutoff adjusted p-value",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2271 cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2272 ))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2273 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2274
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2275 if (nrow(filtered_data_filtered) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2276 # Add Phosphopeptide column to anova_filtered table
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2277 # The assumption here is that the first intensity is unique;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2278 # this is a hokey assumption but almost definitely will
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2279 # be true in the real world unless there is a computation
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2280 # error upstream.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2281 anova_filtered_merge <- base::merge(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2282 x = connect_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2283 y = filtered_data_filtered,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2284 by.x = "Intensity",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2285 by.y = 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2286 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2287 anova_filtered_merge_order <- rownames(filtered_p)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2288
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2289 anova_filtered <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2290 ppep = anova_filtered_merge$Phosphopeptide,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2291 intense = anova_filtered_merge$Intensity,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2292 data = anova_filtered_merge[, 2:number_of_samples + 1]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2293 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2294 colnames(anova_filtered) <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2295 c("Phosphopeptide", colnames(filtered_data_filtered))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2296
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2297 # Merge qualitative columns into the ANOVA data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2298 output_table <- data.frame(anova_filtered$Phosphopeptide)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2299 output_table <- base::merge(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2300 x = output_table,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2301 y = data_table_imp_qn_lt,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2302 by.x = "anova_filtered.Phosphopeptide",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2303 by.y = "Phosphopeptide"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2304 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2305
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2306 # Produce heatmap to visualize significance and the effect of imputation
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2307
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2308 anova_filtered_merge_format <- sapply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2309 X = filtered_p$fdr_adjusted_anova_p
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2310 ,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2311 FUN = function(x) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2312 if (x > 0.0001)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2313 paste0("(%0.", 1 + ceiling(-log10(x)), "f) %s")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2314 else
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2315 paste0("(%0.4e) %s")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2316 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2317 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2318
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2319 cat_hm_heading <- function(m, cutoff) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2320 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2321 if (nrow(m) > intensity_hm_rows) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2322 subsection_header(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2323 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2324 sprintf("Heatmap for the %d most-significant peptides",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2325 intensity_hm_rows),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2326 sprintf("whose adjusted p-value < %0.2f\n", cutoff)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2327 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2328 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2329 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2330 if (nrow(m) == 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2331 return(FALSE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2332 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2333 subsection_header(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2334 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2335 sprintf("Heatmap for %d usable peptides whose", nrow(m)),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2336 sprintf("adjusted p-value < %0.2f\n", cutoff)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2337 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2338 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2339 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2340 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2341 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2342 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2343 return(TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2344 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2345
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2346 # construct matrix with appropriate rownames
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2347 m <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2348 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2349 if (nrow(m) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2350 rownames_m <- rownames(m)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2351 rownames(m) <- sapply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2352 X = seq_len(nrow(m))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2353 ,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2354 FUN = function(i) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2355 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2356 anova_filtered_merge_format[i],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2357 filtered_p$fdr_adjusted_anova_p[i],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2358 rownames_m[i]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2359 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2360 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2361 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2362 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2363 # draw the heading and heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2364 if (nrow(m) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2365 number_of_peptides_found <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2366 draw_intensity_heatmap(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2367 m = m,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2368 cutoff = cutoff,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2369 hm_heading_function = cat_hm_heading,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2370 hm_main_title = "Unimputed, unnormalized log(intensities)",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2371 suppress_row_dendrogram = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2372 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2373 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2374 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2375 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2376 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2377 cat("\\leavevmode\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2378 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2379
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2380 ```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2381
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2382 if (count_of_treatment_levels > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2383 # Prepare two-way contrasts with adjusted p-values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2384 # Strategy:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2385 # - use imputed, log-transformed data:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2386 # - remember this when computing log2(fold-change)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2387 # - each contrast is between a combination of trt levels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2388 # - for each contrast, compute samples that are members
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2389 # - compute one-way test:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2390 # - use `oneway.test` (Welch test) if numbers of samples
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2391 # are not equivalent between trt levels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2392 # - otherwise, aov is fine but offers no advantage
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2393 # - adjust p-value, assuming that
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2394 # (# of pppeps)*(# of contrasts) tests were performed
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2395
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2396 # Each contrast is between a combination of trt levels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2397 m2 <- combn(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2398 x = seq_len(length(levels(sample_treatment_levels))),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2399 m = 2,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2400 simplify = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2401 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2402 contrast_count <- ncol(m2)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2403
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2404 # For each contrast, compute samples that are members
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2405 # - local function to construct a data.frame for each contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2406 # - the contrast in the first "column"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2407 f_m2 <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2408 function(cntrst, lvl1, lvl2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2409 return(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2410 data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2411 contrast = cntrst,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2412 level = sample_treatment_levels[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2413 sample_treatment_levels %in%
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2414 levels(sample_treatment_levels)[c(lvl1, lvl2)]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2415 ],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2416 label = sample_name_matches[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2417 sample_treatment_levels %in%
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2418 levels(sample_treatment_levels)[c(lvl1, lvl2)]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2419 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2420 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2421 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2422 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2423 # - compute a df for each contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2424 sample_level_dfs <- lapply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2425 X = 1:contrast_count,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2426 FUN = function(i) f_m2(i, m2[1, i], m2[2, i])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2427 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2428 # - compute a single df for all contrasts
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2429 combined_contrast_df <- Reduce(f = rbind, x = sample_level_dfs)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2430
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2431 # - dispose objects to free resources
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2432 rm(sample_level_dfs)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2433
