Mercurial > repos > eschen42 > mqppep_preproc

annotate MaxQuantProcessingScript.R @ 31:e103de3e41e6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9
author eschen42
date Fri, 09 Dec 2022 21:06:08 +0000
parents 29775869faba
children 072fe8228dfa
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2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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1 #!/usr/bin/env Rscript
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2
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3 # This is the implementation for the
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4 # "MaxQuant Phosphopeptide Localization Probability Cutoff"
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5 # Galaxy tool (mqppep_lclztn_filter)
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6 # It is adapted from the MaxQuant Processing Script written by Larry Cheng.
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8 # libraries
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9 library(optparse)
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10 library(data.table)
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11 library(stringr)
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12 library(ggplot2)
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14 # title: "MaxQuant Processing Script"
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15 # author: "Larry Cheng"
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16 # date: "February 19, 2018"
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17 #
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18 # # MaxQuant Processing Script
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19 # Takes MaxQuant Phospho (STY)sites.txt file as input
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20 # and performs the following (in order):
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21 # 1) Runs the Proteomics Quality Control software
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22 # 2) Remove contaminant and reverse sequence rows
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23 # 3) Filters rows based on localization probability
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24 # 4) Extract the quantitative data
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25 # 5) Sequences phosphopeptides
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26 # 6) Merges multiply phosphorylated peptides
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27 # 7) Filters out phosphopeptides based on enrichment
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28 # The output file contains the phosphopeptide (first column)
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29 # and the quantitative values for each sample.
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30 #
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31 # ## Revision History
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32 # Rev. 2022-02-10 :wrap for inclusion in Galaxy
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33 # Rev. 2018-02-19 :break up analysis script into "MaxQuant Processing Script"
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34 # and "Phosphopeptide Processing Script"
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35 # Rev. 2017-12-12 :added PTXQC
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36 # added additional plots and table outputs for quality control
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37 # allowed for more than 2 samples to be grouped together
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38 # (up to 26 (eg, 1A, 1B, 1C, etc))
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39 # converted from .r to .rmd file to knit report
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40 # for quality control
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41 # Rev. 2016-09-11 :automated the FDR cutoffs; removed the option to data
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42 # impute multiple times
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43 # Rev. 2016-09-09 :added filter to eliminate contaminant & reverse sequence rows
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44 # Rev. 2016-09-01 :moved the collapse step from after ANOVA filter to prior to
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45 # preANOVA file output
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46 # Rev. 2016-08-22 :use regexSampleNames <- "\\.(\\d + )[AB]$"
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47 # so that it looks at the end of string
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48 # Rev. 2016-08-05 :Removed vestigial line (ppeptides <- ....)
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49 # Rev. 2016-07-03 :Removed row names from the write.table() output for
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50 # ANOVA and PreANOVA
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51 # Rev. 2016-06-25 :Set default Localization Probability cutoff to 0.75
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52 # Rev. 2016-06-23 :fixed a bug in filtering for pY enrichment by resetting
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53 # the row numbers afterwards
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54 # Rev. 2016-06-21 :test18 + standardized the regexpression in protocol
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57 ### FUNCTION DECLARATIONS begin ----------------------------------------------
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59 # Read first line of file at filePath
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60 # adapted from: https://stackoverflow.com/a/35761217/15509512
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61 read_first_line <- function(filepath) {
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62 con <- file(filepath, "r")
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63 line <- readLines(con, n = 1)
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64 close(con)
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65 return(line)
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66 }
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68 # Move columns to the end of dataframe
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69 # - data: the dataframe
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70 # - move: a vector of column names, each of which is an element of names(data)
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71 movetolast <- function(data, move) {
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72 data[c(setdiff(names(data), move), move)]
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73 }
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75 # Generate phosphopeptide and build list when applied
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76 phosphopeptide_func <- function(df) {
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77 # generate peptide sequence and list of phosphopositions
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78 phosphoprobsequence <-
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79 strsplit(as.character(df["Phospho (STY) Score diffs"]), "")[[1]]
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80 output <- vector()
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81 phosphopeptide <- ""
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82 counter <- 0 # keep track of position in peptide
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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83 phosphopositions <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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84 vector() # keep track of phosphorylation positions in peptide
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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85 score_diff <- ""
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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86 for (chara in phosphoprobsequence) {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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87 # build peptide sequence
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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88 if (!(
23
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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89 chara == " " ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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90 chara == "(" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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91 chara == ")" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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92 chara == "." ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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93 chara == "-" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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94 chara == "0" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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95 chara == "1" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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96 chara == "2" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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97 chara == "3" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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98 chara == "4" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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99 chara == "5" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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100 chara == "6" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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101 chara == "7" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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102 chara == "8" ||
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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103 chara == "9")
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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104 ) {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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105 phosphopeptide <- paste(phosphopeptide, chara, sep = "")
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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106 counter <- counter + 1
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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107 }
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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108 # generate score_diff
23
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109 if (chara == "-" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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110 chara == "." ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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111 chara == "0" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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112 chara == "1" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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113 chara == "2" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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114 chara == "3" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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115 chara == "4" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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116 chara == "5" ||
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117 chara == "6" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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118 chara == "7" ||
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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119 chara == "8" ||
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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120 chara == "9"
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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121 ) {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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122 score_diff <- paste(score_diff, chara, sep = "")
0
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123 }
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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124 # evaluate score_diff
