mqppep_anova: MaxQuantProcessingScript.R annotate

annotate MaxQuantProcessingScript.R @ 23:3911581e639a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47

author	eschen42
date	Mon, 11 Jul 2022 13:51:14 +0000
parents
children	5b8e15b2a67c

rev	line source
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	1 #!/usr/bin/env Rscript
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	2
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	3 # This is the implementation for the
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	4 # "MaxQuant Phosphopeptide Localization Probability Cutoff"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	5 # Galaxy tool (mqppep_lclztn_filter)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	6 # It is adapted from the MaxQuant Processing Script written by Larry Cheng.
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	7
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	8 # libraries
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	9 library(optparse)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	10 library(data.table)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	11 library(stringr)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	12 library(ggplot2)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	13
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	14 # title: "MaxQuant Processing Script"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	15 # author: "Larry Cheng"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	16 # date: "February 19, 2018"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	17 #
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	18 # # MaxQuant Processing Script
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	19 # Takes MaxQuant Phospho (STY)sites.txt file as input
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	20 # and performs the following (in order):
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	21 # 1) Runs the Proteomics Quality Control software
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	22 # 2) Remove contaminant and reverse sequence rows
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	23 # 3) Filters rows based on localization probability
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	24 # 4) Extract the quantitative data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	25 # 5) Sequences phosphopeptides
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	26 # 6) Merges multiply phosphorylated peptides
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	27 # 7) Filters out phosphopeptides based on enrichment
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	28 # The output file contains the phosphopeptide (first column)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	29 # and the quantitative values for each sample.
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	30 #
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	31 # ## Revision History
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	32 # Rev. 2022-02-10 :wrap for inclusion in Galaxy
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	33 # Rev. 2018-02-19 :break up analysis script into "MaxQuant Processing Script"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	34 # and "Phosphopeptide Processing Script"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	35 # Rev. 2017-12-12 :added PTXQC
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	36 # added additional plots and table outputs for quality control
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	37 # allowed for more than 2 samples to be grouped together
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	38 # (up to 26 (eg, 1A, 1B, 1C, etc))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	39 # converted from .r to .rmd file to knit report
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	40 # for quality control
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	41 # Rev. 2016-09-11 :automated the FDR cutoffs; removed the option to data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	42 # impute multiple times
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	43 # Rev. 2016-09-09 :added filter to eliminate contaminant & reverse sequence rows
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	44 # Rev. 2016-09-01 :moved the collapse step from after ANOVA filter to prior to
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	45 # preANOVA file output
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	46 # Rev. 2016-08-22 :use regexSampleNames <- "\\.(\\d + )[AB]$"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	47 # so that it looks at the end of string
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	48 # Rev. 2016-08-05 :Removed vestigial line (ppeptides <- ....)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	49 # Rev. 2016-07-03 :Removed row names from the write.table() output for
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	50 # ANOVA and PreANOVA
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	51 # Rev. 2016-06-25 :Set default Localization Probability cutoff to 0.75
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	52 # Rev. 2016-06-23 :fixed a bug in filtering for pY enrichment by resetting
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	53 # the row numbers afterwards
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	54 # Rev. 2016-06-21 :test18 + standardized the regexpression in protocol
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	55
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	56
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	57 ### FUNCTION DECLARATIONS begin ----------------------------------------------
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	58
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	59 # Read first line of file at filePath
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	60 # adapted from: https://stackoverflow.com/a/35761217/15509512
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	61 read_first_line <- function(filepath) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	62 con <- file(filepath, "r")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	63 line <- readLines(con, n = 1)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	64 close(con)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	65 return(line)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	66 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	67
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	68 # Move columns to the end of dataframe
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	69 # - data: the dataframe
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	70 # - move: a vector of column names, each of which is an element of names(data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	71 movetolast <- function(data, move) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	72 data[c(setdiff(names(data), move), move)]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	73 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	74
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	75 # Generate phosphopeptide and build list when applied
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	76 phosphopeptide_func <- function(df) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	77 # generate peptide sequence and list of phosphopositions
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	78 phosphoprobsequence <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	79 strsplit(as.character(df["Phospho (STY) Score diffs"]), "")[[1]]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	80 output <- vector()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	81 phosphopeptide <- ""
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	82 counter <- 0 # keep track of position in peptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	83 phosphopositions <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	84 vector() # keep track of phosphorylation positions in peptide
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	85 score_diff <- ""
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	86 for (chara in phosphoprobsequence) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	87 # build peptide sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	88 if (!(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	89 chara == " " \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	90 chara == "(" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	91 chara == ")" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	92 chara == "." \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	93 chara == "-" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	94 chara == "0" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	95 chara == "1" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	96 chara == "2" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	97 chara == "3" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	98 chara == "4" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	99 chara == "5" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	100 chara == "6" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	101 chara == "7" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	102 chara == "8" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	103 chara == "9")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	104 ) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	105 phosphopeptide <- paste(phosphopeptide, chara, sep = "")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	106 counter <- counter + 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	107 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	108 # generate score_diff