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2434 # - write the df to a DB for later join-per-contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2435 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2436
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2437 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2438 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2439 name = "contrast",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2440 value = combined_contrast_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2441 overwrite = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2442 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2443
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2444 # Create UK for insert
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2445 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2446 CREATE UNIQUE INDEX IF NOT EXISTS contrast__uk__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2447 ON contrast(contrast, label);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2448 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2449 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2450 # Create indexes for join
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2451 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2452 -- index for join in contrast_ppep_smpl_qnlt on a.label < b.label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2453 CREATE INDEX IF NOT EXISTS contrast__label__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2454 ON contrast(label);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2455 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2456 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2457 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2458 -- index for joining two contrast_lvl_ppep_avg_quant on contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2459 CREATE INDEX IF NOT EXISTS contrast__contrast__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2460 ON contrast(contrast);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2461 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2462 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2463 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2464 -- index for joining two contrast_lvl_ppep_avg_quant on phophospep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2465 CREATE INDEX IF NOT EXISTS contrast__level__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2466 ON contrast(level);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2467 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2468 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2469 # - dispose objects to free resources
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2470 rm(combined_contrast_df)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2471
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2472 # Use imputed, log-transformed data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2473 # - remember that this was donoe when computing log2(fold-change)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2474 # - melt data matrix for use in later join-per-contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2475 casted <- cbind(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2476 data.frame(vrbl = rownames(quant_data_imp_qn_log)),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2477 quant_data_imp_qn_log
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2478 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2479 quant_data_imp_qn_log_melted <- reshape2::melt(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2480 casted,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2481 id.vars = "vrbl"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2482 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2483 colnames(quant_data_imp_qn_log_melted) <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2484 c("phosphopep", "sample", "quant")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2485 # - dispose objects to free resources
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2486 rm(casted)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2487
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2488 # - write the df to a DB for use in later join-per-contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2489 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2490 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2491 name = "ppep_smpl_qnlt",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2492 value = quant_data_imp_qn_log_melted,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2493 overwrite = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2494 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2495 # Create UK for insert
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2496 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2497 CREATE UNIQUE INDEX IF NOT EXISTS ppep_smpl_qnlt__uk__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2498 ON ppep_smpl_qnlt(phosphopep, sample);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2499 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2500 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2501 # Create index for join
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2502 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2503 -- index for join in contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2504 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__sample__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2505 ON ppep_smpl_qnlt(sample);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2506 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2507 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2508 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2509 -- index for joining two contrast_lvl_ppep_avg_quant on phopho.pep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2510 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__phosphopep__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2511 ON ppep_smpl_qnlt(phosphopep);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2512 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2513 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2514 # - dispose objects to free resources
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2515 rm(quant_data_imp_qn_log_melted)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2516
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2517 # - drop views if exist
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2518 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2519 -- drop view dependent on contrast_lvl_ppep_avg_quant
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2520 DROP VIEW IF EXISTS v_contrast_log2_fc;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2521 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2522 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2523 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2524 -- drop table dependent on contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2525 DROP TABLE IF EXISTS contrast_lvl_ppep_avg_quant;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2526 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2527 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2528 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2529 DROP TABLE IF EXISTS contrast_lvl_lvl_metadata;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2530 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2531 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2532 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2533 DROP VIEW IF EXISTS v_contrast_lvl_metadata;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2534 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2535 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2536 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2537 -- drop view dependent on contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2538 DROP VIEW IF EXISTS v_contrast_lvl_ppep_avg_quant;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2539 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2540 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2541 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2542 DROP VIEW IF EXISTS v_contrast_lvl_lvl;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2543 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2544 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2545 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2546 -- drop view upon which other views depend
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2547 DROP VIEW IF EXISTS contrast_ppep_smpl_qnlt;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2548 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2549 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2550 # - create view
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2551 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2552 -- view contrast_ppep_smpl_qnlt is used for each phopshopep to
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2553 -- compute p-value for test of trt effect for two trt levels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2554 CREATE VIEW contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2555 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2556 SELECT contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2557 level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2558 phosphopep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2559 sample,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2560 quant
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2561 FROM contrast AS c,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2562 ppep_smpl_qnlt AS q
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2563 WHERE q.sample = c.label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2564 ORDER BY contrast, level, phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2565 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2566 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2567 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2568 # - create simplification views
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2569 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2570 CREATE VIEW v_contrast_lvl_metadata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2571 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2572 SELECT contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2573 level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2574 group_concat(label, ';') AS samples
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2575 FROM contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2576 GROUP BY contrast, level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2577 /* view v_contrast_lvl_metadata is used
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2578 to simplify creation of table contrast_lvl_lvl_metadata */
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2579 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2580 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2581 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2582 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2583 CREATE VIEW v_contrast_lvl_ppep_avg_quant
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2584 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2585 SELECT contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2586 level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2587 phosphopep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2588 avg(quant) AS avg_quant
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2589 FROM contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2590 GROUP BY contrast, level, phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2591 /* view v_contrast_lvl_ppep_avg_quant is used
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2592 to simplify view v_contrast_log2_fc */
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2593 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2594 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2595 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2596
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2597 # - create contrast-metadata table