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125 if (chara == ")") {
0
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126 score_diff <- as.numeric(score_diff)
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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127 # only consider a phosphoresidue if score_diff > 0
0
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128 if (score_diff > 0) {
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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129 phosphopositions <- append(phosphopositions, counter)
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130 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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131 score_diff <- ""
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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132 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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133 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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134
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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135 # generate phosphopeptide sequence (ie, peptide sequence with "p"'s)
0
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136 counter <- 1
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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137 phosphoposition_correction1 <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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138 -1 # used to correct phosphosposition as "p"'s
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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139 # are inserted into the phosphopeptide string
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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140 phosphoposition_correction2 <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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141 0 # used to correct phosphosposition as "p"'s
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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142 # are inserted into the phosphopeptide string
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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143 while (counter <= length(phosphopositions)) {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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144 phosphopeptide <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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145 paste(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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146 substr(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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147 phosphopeptide,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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148 0,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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149 phosphopositions[counter] + phosphoposition_correction1
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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150 ),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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151 "p",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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152 substr(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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153 phosphopeptide,
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154 phosphopositions[counter] + phosphoposition_correction2,
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155 nchar(phosphopeptide)
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156 ),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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157 sep = ""
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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158 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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159 counter <- counter + 1
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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160 phosphoposition_correction1 <- phosphoposition_correction1 + 1
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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161 phosphoposition_correction2 <- phosphoposition_correction2 + 1
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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162 }
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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163 # building phosphopeptide list
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164 output <- append(output, phosphopeptide)
0
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165 return(output)
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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166 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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167
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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168 ### FUNCTION DECLARATIONS end ------------------------------------------------
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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169
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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170
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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171 ### EXTRACT ARGUMENTS begin --------------------------------------------------
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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172
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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173 # parse options
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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174 option_list <- list(
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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175 make_option(
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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176 c("-i", "--input"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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177 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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178 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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179 help = "A MaxQuant Phospho (STY)Sites.txt"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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180 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
181 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
182 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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183 c("-o", "--output"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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184 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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185 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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186 help = "path to output file"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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187 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
188 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
189 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
190 c("-E", "--enrichGraph"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
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191 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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192 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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193 help = "path to enrichment graph PDF"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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194 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
195 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
196 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
197 c("-F", "--enrichGraph_svg"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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198 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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199 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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200 help = "path to enrichment graph SVG"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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201 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
202 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
203 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
204 c("-L", "--locProbCutoffGraph"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
205 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
206 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
207 help = "path to location-proability cutoff graph PDF"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
208 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
209 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
210 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
211 c("-M", "--locProbCutoffGraph_svg"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
212 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
213 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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214 help = "path to location-proability cutoff graph SVG"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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215 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
216 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
217 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
218 c("-e", "--enriched"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
219 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
220 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
221 help = "pY or pST enriched samples (ie, 'Y' or 'ST')"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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222 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
223 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
224 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
225 c("-p", "--phosphoCol"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
226 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
227 type = "character",
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
228 help = paste0("PERL-compatible regular expression matching",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
229 " header of column having number of 'Phospho (STY)'")
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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230 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
231 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
232 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
233 c("-s", "--startCol"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
234 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
235 type = "character",
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
236 help = paste0("PERL-compatible regular expression matching",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
237 " header of column having first sample intensity")
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
238 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
239 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
240 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
241 c("-I", "--intervalCol"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
242 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
243 type = "integer",
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
244 help = paste0("Column interval between the Intensities of samples",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
245 " (eg, 1 if subsequent column; 2 if every other column")
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
246 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
247 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
