Mercurial > repos > lecorguille > xcms_group

comparison xcms.r @ 28:a18fc7554c6d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:43:21 -0500
parents 36b470f3ebcf
children
comparison
equal deleted inserted replaced
27:36b470f3ebcf 28:a18fc7554c6d
11 11
12 12
13 # ----- PACKAGE ----- 13 # ----- PACKAGE -----
14 cat("\tPACKAGE INFO\n") 14 cat("\tPACKAGE INFO\n")
15 #pkgs=c("xcms","batch") 15 #pkgs=c("xcms","batch")
16 pkgs=c("tools","parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") 16 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
17 for(pkg in pkgs) { 17 for(pkg in pkgs) {
18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) 18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") 19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
20 } 20 }
21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
63 if (!is.null(listArguments[["xsetRdataOutput"]])){ 63 if (!is.null(listArguments[["xsetRdataOutput"]])){
64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL 64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
65 } 65 }
66 66
67 #saving the specific parameters 67 #saving the specific parameters
68 rplotspdf = "Rplots.pdf"
69 if (!is.null(listArguments[["rplotspdf"]])){
70 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
71 }
68 sampleMetadataOutput = "sampleMetadata.tsv" 72 sampleMetadataOutput = "sampleMetadata.tsv"
69 if (!is.null(listArguments[["sampleMetadataOutput"]])){ 73 if (!is.null(listArguments[["sampleMetadataOutput"]])){
70 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL 74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
71 } 75 }
72 variableMetadataOutput = "variableMetadata.tsv" 76 variableMetadataOutput = "variableMetadata.tsv"
86 if (!is.null(listArguments[["numDigitsRT"]])){ 90 if (!is.null(listArguments[["numDigitsRT"]])){
87 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL 91 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL
88 } 92 }
89 if (!is.null(listArguments[["intval"]])){ 93 if (!is.null(listArguments[["intval"]])){
90 intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL 94 intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
95 }
96
97 if (thefunction %in% c("xcmsSet","retcor")) {
98 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
91 } 100 }
92 101
93 102
94 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { 103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
95 if (!exists("singlefile")) singlefile=NULL 104 if (!exists("singlefile")) singlefile=NULL
136 145
137 } 146 }
138 147
139 #change the default display settings 148 #change the default display settings
140 #dev.new(file="Rplots.pdf", width=16, height=12) 149 #dev.new(file="Rplots.pdf", width=16, height=12)
141 pdf(file="Rplots.pdf", width=16, height=12) 150 pdf(file=rplotspdf, width=16, height=12)
142 if (thefunction == "group") { 151 if (thefunction == "group") {
143 par(mfrow=c(2,2)) 152 par(mfrow=c(2,2))
144 } 153 }
145 #else if (thefunction == "retcor") { 154 #else if (thefunction == "retcor") {
146 #try to change the legend display 155 #try to change the legend display
186 195
187 # -- TIC -- 196 # -- TIC --
188 if (thefunction == "xcmsSet") { 197 if (thefunction == "xcmsSet") {
189 cat("\t\tGET TIC GRAPH\n") 198 cat("\t\tGET TIC GRAPH\n")
190 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) 199 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
191 getTICs(xcmsSet=xset, rt="raw") 200 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
192 getBPCs(xcmsSet=xset, rt="raw") 201 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
193 } else if (thefunction == "retcor") { 202 } else if (thefunction == "retcor") {
194 cat("\t\tGET TIC GRAPH\n") 203 cat("\t\tGET TIC GRAPH\n")
195 getTICs(xcmsSet=xset, rt="corrected") 204 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
196 getBPCs(xcmsSet=xset, rt="corrected") 205 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
197 } 206 }
198 207
199 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) { 208 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {
200 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput) 209 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
201 } 210 }