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2598 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2599 CREATE TABLE contrast_lvl_lvl_metadata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2600 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2601 SELECT DISTINCT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2602 a.contrast AS ab_contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2603 a.level AS a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2604 b.level AS b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2605 a.samples AS a_samples,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2606 b.samples AS b_samples,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2607 'log2(level_'\|\|a.level\|\|'/level_'\|\|b.level\|\|')'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2608 AS fc_description
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2609 FROM v_contrast_lvl_metadata AS a,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2610 v_contrast_lvl_metadata AS b
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2611 WHERE a.contrast = b.contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2612 AND a.level > b.level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2613 /* view v_contrast_lvl_lvl is used
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2614 to simplify view v_contrast_log2_fc */
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2615 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2616 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2617 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2618 # - create pseudo-materialized view table
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2619 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2620 CREATE VIEW v_contrast_lvl_lvl
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2621 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2622 SELECT DISTINCT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2623 a.contrast AS ab_contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2624 a.level AS a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2625 b.level AS b_level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2626 FROM contrast AS a,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2627 contrast AS b
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2628 WHERE a.contrast = b.contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2629 AND a.level > b.level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2630 /* view v_contrast_lvl_lvl is used
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2631 to simplify view v_contrast_log2_fc */
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2632 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2633 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2634 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2635
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2636 # - create view to compute log2(fold-change)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2637 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2638 CREATE VIEW v_contrast_log2_fc
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2639 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2640 SELECT ab.ab_contrast AS contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2641 m.a_level AS a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2642 c.avg_quant AS a_quant,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2643 m.a_samples AS a_samples,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2644 ab.b_level AS b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2645 d.avg_quant AS b_quant,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2646 m.b_samples AS b_samples,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2647 m.fc_description AS fc_description,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2648 3.32193 * ( d.avg_quant - c.avg_quant) AS log2_fc,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2649 d.phosphopep AS phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2650 FROM contrast_lvl_lvl_metadata AS m,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2651 v_contrast_lvl_ppep_avg_quant AS d,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2652 v_contrast_lvl_lvl AS ab
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2653 INNER JOIN v_contrast_lvl_ppep_avg_quant AS c
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2654 ON c.contrast = ab.ab_contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2655 AND c.level = ab.a_level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2656 WHERE d.contrast = ab.ab_contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2657 AND m.ab_contrast = ab.ab_contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2658 AND d.level = ab.b_level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2659 AND d.phosphopep = c.phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2660 /* view to compute log2(fold-change) */
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2661 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2662 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2663 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2664
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2665 # For each contrast, compute samples that are members
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2666 # compute one-way test:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2667 # - use `oneway.test` (Welch test) if numbers of samples
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2668 # are not equivalent between trt levels
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2669 # - otherwise, aov is fine but offers no advantage
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2670 for (contrast in contrast_count:2) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2671 invisible(contrast)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2672 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2673 for (contrast in 1:contrast_count) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2674 contrast_df <- sqldf::sqldf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2675 x = paste0("
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2676 SELECT level, phosphopep, sample, quant
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2677 FROM contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2678 WHERE contrast = ", contrast, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2679 ORDER BY phosphopep, level, sample
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2680 "),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2681 connection = db
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2682 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2683 contrast_cast <- reshape2::dcast(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2684 data = contrast_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2685 formula = phosphopep ~ sample,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2686 value.var = "quant"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2687 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2688 contrast_cast_ncol <- ncol(contrast_cast)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2689 contrast_cast_data <- contrast_cast[, 2:contrast_cast_ncol]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2690 contrast_cast_samples <- colnames(contrast_cast_data)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2691
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2692 # - order grouping_factor by order of sample columns of contrast_cast_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2693 grouping_factor <- sqldf::sqldf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2694 x = paste0("
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2695 SELECT sample, level
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2696 FROM contrast_ppep_smpl_qnlt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2697 WHERE contrast = ", contrast, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2698 ORDER BY phosphopep, level, sample
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2699 LIMIT ", contrast_cast_ncol - 1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2700 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2701 connection = db
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2702 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2703 rownames(grouping_factor) <- grouping_factor$sample
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2704 grouping_factor <- grouping_factor[, "level", drop = FALSE]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2705
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2706 # - run the two-level (one-way) test
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2707 p_value_data_contrast_ps <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2708 apply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2709 X = contrast_cast_data,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2710 MARGIN = 1, # apply to rows
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2711 FUN = anova_func,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2712 grouping_factor =
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2713 as.factor(as.numeric(grouping_factor$level)), # anova_func arg2
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2714 one_way_f = one_way_two_categories, # anova_func arg3
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2715 simplify = TRUE # TRUE is the default for simplify
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2716 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2717 contrast_data_adj_p_values <- p.adjust(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2718 p = p_value_data_contrast_ps,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2719 method = "fdr",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2720 n = length(p_value_data_contrast_ps) # this is the default, length(p)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2721 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2722 # - compute the fold-change
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2723 contrast_p_df <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2724 data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2725 contrast = contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2726 phosphopep = contrast_cast$phosphopep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2727 p_value_raw = p_value_data_contrast_ps,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2728 p_value_adj = contrast_data_adj_p_values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2729 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2730 db_write_table_overwrite <- (contrast < 2)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2731 db_write_table_append <- !db_write_table_overwrite
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2732 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2733 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2734 name = "contrast_ppep_p_val",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2735 value = contrast_p_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2736 append = db_write_table_append
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2737 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2738 # Create UK for insert
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2739 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2740 CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2741 ON contrast_ppep_p_val(phosphopep, contrast);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2742 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2743 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2744 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2745 # Perhaps this could be done more elegantly using unique keys
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2746 # or creating the tables before saving data to them, but this
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2747 # is fast and, if the database exists on disk rather than in
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2748 # memory, it doesn't stress memory.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2749 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2750 CREATE TEMP table contrast_log2_fc
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2751 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2752 SELECT *
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2753 FROM v_contrast_log2_fc