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	109 if (chara == "-" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	110 chara == "." \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	111 chara == "0" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	112 chara == "1" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	113 chara == "2" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	114 chara == "3" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	115 chara == "4" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	116 chara == "5" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	117 chara == "6" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	118 chara == "7" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	119 chara == "8" \|\|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	120 chara == "9"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	121 ) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	122 score_diff <- paste(score_diff, chara, sep = "")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	123 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	124 # evaluate score_diff
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	125 if (chara == ")") {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	126 score_diff <- as.numeric(score_diff)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	127 # only consider a phosphoresidue if score_diff > 0
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	128 if (score_diff > 0) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	129 phosphopositions <- append(phosphopositions, counter)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	130 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	131 score_diff <- ""
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	132 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	133 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	134
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	135 # generate phosphopeptide sequence (ie, peptide sequence with "p"'s)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	136 counter <- 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	137 phosphoposition_correction1 <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	138 -1 # used to correct phosphosposition as "p"'s
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	139 # are inserted into the phosphopeptide string
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	140 phosphoposition_correction2 <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	141 0 # used to correct phosphosposition as "p"'s
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	142 # are inserted into the phosphopeptide string
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	143 while (counter <= length(phosphopositions)) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	144 phosphopeptide <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	145 paste(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	146 substr(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	147 phosphopeptide,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	148 0,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	149 phosphopositions[counter] + phosphoposition_correction1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	150 ),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	151 "p",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	152 substr(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	153 phosphopeptide,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	154 phosphopositions[counter] + phosphoposition_correction2,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	155 nchar(phosphopeptide)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	156 ),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	157 sep = ""
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	158 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	159 counter <- counter + 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	160 phosphoposition_correction1 <- phosphoposition_correction1 + 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	161 phosphoposition_correction2 <- phosphoposition_correction2 + 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	162 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	163 # building phosphopeptide list
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	164 output <- append(output, phosphopeptide)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	165 return(output)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	166 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	167
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	168 ### FUNCTION DECLARATIONS end ------------------------------------------------
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	169
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	170
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	171 ### EXTRACT ARGUMENTS begin --------------------------------------------------
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	172
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	173 # parse options
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	174 option_list <- list(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	175 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	176 c("-i", "--input"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	177 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	178 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	179 help = "A MaxQuant Phospho (STY)Sites.txt"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	180 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	181 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	182 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	183 c("-o", "--output"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	184 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	185 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	186 help = "path to output file"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	187 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	188 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	189 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	190 c("-E", "--enrichGraph"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	191 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	192 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	193 help = "path to enrichment graph PDF"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	194 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	195 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	196 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	197 c("-F", "--enrichGraph_svg"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	198 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	199 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	200 help = "path to enrichment graph SVG"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	201 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	202 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	203 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	204 c("-L", "--locProbCutoffGraph"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	205 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	206 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	207 help = "path to location-proability cutoff graph PDF"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	208 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	209 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	210 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	211 c("-M", "--locProbCutoffGraph_svg"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	212 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	213 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	214 help = "path to location-proability cutoff graph SVG"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	215 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	216 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	217 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	218 c("-e", "--enriched"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	219 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	220 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	221 help = "pY or pST enriched samples (ie, 'Y' or 'ST')"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	222 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	223 # default = "^Number of Phospho [(]STY[)]$",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	224 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	225 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	226 c("-p", "--phosphoCol"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	227 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	228 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	229 help = paste0("PERL-compatible regular expression matching",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	230 " header of column having number of 'Phospho (STY)'")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	231 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	232 # default = "^Intensity[^_]",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	233 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	234 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	235 c("-s", "--startCol"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	236 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	237 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	238 help = paste0("PERL-compatible regular expression matching",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	239 " header of column having first sample intensity")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	240 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	241 # default = 1,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	242 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	243 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	244 c("-I", "--intervalCol"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	245 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	246 type = "integer",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	247 help = paste0("Column interval between the Intensities of samples",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	248 " (eg, 1 if subsequent column; 2 if every other column")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	249 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	250 # default = 0.75,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	251 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	252 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	253 c("-l", "--localProbCutoff"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	