248 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
249 c("-l", "--localProbCutoff"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
250 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
251 type = "double",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
252 help = "Localization Probability Cutoff"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
253 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
254 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
255 make_option(
0
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256 c("-f", "--collapse_func"),
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257 action = "store",
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258 type = "character",
5
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259 help = paste0("merge identical phosphopeptides",
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260 " by ('sum' or 'average') the intensities")
0
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261 )
5
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262 ,
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263 make_option(
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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264 c("-r", "--filtered_data"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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265 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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266 type = "character",
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267 help = "filtered_data.txt"
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268 )
5
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269 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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270 make_option(
0
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271 c("-q", "--quant_data"),
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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272 action = "store",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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273 type = "character",
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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274 help = "quantData.txt"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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275 )
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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276 )
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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277 args <- parse_args(OptionParser(option_list = option_list))
0
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278 # Check parameter values
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279
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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280 ### EXTRACT ARGUMENTS end ----------------------------------------------------
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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281
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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282
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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283 ### EXTRACT PARAMETERS from arguments begin ----------------------------------
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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284
5
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285 if (!file.exists(args$input)) {
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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286 stop((paste("File", args$input, "does not exist")))
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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287 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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288
5
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289 phospho_col_pattern <- "^Number of Phospho [(][STY][STY]*[)]$"
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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290 start_col_pattern <- "^Intensity[^_]"
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291 phospho_col_pattern <- read_first_line(args$phosphoCol)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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292 start_col_pattern <- read_first_line(args$startCol)
0
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293
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294 sink(getConnection(2))
5
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295
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296 input_file_name <- args$input
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297 filtered_filename <- args$filtered_data
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298 quant_file_name <- args$quant_data
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299 interval_col <- as.integer(args$intervalCol)
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300
5
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301 first_line <- read_first_line(input_file_name)
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302 col_headers <-
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303 unlist(strsplit(
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304 x = first_line,
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305 split = c("\t"),
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306 fixed = TRUE
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diff changeset
307 ))
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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308 sink(getConnection(2))
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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309 sink()
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310
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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311
5
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312 intensity_header_cols <-
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313 grep(pattern = start_col_pattern, x = col_headers, perl = TRUE)
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diff changeset
314 if (length(intensity_header_cols) == 0) {
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diff changeset
315 err_msg <-
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diff changeset
316 paste("Found no intensity columns matching pattern:",
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diff changeset
317 start_col_pattern)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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318 # Divert output to stderr
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319 sink(getConnection(2))
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320 print(err_msg)
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diff changeset
321 sink()
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322 stop(err_msg)
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diff changeset
323 }
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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324
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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325
5
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326 phospho_col <-
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327 grep(pattern = phospho_col_pattern, x = col_headers, perl = TRUE)[1]
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diff changeset
328 if (is.na(phospho_col)) {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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329 err_msg <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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330 paste("Found no 'number of phospho sites' columns matching pattern:",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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331 phospho_col_pattern)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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332 # Divert output to stderr
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333 sink(getConnection(2))
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
334 print(err_msg)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
335 sink()
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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336 stop(err_msg)
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diff changeset
337 }
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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338
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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339
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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340 i_count <- 0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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341 this_column <- 1
5
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342 last_value <- intensity_header_cols[1]
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343 intensity_cols <- c(last_value)
0
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344
5
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345 while (length(intensity_header_cols) >= interval_col * i_count) {
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346 i_count <- 1 + i_count
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347 this_column <- interval_col + this_column
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348 if (last_value + interval_col != intensity_header_cols[this_column])
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349 break
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350 last_value <- intensity_header_cols[this_column]
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351 if (length(intensity_header_cols) < interval_col * i_count)
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352 break
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353 intensity_cols <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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354 c(intensity_cols, intensity_header_cols[this_column])
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355 }
0
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356
5
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357 start_col <- intensity_cols[1]
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358 num_samples <- i_count
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359
5
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360 output_filename <- args$output
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361 enrich_graph_filename <- args$enrichGraph
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362 loc_prob_cutoff_graph_filename <- args$locProbCutoffGraph
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363 enrich_graph_filename_svg <- args$enrichGraph_svg
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364 loc_prob_cutoff_graph_fn_svg <- args$locProbCutoffGraph_svg
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365
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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366 local_prob_cutoff <- args$localProbCutoff
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367 enriched <- args$enriched
5
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368 collapse_fn <- args$collapse_func
0
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369
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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370 ### EXTRACT PARAMETERS from arguments end ------------------------------------
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371
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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372
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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373 # Proteomics Quality Control for MaxQuant Results
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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374 # (Bielow C et al. J Proteome Res. 2016 PMID: 26653327)
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375 # is run by the Galaxy MaxQuant wrapper and need not be invoked here.