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2754 ORDER BY contrast, phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2755 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2756 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2757 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2758 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2759 CREATE TEMP table ppep_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2760 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2761 SELECT p_value_raw,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2762 p_value_adj,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2763 contrast AS p_val_contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2764 phosphopep AS p_val_ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2765 FROM contrast_ppep_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2766 ORDER BY contrast, phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2767 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2768 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2769 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2770 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2771 DROP TABLE IF EXISTS contrast_log2_fc_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2772 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2773 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2774 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2775 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2776 CREATE TABLE contrast_log2_fc_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2777 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2778 SELECT a.*,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2779 b.p_value_raw,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2780 b.p_value_adj,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2781 b.p_val_contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2782 b.p_val_ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2783 FROM contrast_log2_fc a, ppep_p_val b
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2784 WHERE a.rowid = b.rowid
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2785 AND a.phosphopep = b.p_val_ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2786 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2787 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2788 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2789 # Create UK
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2790 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2791 CREATE UNIQUE INDEX IF NOT EXISTS contrast_log2_fc_p_val__uk__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2792 ON contrast_log2_fc_p_val(phosphopep, contrast);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2793 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2794 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2795 # Create indices for future queries
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2796 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2797 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__contrast__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2798 ON contrast_log2_fc_p_val(contrast);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2799 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2800 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2801 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2802 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__phosphopep__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2803 ON contrast_log2_fc_p_val(phosphopep);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2804 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2805 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2806 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2807 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_raw__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2808 ON contrast_log2_fc_p_val(p_value_raw);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2809 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2810 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2811 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2812 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_adj__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2813 ON contrast_log2_fc_p_val(p_value_adj);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2814 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2815 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2816 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2817 DROP VIEW IF EXISTS v_contrast_log2_fc_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2818 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2819 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2820 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2821 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2822 CREATE VIEW v_contrast_log2_fc_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2823 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2824 SELECT contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2825 a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2826 a_samples,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2827 b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2828 b_samples,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2829 a_quant,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2830 b_quant,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2831 fc_description,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2832 log2_fc,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2833 p_value_raw,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2834 p_value_adj,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2835 phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2836 FROM contrast_log2_fc_p_val
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2837 ORDER BY contrast, phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2838 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2839 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2840 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2841 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2842 DROP TABLE IF EXISTS kseaapp_metadata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2843 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2844 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2845 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2846 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2847 CREATE TABLE kseaapp_metadata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2848 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2849 WITH extended(deppep, ppep, gene_name, uniprot_id, phosphoresidue) AS (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2850 SELECT DISTINCT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2851 deppep.seq,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2852 ppep.seq,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2853 GeneName\|\|';',
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2854 UniProtID\|\|';',
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2855 PhosphoResidue\|\|';'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2856 FROM
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2857 ppep, deppep, mrgfltr_metadata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2858 WHERE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2859 mrgfltr_metadata.ppep_id = ppep.id
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2860 AND
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2861 ppep.deppep_id = deppep.id
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2862 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2863 SELECT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2864 ppep AS `ppep`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2865 SUBSTR(uniprot_id, 1, INSTR(uniprot_id,';') - 1 ) AS `Protein`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2866 SUBSTR(gene_name, 1, INSTR(gene_name,';') - 1 ) AS `Gene`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2867 deppep AS `Peptide`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2868 REPLACE(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2869 REPLACE(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2870 SUBSTR(phosphoresidue, 1, INSTR(phosphoresidue,';') - 1 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2871 'p',
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2872 ''
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2873 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2874 ', ',
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2875 ';'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2876 ) AS `Residue.Both`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2877 FROM extended
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2878 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2879 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2880 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2881 # Create indexes for join
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2882 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2883 CREATE INDEX IF NOT EXISTS kseaapp_metadata__ppep__idx
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2884 ON kseaapp_metadata(ppep);
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2885 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2886 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2887 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2888 DROP VIEW IF EXISTS v_kseaapp_contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2889 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2890 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2891 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2892 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2893 CREATE VIEW v_kseaapp_contrast
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2894 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2895 SELECT a.*, b.Protein, b.Gene, b.Peptide, b.`Residue.Both`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2896 FROM v_contrast_log2_fc_p_val a, kseaapp_metadata b
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2897 WHERE b.ppep = a.phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2898 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2899 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2900 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2901 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2902 DROP VIEW IF EXISTS v_kseaapp_input
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2903 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2904 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2905 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2906 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2907 CREATE VIEW v_kseaapp_input
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2908 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2909 SELECT v.contrast,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2910 v.phosphopep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2911 m.`Protein`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2912 m.`Gene`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2913 m.`Peptide`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2914 m.`Residue.Both`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2915 v.p_value_raw AS `p`,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2916 v.log2_fc AS `FC`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2917 FROM kseaapp_metadata AS m,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2918 v_contrast_log2_fc_p_val AS v
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2919 WHERE m.ppep = v.phosphopep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2920 AND NOT m.`Gene` = 'No_Gene_Name'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2921 AND NOT v.log2_fc = 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2922 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2923 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2924 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2925 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2926 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2927
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2928 ```{r echo = FALSE, results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2929 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2930 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2931
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2932 # KSEA Analysis
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2933
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2934 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:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2935
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2936 - The package is available on CRAN, at https:/cran.r-project.org/package=KSEAapp
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2937 - 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).