254 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	255 type = "double",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	256 help = "Localization Probability Cutoff"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	257 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	258 # default = "sum",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	259 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	260 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	261 c("-f", "--collapse_func"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	262 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	263 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	264 help = paste0("merge identical phosphopeptides",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	265 " by ('sum' or 'average') the intensities")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	266 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	267 # default = "filtered_data.txt",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	268 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	269 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	270 c("-r", "--filtered_data"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	271 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	272 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	273 help = "filtered_data.txt"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	274 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	275 # default = "quantData.txt",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	276 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	277 make_option(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	278 c("-q", "--quant_data"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	279 action = "store",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	280 type = "character",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	281 help = "quantData.txt"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	282 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	283 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	284 args <- parse_args(OptionParser(option_list = option_list))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	285 # Check parameter values
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	286
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	287 ### EXTRACT ARGUMENTS end ----------------------------------------------------
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	288
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	289
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	290 ### EXTRACT PARAMETERS from arguments begin ----------------------------------
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	291
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	292 if (!file.exists(args$input)) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	293 stop((paste("File", args$input, "does not exist")))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	294 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	295
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	296 phospho_col_pattern <- "^Number of Phospho [(][STY][STY]*[)]$"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	297 start_col_pattern <- "^Intensity[^_]"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	298 phospho_col_pattern <- read_first_line(args$phosphoCol)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	299 start_col_pattern <- read_first_line(args$startCol)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	300
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	301 sink(getConnection(2))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	302
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	303 input_file_name <- args$input
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	304 filtered_filename <- args$filtered_data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	305 quant_file_name <- args$quant_data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	306 interval_col <- as.integer(args$intervalCol)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	307
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	308 first_line <- read_first_line(input_file_name)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	309 col_headers <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	310 unlist(strsplit(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	311 x = first_line,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	312 split = c("\t"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	313 fixed = TRUE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	314 ))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	315 sink(getConnection(2))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	316 sink()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	317
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	318
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	319 intensity_header_cols <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	320 grep(pattern = start_col_pattern, x = col_headers, perl = TRUE)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	321 if (length(intensity_header_cols) == 0) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	322 err_msg <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	323 paste("Found no intensity columns matching pattern:",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	324 start_col_pattern)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	325 # Divert output to stderr
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	326 sink(getConnection(2))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	327 print(err_msg)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	328 sink()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	329 stop(err_msg)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	330 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	331
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	332
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	333 phospho_col <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	334 grep(pattern = phospho_col_pattern, x = col_headers, perl = TRUE)[1]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	335 if (is.na(phospho_col)) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	336 err_msg <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	337 paste("Found no 'number of phospho sites' columns matching pattern:",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	338 phospho_col_pattern)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	339 # Divert output to stderr
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	340 sink(getConnection(2))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	341 print(err_msg)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	342 sink()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	343 stop(err_msg)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	344 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	345
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	346
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	347 i_count <- 0
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	348 this_column <- 1
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	349 last_value <- intensity_header_cols[1]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	350 intensity_cols <- c(last_value)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	351
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	352 while (length(intensity_header_cols) >= interval_col * i_count) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	353 i_count <- 1 + i_count
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	354 this_column <- interval_col + this_column
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	355 if (last_value + interval_col != intensity_header_cols[this_column])
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	356 break
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	357 last_value <- intensity_header_cols[this_column]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	358 if (length(intensity_header_cols) < interval_col * i_count)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	359 break
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	360 intensity_cols <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	361 c(intensity_cols, intensity_header_cols[this_column])
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	362 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	363
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	364 start_col <- intensity_cols[1]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	365 num_samples <- i_count
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	366
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	367 output_filename <- args$output
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	368 enrich_graph_filename <- args$enrichGraph
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	369 loc_prob_cutoff_graph_filename <- args$locProbCutoffGraph
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	370 enrich_graph_filename_svg <- args$enrichGraph_svg
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	371 loc_prob_cutoff_graph_fn_svg <- args$locProbCutoffGraph_svg
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	372
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	373 local_prob_cutoff <- args$localProbCutoff
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	374 enriched <- args$enriched
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	375 collapse_fn <- args$collapse_func
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	376
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	377 ### EXTRACT PARAMETERS from arguments end ------------------------------------
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	378
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	379
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	380 # Proteomics Quality Control for MaxQuant Results
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	381 # (Bielow C et al. J Proteome Res. 2016 PMID: 26653327)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	382 # is run by the Galaxy MaxQuant wrapper and need not be invoked here.
