Mercurial > repos > lecorguille > xcms_fillpeaks

comparison xcms.r @ 29:f6d3e6be4ea3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:48:31 -0400
parents 4db7afa8284d
children 6b5ed508f81f
comparison
equal deleted inserted replaced
28:9b0bf28bcbaf 29:f6d3e6be4ea3
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("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") 16 pkgs=c("tools","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 }
72 sampleMetadataOutput = "sampleMetadata.tsv" 68 sampleMetadataOutput = "sampleMetadata.tsv"
73 if (!is.null(listArguments[["sampleMetadataOutput"]])){ 69 if (!is.null(listArguments[["sampleMetadataOutput"]])){
74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL 70 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
75 } 71 }
76 variableMetadataOutput = "variableMetadata.tsv" 72 variableMetadataOutput = "variableMetadata.tsv"
90 if (!is.null(listArguments[["numDigitsRT"]])){ 86 if (!is.null(listArguments[["numDigitsRT"]])){
91 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL 87 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL
92 } 88 }
93 if (!is.null(listArguments[["intval"]])){ 89 if (!is.null(listArguments[["intval"]])){
94 intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL 90 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
100 } 91 }
101 92
102 93
103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { 94 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
104 if (!exists("singlefile")) singlefile=NULL 95 if (!exists("singlefile")) singlefile=NULL
145 136
146 } 137 }
147 138
148 #change the default display settings 139 #change the default display settings
149 #dev.new(file="Rplots.pdf", width=16, height=12) 140 #dev.new(file="Rplots.pdf", width=16, height=12)
150 pdf(file=rplotspdf, width=16, height=12) 141 pdf(file="Rplots.pdf", width=16, height=12)
151 if (thefunction == "group") { 142 if (thefunction == "group") {
152 par(mfrow=c(2,2)) 143 par(mfrow=c(2,2))
153 } 144 }
154 #else if (thefunction == "retcor") { 145 #else if (thefunction == "retcor") {
155 #try to change the legend display 146 #try to change the legend display
195 186
196 # -- TIC -- 187 # -- TIC --
197 if (thefunction == "xcmsSet") { 188 if (thefunction == "xcmsSet") {
198 cat("\t\tGET TIC GRAPH\n") 189 cat("\t\tGET TIC GRAPH\n")
199 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) 190 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
200 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") 191 getTICs(xcmsSet=xset, rt="raw")
201 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) 192 getBPCs(xcmsSet=xset, rt="raw")
202 } else if (thefunction == "retcor") { 193 } else if (thefunction == "retcor") {
203 cat("\t\tGET TIC GRAPH\n") 194 cat("\t\tGET TIC GRAPH\n")
204 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") 195 getTICs(xcmsSet=xset, rt="corrected")
205 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) 196 getBPCs(xcmsSet=xset, rt="corrected")
206 } 197 }
207 198
208 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) { 199 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {
209 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput) 200 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
210 } 201 }