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2938 - An online alternative (supporting only analysis of human data) is available at [https:/casecpb.shinyapps.io/ksea/](https:/casecpb.shinyapps.io/ksea/).
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2939
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2940 For each kinase, $i$, and each two-way contrast of treatments, $j$, an enrichment $z$-score is computed as:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2941
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2942 $$
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2943 \text{kinase enrichment score}_{j,i} = \frac{(\overline{s}_{j,i} - \overline{p}_j)\sqrt{m_{j,i}}}{\delta_j}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2944 $$
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2945
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2946 and fold-enrichment is computed as:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2947
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2948 $$
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2949 \text{Enrichment}_{j,i} = \frac{\overline{s}_{j,i}}{\overline{p}_j}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2950 $$
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2951
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2952 where:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2953
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2954 - $\overline{s}_{j,i}$ is the mean $\log_2 (\|\text{fold-change\|})$ in intensities (for contrast $j$) of known substrates of the kinase $i$,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2955 - $\overline{p}_j$ is the mean $\log_2 (\|\text{fold-change}\|)$ of all phosphosites identified in contrast $j$, and
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2956 - $m_{j,i}$ is the total number of phosphosite substrates of kinase $i$ identified in contrast $j$,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2957 - $\delta_j$ is the standard deviation of the $\log_2 (\|\text{fold-change}\|)$ for contrast $j$ across all phosphosites in the dataset.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2958 - 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.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2959
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2960 $\text{FDR}_{j,i}$ is computed from the $p$-value for the z-score using the R `stats::p.adjust` function, applying the False Discovery Rate 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)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2961
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2962 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).
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2963
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2964 Asterisks in heatmaps reflect enrichments that are significant at `r ksea_cutoff_statistic` < `r ksea_cutoff_threshold`.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2965
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2966 - 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.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2967 - 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)).
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2968 - Kinase-strate deata 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).
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2969
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2970 ```{r ksea, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2971
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2972 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2973
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2974 # -- eliminate the table that's about to be defined
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2975 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2976 DROP TABLE IF EXISTS site_metadata;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2977 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2978
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2979 # -- define the site_metadata table
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2980 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2981 CREATE TABLE site_metadata(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2982 id INTEGER PRIMARY KEY
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2983 , site_type_id INTEGER REFERENCES site_type(id)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2984 , full TEXT UNIQUE ON CONFLICT IGNORE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2985 , abbrev TEXT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2986 , pattern TEXT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2987 , motif TEXT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2988 );
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2989 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2990
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2991 # -- populate the table with initial values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2992 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2993 INSERT INTO site_metadata(full, abbrev, site_type_id)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2994 SELECT DISTINCT kinase_map, kinase_map, site_type_id
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2995 FROM ppep_gene_site
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2996 ORDER BY kinase_map;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2997 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2998
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2999 # -- drop bogus KSData view if exists
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3000 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3001 DROP VIEW IF EXISTS ks_data_v;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3002 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3003
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3004 # -- create view to serve as an impostor for KSEAapp::KSData
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3005 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3006 CREATE VIEW IF NOT EXISTS ks_data_v
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3007 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3008 SELECT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3009 'NA' AS KINASE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3010 'NA' AS KIN_ACC_ID,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3011 kinase_map AS GENE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3012 'NA' AS KIN_ORGANISM,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3013 'NA' AS SUBSTRATE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3014 0 AS SUB_GENE_ID,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3015 'NA' AS SUB_ACC_ID,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3016 gene_names AS SUB_GENE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3017 'NA' AS SUB_ORGANISM,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3018 phospho_peptide AS SUB_MOD_RSD,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3019 0 AS SITE_GROUP_ID,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3020 'NA' AS 'SITE_7AA',
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3021 2 AS networkin_score,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3022 type_name AS Source
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3023 FROM ppep_gene_site_view;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3024 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3025
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3026 contrast_metadata_df <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3027 sqldf::sqldf("select * from contrast_lvl_lvl_metadata", connection = db)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3028 rslt <- new_env()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3029 rslt$score_list <- list()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3030 rslt$name_list <- list()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3031 rslt$longname_list <- list()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3032
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3033 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3034 DROP TABLE IF EXISTS contrast_ksea_scores;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3035 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3036 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3037
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3038 next_index <- 0
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3039 err_na_subscr_df_const <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3040 "missing values are not allowed in subscripted assignments of data frames"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3041
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3042 for (i_cntrst in seq_len(nrow(contrast_metadata_df))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3043 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3044 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3045 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3046 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3047 contrast_longlabel <- (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3048 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3049 "Trt %s {%s} -> Trt %s {%s}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3050 contrast_metadata_df[i_cntrst, "b_level"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3051 gsub(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3052 pattern = ";",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3053 replacement = ", ",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3054 x = contrast_metadata_df[i_cntrst, "b_samples"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3055 fixed = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3056 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3057 contrast_metadata_df[i_cntrst, "a_level"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3058 gsub(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3059 pattern = ";",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3060 replacement = ", ",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3061 x = contrast_metadata_df[i_cntrst, "a_samples"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3062 fixed = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3063 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3064 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3065 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3066 kseaapp_input <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3067 sqldf::sqldf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3068 x = sprintf("
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3069 SELECT `Protein`, `Gene`, `Peptide`, phosphopep AS `Residue.Both`, `p`, `FC`
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3070 FROM v_kseaapp_input
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3071 WHERE contrast = %d
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3072 ",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3073 i_cntrst
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3074 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3075 connection = db
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3076 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3077
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3078 pseudo_ksdata <- dbReadTable(db, "ks_data_v")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3079
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3080 # This hack is because SQL table has the log2-transformed values