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	383
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	384
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	385 # Read & filter out contaminants, reverse sequences, & localization probability
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	386 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	387 full_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	388 read.table(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	389 file = input_file_name,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	390 sep = "\t",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	391 header = TRUE,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	392 quote = ""
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	393 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	394
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	395 # Filter out contaminant rows and reverse rows
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	396 filtered_data <- subset(full_data, !grepl("CON__", Proteins))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	397 filtered_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	398 subset(filtered_data, !grepl("_MYCOPLASMA", Proteins))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	399 filtered_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	400 subset(filtered_data, !grepl("CONTAMINANT_", Proteins))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	401 filtered_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	402 subset(filtered_data, !grepl("REV__", Protein)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	403 ) # since REV__ rows are blank in the first column (Proteins)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	404 write.table(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	405 filtered_data,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	406 file = filtered_filename,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	407 sep = "\t",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	408 quote = FALSE,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	409 col.names = TRUE,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	410 row.names = FALSE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	411 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	412 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	413
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	414
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	415 # Filter out data with localization probability below localProbCutoff
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	416 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	417 # Data filtered by localization probability
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	418 loc_prob_filtered_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	419 filtered_data[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	420 filtered_data$Localization.prob >= local_prob_cutoff,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	421 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	422 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	423
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	424
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	425 # Localization probability -- visualize locprob cutoff
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	426 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	427 loc_prob_graph_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	428 data.frame(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	429 group = c(paste(">", toString(local_prob_cutoff), sep = ""),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	430 paste("<", toString(local_prob_cutoff), sep = "")),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	431 value = c(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	432 nrow(loc_prob_filtered_data) / nrow(filtered_data) * 100,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	433 (nrow(filtered_data) - nrow(loc_prob_filtered_data))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	434 / nrow(filtered_data) * 100
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	435 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	436 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	437 gigi <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	438 ggplot(loc_prob_graph_data, aes(x = "", y = value, fill = group)) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	439 geom_bar(width = 0.5,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	440 stat = "identity",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	441 color = "black") +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	442 labs(x = NULL,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	443 y = "percent",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	444 title = "Phosphopeptides partitioned by localization-probability cutoff"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	445 ) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	446 scale_fill_discrete(name = "phosphopeptide\nlocalization-\nprobability") +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	447 theme_minimal() +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	448 theme(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	449 legend.position = "right",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	450 legend.title = element_text(),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	451 plot.title = element_text(hjust = 0.5),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	452 plot.subtitle = element_text(hjust = 0.5),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	453 plot.title.position = "plot"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	454 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	455 pdf(loc_prob_cutoff_graph_filename)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	456 print(gigi)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	457 dev.off()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	458 svg(loc_prob_cutoff_graph_fn_svg)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	459 print(gigi)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	460 dev.off()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	461 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	462
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	463
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	464 # Extract quantitative values from filtered data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	465 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	466 quant_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	467 loc_prob_filtered_data[, seq(from = start_col,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	468 by = interval_col,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	469 length.out = num_samples)]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	470 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	471
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	472
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	473 # Generate Phosphopeptide Sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	474 # for latest version of MaxQuant (Version 1.5.3.30)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	475 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	476 metadata_df <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	477 data.frame(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	478 loc_prob_filtered_data[, 1:8],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	479 loc_prob_filtered_data[, phospho_col],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	480 loc_prob_filtered_data[, phospho_col + 1],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	481 loc_prob_filtered_data[, phospho_col + 2],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	482 loc_prob_filtered_data[, phospho_col + 3],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	483 loc_prob_filtered_data[, phospho_col + 4],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	484 loc_prob_filtered_data[, phospho_col + 5],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	485 loc_prob_filtered_data[, phospho_col + 6],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	486 loc_prob_filtered_data[, phospho_col + 7],
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	487 quant_data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	488 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	489 colnames(metadata_df) <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	490 c(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	491 "Proteins",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	492 "Positions within proteins",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	493 "Leading proteins",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	494 "Protein",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	495 "Protein names",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	496 "Gene names",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	497 "Fasta headers",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	498 "Localization prob",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	499 "Number of Phospho (STY)",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	500 "Amino Acid",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	501 "Sequence window",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	502 "Modification window",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	503 "Peptide window coverage",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	504 "Phospho (STY) Probabilities",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	505 "Phospho (STY) Score diffs",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	506 "Position in peptide",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	507 colnames(quant_data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	508 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	509 # 'phosphopeptide_func' generates a phosphopeptide sequence
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	510 # for each row of data.