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376
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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377
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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378 # Read & filter out contaminants, reverse sequences, & localization probability
0
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379 # ---
5
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380 full_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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381 read.table(
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382 file = input_file_name,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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383 sep = "\t",
23
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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384 header = TRUE,
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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385 quote = ""
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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386 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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387
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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388 # Filter out contaminant rows and reverse rows
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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389 filtered_data <- subset(full_data, !grepl("CON__", Proteins))
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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390 filtered_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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391 subset(filtered_data, !grepl("_MYCOPLASMA", Proteins))
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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392 filtered_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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393 subset(filtered_data, !grepl("CONTAMINANT_", Proteins))
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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394 filtered_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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395 subset(filtered_data, !grepl("REV__", Protein)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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396 ) # since REV__ rows are blank in the first column (Proteins)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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397 write.table(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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398 filtered_data,
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399 file = filtered_filename,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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400 sep = "\t",
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401 quote = FALSE,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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402 col.names = TRUE,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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403 row.names = FALSE
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
404 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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405 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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406
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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407
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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408 # Filter out data with localization probability below localProbCutoff
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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409 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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410 # Data filtered by localization probability
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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411 loc_prob_filtered_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
412 filtered_data[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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413 filtered_data$Localization.prob >= local_prob_cutoff,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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414 ]
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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415 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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416
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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417
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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418 # Localization probability -- visualize locprob cutoff
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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419 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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420 loc_prob_graph_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
421 data.frame(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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422 group = c(paste(">", toString(local_prob_cutoff), sep = ""),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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423 paste("<", toString(local_prob_cutoff), sep = "")),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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424 value = c(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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425 nrow(loc_prob_filtered_data) / nrow(filtered_data) * 100,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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426 (nrow(filtered_data) - nrow(loc_prob_filtered_data))
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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427 / nrow(filtered_data) * 100
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
428 )
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
429 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
430 gigi <-
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
431 ggplot(loc_prob_graph_data, aes(x = "", y = value, fill = group)) +
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
432 geom_bar(width = 0.5,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
433 stat = "identity",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
434 color = "black") +
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
435 labs(x = NULL,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
436 y = "percent",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
437 title = "Phosphopeptides partitioned by localization-probability cutoff"
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
438 ) +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
439 scale_fill_discrete(name = "phosphopeptide\nlocalization-\nprobability") +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
440 theme_minimal() +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
441 theme(
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
442 legend.position = "right",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
443 legend.title = element_text(),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
444 plot.title = element_text(hjust = 0.5),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
445 plot.subtitle = element_text(hjust = 0.5),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
446 plot.title.position = "plot"
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
447 )
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
448 pdf(loc_prob_cutoff_graph_filename)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
449 print(gigi)
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
450 dev.off()
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
451 svg(loc_prob_cutoff_graph_fn_svg)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
452 print(gigi)
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
453 dev.off()
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
454 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
455
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
456
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
457 # Extract quantitative values from filtered data
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
458 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
459 quant_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
460 loc_prob_filtered_data[, seq(from = start_col,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
461 by = interval_col,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
462 length.out = num_samples)]
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
463 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
464
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
465
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
466 # Generate Phosphopeptide Sequence
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
467 # for latest version of MaxQuant (Version 1.5.3.30)
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
468 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
469 metadata_df <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
470 data.frame(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
471 loc_prob_filtered_data[, 1:8],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
472 loc_prob_filtered_data[, phospho_col],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
473 loc_prob_filtered_data[, phospho_col + 1],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
474 loc_prob_filtered_data[, phospho_col + 2],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
475 loc_prob_filtered_data[, phospho_col + 3],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
476 loc_prob_filtered_data[, phospho_col + 4],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
477 loc_prob_filtered_data[, phospho_col + 5],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
478 loc_prob_filtered_data[, phospho_col + 6],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
479 loc_prob_filtered_data[, phospho_col + 7],
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
480 quant_data
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
481 )
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
482 colnames(metadata_df) <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
483 c(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
484 "Proteins",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
485 "Positions within proteins",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
486 "Leading proteins",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
487 "Protein",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
488 "Protein names",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
489 "Gene names",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
490 "Fasta headers",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
491 "Localization prob",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
492 "Number of Phospho (STY)",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
493 "Amino Acid",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
494 "Sequence window",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
495 "Modification window",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
496 "Peptide window coverage",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
497 "Phospho (STY) Probabilities",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
498 "Phospho (STY) Score diffs",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
499 "Position in peptide",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
500 colnames(quant_data)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
501 )
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
502 # 'phosphopeptide_func' generates a phosphopeptide sequence
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
503 # for each row of data.