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3081 kseaapp_input[, "FC"] <- 2 ** kseaapp_input[, "FC", drop = TRUE]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3082 main_title <- (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3083 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3084 "Change from treatment %s to treatment %s",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3085 contrast_metadata_df[i_cntrst, "b_level"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3086 contrast_metadata_df[i_cntrst, "a_level"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3087 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3088 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3089 sub_title <- contrast_longlabel
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3090 tryCatch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3091 expr = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3092 ksea_scores_rslt <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3093 ksea_scores(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3094 ksdata = pseudo_ksdata, # KSEAapp::KSData,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3095 px = kseaapp_input,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3096 networkin = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3097 networkin_cutoff = 2
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3098 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3099
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3100 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3101 next_index <- 1 + next_index
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3102 rslt$score_list[[next_index]] <- ksea_scores_rslt
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3103 rslt$name_list[[next_index]] <- contrast_label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3104 rslt$longname_list[[next_index]] <- contrast_longlabel
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3105 low_fdr_print(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3106 rslt = rslt,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3107 i_cntrst = i_cntrst,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3108 i = next_index,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3109 a_level = cntrst_a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3110 b_level = cntrst_b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3111 fold_change = cntrst_fold_change,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3112 caption = contrast_longlabel
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3113 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3114 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3115 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3116 error = function(e) str(e)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3117 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3118 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3119
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3120 plotted_kinases <- NULL
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3121 if (length(rslt$score_list) > 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3122 for (i in seq_len(length(ksea_heatmap_titles))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3123 hdr <- ksea_heatmap_titles[[i]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3124 which_kinases <- i
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3125
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3126 cat("\\clearpage\n\\begin{center}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3127 if (i == const_ksea_astrsk_kinases) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3128 subsection_header(hdr)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3129 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3130 subsection_header(hdr)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3131 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3132 cat("\\end{center}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3133
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3134 plotted_kinases <- ksea_heatmap(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3135 # the data frame outputs from the KSEA.Scores() function, in list format
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3136 score_list = rslt$score_list,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3137 # a character vector of all the sample names for heatmap annotation:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3138 # - the names must be in the same order as the data in score_list
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3139 # - please avoid long names, as they may get cropped in the final image
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3140 sample_labels = rslt$name_list,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3141 # character string of either "p.value" or "FDR" indicating the data column
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3142 # to use for marking statistically significant scores
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3143 stats = c("p.value", "FDR")[2],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3144 # a numeric value between 0 and infinity indicating the min. number of
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3145 # substrates a kinase must have to be included in the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3146 m_cutoff = 1,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3147 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3148 # for indicating significant kinases in the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3149 p_cutoff = 0.05,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3150 # a binary input of TRUE or FALSE, indicating whether or not to perform
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3151 # hierarchical clustering of the sample columns
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3152 sample_cluster = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3153 # a binary input of TRUE or FALSE, indicating whether or not to export
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3154 # the heatmap as a .png image into the working directory
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3155 export = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3156 # additional arguments to gplots::heatmap.2, such as:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3157 # - main: main title of plot
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3158 # - xlab: x-axis label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3159 # - ylab: y-axis label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3160 xlab = "Contrast",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3161 ylab = "Kinase",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3162 # print which kinases:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3163 # - 1 : all kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3164 # - 2 : significant kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3165 # - 3 : non-significant kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3166 which_kinases = which_kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3167 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3168 cat("\\begin{center}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3169 cat("Color intensities reflects $z$-score magnitudes; hue reflects $z$-score sign. Asterisks reflect significance.\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3170 cat("\\end{center}\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3171 } # end for (i in ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3172 } # end if (length ...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3173
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3174 for (i_cntrst in seq_len(length(rslt$score_list))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3175 next_index <- i_cntrst
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3176 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3177 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3178 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3179 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3180 contrast_longlabel <- (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3181 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3182 "Trt %s {%s} -> Trt %s {%s}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3183 contrast_metadata_df[i_cntrst, "b_level"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3184 gsub(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3185 pattern = ";",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3186 replacement = ", ",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3187 x = contrast_metadata_df[i_cntrst, "b_samples"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3188 fixed = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3189 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3190 contrast_metadata_df[i_cntrst, "a_level"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3191 gsub(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3192 pattern = ";",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3193 replacement = ", ",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3194 x = contrast_metadata_df[i_cntrst, "a_samples"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3195 fixed = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3196 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3197 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3198 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3199 main_title <- (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3200 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3201 "Change from treatment %s to treatment %s",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3202 contrast_metadata_df[i_cntrst, "b_level"],
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3203 contrast_metadata_df[i_cntrst, "a_level"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3204 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3205 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3206 sub_title <- contrast_longlabel
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3207 tryCatch(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3208 expr = {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3209 ksea_scores_rslt <- rslt$score_list[[next_index]]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3210
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3211 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3212 low_fdr_barplot(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3213 rslt = rslt,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3214 i_cntrst = i_cntrst,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3215 i = next_index,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3216 a_level = cntrst_a_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3217 b_level = cntrst_b_level,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3218 fold_change = cntrst_fold_change,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3219 caption = contrast_longlabel
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3220 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3221 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3222 },
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3223 error = function(e) str(e)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3224 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3225 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3226 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3227