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	511 # for the 'apply' function: MARGIN 1 == rows, 2 == columns, c(1, 2) = both
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	512 metadata_df$phosphopeptide <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	513 apply(X = metadata_df, MARGIN = 1, FUN = phosphopeptide_func)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	514 colnames(metadata_df)[1] <- "Phosphopeptide"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	515 # Move the quant data columns to the right end of the data.frame
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	516 metadata_df <- movetolast(metadata_df, c(colnames(quant_data)))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	517 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	518
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	519
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	520 # Write quantitative values for debugging purposes
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	521 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	522 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	523 colnames(quant_write)[1] <- "Sequence.Window"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	524 write.table(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	525 quant_write,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	526 file = quant_file_name,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	527 sep = "\t",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	528 quote = FALSE,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	529 col.names = TRUE,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	530 row.names = FALSE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	531 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	532 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	533
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	534
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	535 # Make new data frame containing only Phosphopeptides
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	536 # that are to be mapped to quant data (merge_df)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	537 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	538 metadata_df <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	539 setDT(metadata_df, keep.rownames = TRUE) # row name will be used to map
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	540 merge_df <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	541 data.frame(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	542 as.integer(metadata_df$rn),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	543 metadata_df$phosphopeptide # row index to merge data frames
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	544 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	545 colnames(merge_df) <- c("rn", "Phosphopeptide")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	546 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	547
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	548
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	549 # Add Phosphopeptide column to quant columns for quality control checking
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	550 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	551 quant_data_qc <- as.data.frame(quant_data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	552 setDT(quant_data_qc, keep.rownames = TRUE) # will use to match rowname to data
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	553 quant_data_qc$rn <- as.integer(quant_data_qc$rn)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	554 quant_data_qc <- merge(merge_df, quant_data_qc, by = "rn")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	555 quant_data_qc$rn <- NULL # remove rn column
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	556 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	557
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	558
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	559 # Collapse multiphosphorylated peptides
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	560 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	561 quant_data_qc_collapsed <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	562 data.table(quant_data_qc, key = "Phosphopeptide")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	563 quant_data_qc_collapsed <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	564 aggregate(. ~ Phosphopeptide, quant_data_qc, FUN = collapse_fn)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	565 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	566 print("quant_data_qc_collapsed")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	567 head(quant_data_qc_collapsed)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	568
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	569 # Compute (as string) % of phosphopeptides that are multiphosphorylated
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	570 # (for use in next step)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	571 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	572 pct_multiphos <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	573 (
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	574 nrow(quant_data_qc) - nrow(quant_data_qc_collapsed)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	575 ) / (2 * nrow(quant_data_qc))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	576 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	577 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	578
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	579
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	580 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	581 # ---
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	582 py_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	583 quant_data_qc_collapsed[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	584 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pY"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	585 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	586 ps_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	587 quant_data_qc_collapsed[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	588 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pS"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	589 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	590 pt_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	591 quant_data_qc_collapsed[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	592 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pT"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	593 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	594
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	595 py_num <- nrow(py_data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	596 ps_num <- nrow(ps_data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	597 pt_num <- nrow(pt_data)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	598
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	599 # Visualize enrichment
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	600 enrich_graph_data <- data.frame(group = c("pY", "pS", "pT"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	601 value = c(py_num, ps_num, pt_num))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	602
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	603 enrich_graph_data <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	604 enrich_graph_data[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	605 enrich_graph_data$value > 0,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	606 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	607
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	608 # Plot pie chart with legend
