Mercurial > repos > lecorguille > xcms_plot_chromatogram
view xcms_plot_chromatogram.r @ 10:dbd877060ac3 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author | workflow4metabolomics |
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date | Wed, 12 Feb 2020 08:30:06 -0500 |
parents | 271c9d5f0d10 |
children | 024974037c4e |
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#!/usr/bin/env Rscript # ----- PACKAGE ----- cat("\tSESSION INFO\n") #Import the different functions source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } source_local("lib.r") pkgs <- c("xcms","batch","RColorBrewer") loadAndDisplayPackages(pkgs) cat("\n\n"); # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects write.table(as.matrix(args), col.names=F, quote=F, sep='\t') cat("\n\n") # ----- PROCESSING INFILE ----- cat("\tARGUMENTS PROCESSING INFO\n") cat("\n\n") # ----- ARGUMENTS PROCESSING ----- cat("\tINFILE PROCESSING INFO\n") mergeXDataReturn <- mergeXData(args) xdata <- mergeXDataReturn$xdata singlefile <- mergeXDataReturn$singlefile md5sumList <- mergeXDataReturn$md5sumList sampleNamesList <- mergeXDataReturn$sampleNamesList chromTIC <- mergeXDataReturn$chromTIC chromBPI <- mergeXDataReturn$chromBPI chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted cat("\n\n") # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") cat("\t\tDRAW GRAPHICS\n") register(SerialParam()) if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max") cat("\n\n") # ----- EXPORT ----- cat("\tXCMSnExp OBJECT INFO\n") print(xdata) cat("\n\n") # 2020-01-17 - disable because xcms 3.4.4 raises an error with xdata build with xcms 3.6.1 #cat("\txcmsSet OBJECT INFO\n") # Get the legacy xcmsSet object #xset <- getxcmsSetObject(xdata) #print(xset) #cat("\n\n") cat("\tDONE\n")