Mercurial > repos > galaxyp > mqppep_preproc

comparison mqppep_anova_script.Rmd @ 4:17e7a50939b3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1
author galaxyp
date Tue, 14 Feb 2023 17:36:58 +0000
parents de65777a9baa
children
comparison
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3:de65777a9baa 4:17e7a50939b3
79 # what should be the primary criterion to eliminate excessive heatmap rows 79 # what should be the primary criterion to eliminate excessive heatmap rows
80 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1] 80 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
81 # should correlation among substrates be used (rather than covariance) 81 # should correlation among substrates be used (rather than covariance)
82 correlateSubstrates: TRUE 82 correlateSubstrates: TRUE
83 # only show covariance among variables having variance > 1 83 # only show covariance among variables having variance > 1
84 filterCovVarGT1: TRUE 84 filterCovVarGT1: FALSE
85 # maximum number of residues to display for ppeps in rownames or columnames 85 # maximum number of residues to display for ppeps in rownames or columnames
86 ppepTruncN: 10 86 ppepTruncN: 10
87 # maximum number of characters of subgenes to display in rownames or columnames 87 # maximum number of characters of subgenes to display in rownames or columnames
88 subgeneTruncN: 10 88 subgeneTruncN: 10
89 # maximum number of characters for paste(subgene, ppep) for enrichment plots 89 # maximum number of characters for paste(subgene, ppep) for enrichment plots
95 # look-up tables for kinase descriptions 95 # look-up tables for kinase descriptions
96 kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2" 96 kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
97 kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2" 97 kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
98 # should debugging trace messages be printed? 98 # should debugging trace messages be printed?
99 showEnrichedSubstrates: FALSE 99 showEnrichedSubstrates: FALSE
100 # should debugging nb/nbe messages be printed?
101 printNBMsgs: FALSE
102 #printNBMsgs: TRUE
103 # should row-scaling be applied to heatmaps: "none" or "row" 100 # should row-scaling be applied to heatmaps: "none" or "row"
104 defaultHeatMapRowScaling: !r c("none", "row")[1] 101 defaultHeatMapRowScaling: !r c("none", "row")[1]
105 # how missing values be displayed on heat maps: "NA" or " " 102 # how missing values be displayed on heat maps: "NA" or " "
106 heatMapNAcellNote: !r c(" ", "NA")[1] 103 heatMapNAcellNote: !r c(" ", "NA")[1]
107 # how missing values be displayed on heat maps: "NA" or " " 104 # how missing values be displayed on heat maps: "NA" or " "
113 # should debugging trace messages be printed? 110 # should debugging trace messages be printed?
114 printTraceMsgs: FALSE 111 printTraceMsgs: FALSE
115 # when debugging files are needed, set debugFileBasePath to the path 112 # when debugging files are needed, set debugFileBasePath to the path
116 # to the directory where they should be written 113 # to the directory where they should be written
117 debugFileBasePath: !r if (TRUE) NULL else "test-data" 114 debugFileBasePath: !r if (TRUE) NULL else "test-data"
115 # should debugging nb/nbe messages be printed?
116 printNBMsgs: FALSE
117 #printNBMsgs: TRUE
118 --- 118 ---
119 119
120 ```{r setup, include = FALSE, results = 'asis'} 120 ```{r setup, include = FALSE, results = 'asis'}
121 121
122 # simple debug messaging 122 # simple debug messaging
6009 WHERE gene IN (SELECT kinase FROM enriched_kinases) 6009 WHERE gene IN (SELECT kinase FROM enriched_kinases)
6010 ), 6010 ),
6011 p_value_data 6011 p_value_data
6012 WHERE ppep = phosphopeptide 6012 WHERE ppep = phosphopeptide
6013 GROUP BY kinase, ppep 6013 GROUP BY kinase, ppep
6014 ORDER BY kinase, ppep, p_value_data.quality DESC 6014 ORDER BY kinase, p_value_data.quality DESC
6015 "), 6015 "),
6016 justification = "l l l l l l l", 6016 justification = "l l l l l l l",
6017 centered = TRUE, 6017 centered = TRUE,
6018 caption = "labeled substrates of enriched kinases", 6018 caption = "labeled substrates of enriched kinases",
6019 anchor = c(const_table_anchor_p, const_table_anchor_t), 6019 anchor = c(const_table_anchor_p, const_table_anchor_t),