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	609 # start: https://stackoverflow.com/a/62522478/15509512
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	610 # refine: https://www.statology.org/ggplot-pie-chart/
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	611 # colors: https://colorbrewer2.org/#type=diverging&scheme=BrBG&n=8
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	612 slices <- enrich_graph_data$value
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	613 phosphoresidue <- enrich_graph_data$group
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	614 pct <- round(100 * slices / sum(slices))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	615 lbls <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	616 paste(enrich_graph_data$group, "\n", pct, "%\n(", slices, ")", sep = "")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	617 slc_ctr <- c()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	618 run_tot <- 0
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	619 for (p in pct) {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	620 slc_ctr <- c(slc_ctr, run_tot + p / 2.0)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	621 run_tot <- run_tot + p
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	622 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	623 lbl_y <- 100 - slc_ctr
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	624 df <-
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	625 data.frame(slices,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	626 pct,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	627 lbls,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	628 phosphoresidue = factor(phosphoresidue, levels = phosphoresidue))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	629 gigi <- ggplot(df
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	630 , aes(x = 1, y = pct, fill = phosphoresidue)) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	631 geom_col(position = "stack", orientation = "x") +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	632 geom_text(aes(x = 1, y = lbl_y, label = lbls), col = "black") +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	633 coord_polar(theta = "y", direction = -1) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	634 labs(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	635 x = NULL
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	636 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	637 y = NULL
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	638 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	639 title = "Percentages (and counts) of phosphosites, by type of residue"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	640 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	641 caption = sprintf(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	642 "Roughly %s of peptides have multiple phosphosites.",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	643 pct_multiphos
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	644 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	645 ) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	646 labs(x = NULL, y = NULL, fill = NULL) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	647 theme_classic() +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	648 theme(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	649 legend.position = "right"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	650 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	651 axis.line = element_blank()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	652 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	653 axis.text = element_blank()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	654 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	655 axis.ticks = element_blank()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	656 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	657 plot.title = element_text(hjust = 0.5)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	658 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	659 plot.subtitle = element_text(hjust = 0.5)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	660 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	661 plot.caption = element_text(hjust = 0.5)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	662 ,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	663 plot.title.position = "plot"
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	664 ) +
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	665 scale_fill_manual(breaks = phosphoresidue,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	666 values = c("#c7eae5", "#f6e8c3", "#dfc27d"))
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	667
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	668 pdf(enrich_graph_filename)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	669 print(gigi)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	670 dev.off()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	671 svg(enrich_graph_filename_svg)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	672 print(gigi)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	673 dev.off()
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	674 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	675
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	676
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	677 # Filter phosphopeptides by enrichment
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	678 # --
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	679 if (enriched == "Y") {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	680 quant_data_qc_enrichment <- quant_data_qc_collapsed[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	681 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pY"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	682 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	683 } else if (enriched == "ST") {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	684 quant_data_qc_enrichment <- quant_data_qc_collapsed[
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	685 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pS") \|
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	686 str_detect(quant_data_qc_collapsed$Phosphopeptide, "pT"),
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	687 ]
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	688 } else {
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	689 print("Error in enriched variable. Set to either 'Y' or 'ST'")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	690 }
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	691 # ...
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	692
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	693 print("quant_data_qc_enrichment")
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	694 head(quant_data_qc_enrichment)
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	695
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	696 # Write phosphopeptides filtered by enrichment
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	697 # --
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	698 write.table(
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	699 quant_data_qc_enrichment,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	700 file = output_filename,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	701 sep = "\t",
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	702 quote = FALSE,
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	703 row.names = FALSE
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	704 )
3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: diff changeset	705 # ...

Mercurial > repos > eschen42 > mqppep_anova

annotate MaxQuantProcessingScript.R @ 23:3911581e639a draft