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3228 ```{r enriched, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3229
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3230 # Use enriched kinases to find enriched kinase-substrate pairs
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3231 enriched_kinases <- data.frame(kinase = ls(ksea_asterisk_hash))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3232 all_enriched_substrates <- sqldf("
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3233 SELECT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3234 gene AS kinase,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3235 ppep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3236 '('\|\|group_concat(gene\|\|'-'\|\|sub_gene)\|\|') '\|\|ppep AS label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3237 FROM (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3238 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3239 FROM pseudo_ksdata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3240 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3241 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3242 GROUP BY ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3243 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3244
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3245 # helper used to label per-kinase substrate enrichment figure
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3246 cat_enriched_heading <- function(m, cut_args) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3247 cutoff <- cut_args$cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3248 kinase <- cut_args$kinase
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3249 statistic <- cut_args$statistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3250 threshold <- cut_args$threshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3251 cat("\\newpage\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3252 if (nrow(m) > intensity_hm_rows) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3253 subsection_header(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3254 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3255 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3256 "Lowest p-valued %d (of %d) enriched %s-substrates,",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3257 intensity_hm_rows,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3258 nrow(m),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3259 kinase
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3260 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3261 sprintf(" KSEA %s < %0.2f\n", statistic, threshold)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3262 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3263 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3264 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3265 if (nrow(m) == 1) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3266 return(FALSE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3267 } else {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3268 subsection_header(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3269 paste(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3270 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3271 "%d enriched %s-substrates,",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3272 nrow(m),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3273 kinase
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3274 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3275 sprintf(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3276 " KSEA %s < %0.2f\n",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3277 statistic,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3278 threshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3279 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3280 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3281 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3282 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3283 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3284 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3285 cat("\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3286 return(TRUE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3287 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3288
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3289 # Disabling heatmaps for substrates pending decision whether to eliminate them altogether
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3290 if (FALSE)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3291 for (kinase_name in sort(enriched_kinases$kinase)) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3292 enriched_substrates <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3293 all_enriched_substrates[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3294 all_enriched_substrates$kinase == kinase_name,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3295 ,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3296 drop = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3297 ]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3298 # Get the intensity values for the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3299 enriched_intensities <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3300 as.matrix(unimputed_quant_data_log[enriched_substrates$ppep, , drop = FALSE])
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3301 # Remove rows having too many NA values to be relevant
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3302 na_counter <- is.na(enriched_intensities)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3303 na_counts <- apply(na_counter, 1, sum)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3304 enriched_intensities <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3305 enriched_intensities[na_counts < ncol(enriched_intensities) / 2, , drop = FALSE]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3306 # Rename the rows with the display-name for the heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3307 rownames(enriched_intensities) <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3308 sapply(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3309 X = rownames(enriched_intensities),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3310 FUN = function(rn) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3311 enriched_substrates[enriched_substrates$ppep == rn, "label"]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3312 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3313 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3314 # Format as matrix for heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3315 m <- as.matrix(enriched_intensities)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3316 # Draw the heading and heatmap
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3317 if (nrow(m) > 0) {
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3318 cut_args <- new_env()
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3319 cut_args$cutoff <- cutoff
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3320 cut_args$kinase <- kinase_name
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3321 cut_args$statistic <- ksea_cutoff_statistic
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3322 cut_args$threshold <- ksea_cutoff_threshold
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3323 number_of_peptides_found <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3324 draw_intensity_heatmap(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3325 m = m,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3326 cutoff = cut_args,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3327 hm_heading_function = cat_enriched_heading,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3328 hm_main_title
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3329 = "Unnormalized (zero-imputed) intensities of enriched kinase-substrates",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3330 suppress_row_dendrogram = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3331 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3332 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3333 }
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3334
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3335 # Write output tabular files
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3336
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3337 # get kinase, ppep, concat(kinase) tuples for enriched kinases
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3338
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3339 kinase_ppep_label <- sqldf("
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3340 WITH
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3341 t(ppep, label) AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3342 (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3343 SELECT DISTINCT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3344 SUB_MOD_RSD AS ppep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3345 group_concat(gene, '; ') AS label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3346 FROM pseudo_ksdata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3347 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3348 GROUP BY ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3349 ),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3350 k(kinase, ppep_join) AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3351 (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3352 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep_join
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3353 FROM pseudo_ksdata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3354 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3355 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3356 SELECT k.kinase, t.ppep, t.label
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3357 FROM t, k
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3358 WHERE t.ppep = k.ppep_join
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3359 ORDER BY k.kinase, t.ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3360 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3361
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3362 # extract what we need from full_data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3363 impish <- cbind(rownames(quant_data_imp), quant_data_imp)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3364 colnames(impish)[1] <- "Phosphopeptide"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3365 data_table_imputed_sql <- "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3366 SELECT
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3367 f.*,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3368 k.label AS KSEA_enrichments,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3369 q.*
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3370 FROM
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3371 metadata_plus_p f
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3372 LEFT JOIN kinase_ppep_label k
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3373 ON f.Phosphopeptide = k.ppep,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3374 impish q
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3375 WHERE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3376 f.Phosphopeptide = q.Phosphopeptide