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
504 # for the 'apply' function: MARGIN 1 == rows, 2 == columns, c(1, 2) = both
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
505 metadata_df$phosphopeptide <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
506 apply(X = metadata_df, MARGIN = 1, FUN = phosphopeptide_func)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
507 colnames(metadata_df)[1] <- "Phosphopeptide"
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
508 # Move the quant data columns to the right end of the data.frame
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
509 metadata_df <- movetolast(metadata_df, c(colnames(quant_data)))
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
510 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
511
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
512
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
513 # Write quantitative values for debugging purposes
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
514 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
515 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
516 colnames(quant_write)[1] <- "Sequence.Window"
6
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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diff changeset
517 write.table(
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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parents: 5
diff changeset
518 quant_write,
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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diff changeset
519 file = quant_file_name,
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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parents: 5
diff changeset
520 sep = "\t",
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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parents: 5
diff changeset
521 quote = FALSE,
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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parents: 5
diff changeset
522 col.names = TRUE,
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
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parents: 5
diff changeset
523 row.names = FALSE
42daf70d4ed4 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
eschen42
parents: 5
diff changeset
524 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
525 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
526
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
527
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
528 # Make new data frame containing only Phosphopeptides
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
529 # that are to be mapped to quant data (merge_df)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
530 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
531 metadata_df <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
532 setDT(metadata_df, keep.rownames = TRUE) # row name will be used to map
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
533 merge_df <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
534 data.frame(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
535 as.integer(metadata_df$rn),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
536 metadata_df$phosphopeptide # row index to merge data frames
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
537 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
538 colnames(merge_df) <- c("rn", "Phosphopeptide")
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
539 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
540
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
541
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
542 # Add Phosphopeptide column to quant columns for quality control checking
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
543 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
544 quant_data_qc <- as.data.frame(quant_data)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
545 setDT(quant_data_qc, keep.rownames = TRUE) # will use to match rowname to data
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
546 quant_data_qc$rn <- as.integer(quant_data_qc$rn)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
547 quant_data_qc <- merge(merge_df, quant_data_qc, by = "rn")
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
548 quant_data_qc$rn <- NULL # remove rn column
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
549 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
550
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
551
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
552 # Collapse multiphosphorylated peptides
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
553 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
554 quant_data_qc_collapsed <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
555 data.table(quant_data_qc, key = "Phosphopeptide")
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
556 quant_data_qc_collapsed <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
557 aggregate(. ~ Phosphopeptide, quant_data_qc, FUN = collapse_fn)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
558 # ...