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3377 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3378 data_table_imputed <- sqldf(data_table_imputed_sql)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3379 # Zap the duplicated 'Phosphopeptide' column named 'ppep'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3380 data_table_imputed <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3381 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3382
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3383 # Output with imputed, un-normalized data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3384
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3385 write.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3386 data_table_imputed
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3387 , file = imputed_data_filename
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3388 , sep = "\t"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3389 , col.names = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3390 , row.names = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3391 , quote = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3392 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3393
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3394
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3395 #output quantile normalized data
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3396 impish <- cbind(rownames(quant_data_imp_qn_log), quant_data_imp_qn_log)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3397 colnames(impish)[1] <- "Phosphopeptide"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3398 data_table_imputed <- sqldf(data_table_imputed_sql)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3399 # Zap the duplicated 'Phosphopeptide' column named 'ppep'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3400 data_table_imputed <-
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3401 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3402 write.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3403 data_table_imputed,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3404 file = imp_qn_lt_data_filenm,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3405 sep = "\t",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3406 col.names = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3407 row.names = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3408 quote = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3409 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3410
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3411 ppep_kinase <- sqldf("
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3412 SELECT DISTINCT k.ppep, k.kinase
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3413 FROM (
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3414 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3415 FROM pseudo_ksdata
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3416 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3417 ) k
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3418 ORDER BY k.ppep, k.kinase
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3419 ")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3420
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3421 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3422 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3423 name = "ksea_enriched_ks",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3424 value = ppep_kinase,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3425 append = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3426 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3427
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3428 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3429 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3430 name = "anova_signif",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3431 value = p_value_data,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3432 append = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3433 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3434
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3435 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3436 DROP VIEW IF EXISTS stats_metadata_v;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3437 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3438 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3439 dml_no_rows_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3440 CREATE VIEW stats_metadata_v
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3441 AS
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3442 SELECT DISTINCT m.*,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3443 p.raw_anova_p,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3444 p.fdr_adjusted_anova_p,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3445 kek.kinase AS ksea_enrichments
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3446 FROM
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3447 mrgfltr_metadata_view m
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3448 LEFT JOIN anova_signif p
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3449 ON m.phospho_peptide = p.phosphopeptide
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3450 LEFT JOIN ksea_enriched_ks kek
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3451 ON m.phospho_peptide = kek.ppep
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3452 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3453 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3454 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3455
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3456 write.table(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3457 dbReadTable(db, "stats_metadata_v"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3458 file = anova_ksea_mtdt_file,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3459 sep = "\t",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3460 col.names = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3461 row.names = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3462 quote = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3463 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3464
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3465
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3466 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3467
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3468 ```{r parmlist, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3469 cat("\\leavevmode\n\n\n")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3470
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3471 # write parameters to report
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3472
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3473 param_unlist <- unlist(as.list(params))
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3474 param_df <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3475 parameter = paste0("\\verb@", names(param_unlist), "@"),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3476 value = paste0("\\verb@", gsub("$", "\\$", param_unlist, fixed = TRUE), "@")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3477 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3478
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3479 data_frame_latex(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3480 x = param_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3481 justification = "p{0.35\\linewidth} p{0.6\\linewidth}",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3482 centered = TRUE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3483 caption = "Input parameters",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3484 anchor = const_table_anchor_bp,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3485 underscore_whack = FALSE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3486 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3487
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3488 # write parameters to SQLite output
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3489
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3490 mqppep_anova_script_param_df <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3491 script = "mqppep_anova_script.Rmd",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3492 parameter = names(param_unlist),
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3493 value = param_unlist
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3494 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3495 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3496 DROP TABLE IF EXISTS script_parameter;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3497 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3498 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3499 ddl_exec(db, "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3500 CREATE TABLE IF NOT EXISTS script_parameter(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3501 script TEXT,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3502 parameter TEXT,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3503 value ANY,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3504 UNIQUE (script, parameter) ON CONFLICT REPLACE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3505 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3506 ;
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3507 "
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3508 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3509 RSQLite::dbWriteTable(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3510 conn = db,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3511 name = "script_parameter",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3512 value = mqppep_anova_script_param_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3513 append = TRUE
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3514 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3515
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3516 # We are done with output
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3517 RSQLite::dbDisconnect(db)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3518 ```
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3519 <!--
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3520 There's gotta be a better way...
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3521
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3522 loaded_packages_df <- sessioninfo::package_info("loaded")
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3523 loaded_packages_df[, "library"] <- as.character(loaded_packages_df$library)
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3524 loaded_packages_df <- data.frame(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3525 package = loaded_packages_df$package,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3526 version = loaded_packages_df$loadedversion,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3527 date = loaded_packages_df$date
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3528 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3529 data_frame_latex(
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3530 x = loaded_packages_df,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3531 justification = "l \| l l",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3532 centered = FALSE,
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3533 caption = "Loaded R packages",
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3534 anchor = const_table_anchor_bp
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3535 )
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3536 -->

Mercurial > repos > galaxyp > mqppep_anova

annotate mqppep_anova_script.Rmd @ 0:d9b68bedbc91 draft