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
559 print("quant_data_qc_collapsed")
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
560 head(quant_data_qc_collapsed)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
561
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
562 # Compute (as string) % of phosphopeptides that are multiphosphorylated
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
563 # (for use in next step)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
564 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
565 pct_multiphos <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
566 (
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
567 nrow(quant_data_qc) - nrow(quant_data_qc_collapsed)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
568 ) / (2 * nrow(quant_data_qc))
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
569 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%")
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
570 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
571
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
572
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
573 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
574 # ---
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
575 py_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
576 quant_data_qc_collapsed[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
577 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pY"),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
578 ]
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
579 ps_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
580 quant_data_qc_collapsed[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
581 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pS"),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
582 ]
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
583 pt_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
584 quant_data_qc_collapsed[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
585 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pT"),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
586 ]
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
587
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
588 py_num <- nrow(py_data)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
589 ps_num <- nrow(ps_data)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
590 pt_num <- nrow(pt_data)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
591
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
592 # Visualize enrichment
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
593 enrich_graph_data <- data.frame(group = c("pY", "pS", "pT"),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
594 value = c(py_num, ps_num, pt_num))
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
595
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
596 enrich_graph_data <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
597 enrich_graph_data[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
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diff changeset
598 enrich_graph_data$value > 0,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
599 ]
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
600
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
601 # Plot pie chart with legend
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
602 # start: https://stackoverflow.com/a/62522478/15509512
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
603 # refine: https://www.statology.org/ggplot-pie-chart/
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
604 # colors: https://colorbrewer2.org/#type=diverging&scheme=BrBG&n=8
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
605 slices <- enrich_graph_data$value
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
606 phosphoresidue <- enrich_graph_data$group
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
607 pct <- round(100 * slices / sum(slices))
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
608 lbls <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
609 paste(enrich_graph_data$group, "\n", pct, "%\n(", slices, ")", sep = "")
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
610 slc_ctr <- c()
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
611 run_tot <- 0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
612 for (p in pct) {
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
613 slc_ctr <- c(slc_ctr, run_tot + p / 2.0)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
614 run_tot <- run_tot + p
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
615 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
616 lbl_y <- 100 - slc_ctr
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
617 df <-
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
618 data.frame(slices,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
619 pct,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
620 lbls,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
621 phosphoresidue = factor(phosphoresidue, levels = phosphoresidue))
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
622 gigi <- ggplot(df
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
623 , aes(x = 1, y = pct, fill = phosphoresidue)) +
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
624 geom_col(position = "stack", orientation = "x") +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
625 geom_text(aes(x = 1, y = lbl_y, label = lbls), col = "black") +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
626 coord_polar(theta = "y", direction = -1) +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
627 labs(
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
628 x = NULL
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
629 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
630 y = NULL
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
631 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
632 title = "Percentages (and counts) of phosphosites, by type of residue"
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
633 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
634 caption = sprintf(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
635 "Roughly %s of peptides have multiple phosphosites.",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
636 pct_multiphos
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
637 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
638 ) +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
639 labs(x = NULL, y = NULL, fill = NULL) +
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
640 theme_classic() +
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
641 theme(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
642 legend.position = "right"
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
643 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
644 axis.line = element_blank()
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
645 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
646 axis.text = element_blank()
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
647 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
648 axis.ticks = element_blank()
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
649 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
650 plot.title = element_text(hjust = 0.5)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
651 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
652 plot.subtitle = element_text(hjust = 0.5)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
653 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
654 plot.caption = element_text(hjust = 0.5)
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
eschen42
parents: 0
diff changeset
655 ,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
656 plot.title.position = "plot"
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
657 ) +
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
658 scale_fill_manual(breaks = phosphoresidue,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
659 values = c("#c7eae5", "#f6e8c3", "#dfc27d"))
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
660
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
661 pdf(enrich_graph_filename)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
662 print(gigi)
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
663 dev.off()
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
664 svg(enrich_graph_filename_svg)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
665 print(gigi)
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
666 dev.off()
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
667 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
668
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
669
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
670 # Filter phosphopeptides by enrichment
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
671 # --
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
672 if (enriched == "Y") {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
673 quant_data_qc_enrichment <- quant_data_qc_collapsed[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
674 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pY"),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
675 ]
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
676 } else if (enriched == "ST") {
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
677 quant_data_qc_enrichment <- quant_data_qc_collapsed[
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
678 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pS") |
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
679 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pT"),
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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parents: 0
diff changeset
680 ]
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
681 } else {
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
682 print("Error in enriched variable. Set to either 'Y' or 'ST'")
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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683 }
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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684 # ...
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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685
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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686 print("quant_data_qc_enrichment")
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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687 head(quant_data_qc_enrichment)
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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688
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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689 # Write phosphopeptides filtered by enrichment
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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690 # --
5
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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691 write.table(
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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692 quant_data_qc_enrichment,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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693 file = output_filename,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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694 sep = "\t",
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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695 quote = FALSE,
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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696 row.names = FALSE
b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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diff changeset
697 )
0
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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698 # ...