Mercurial > repos > lecorguille > xcms_plot_chromatogram
diff xcms_plot_chromatogram.r @ 0:c749bfd3410e draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
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date | Tue, 18 Sep 2018 16:06:05 -0400 |
parents | |
children | 7c0cc7a3c3db |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_plot_chromatogram.r Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,76 @@ +#!/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") +source_local("lib-xcms3.x.x.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") + +if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } +if (!is.null(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") + +cat("\txcmsSet OBJECT INFO\n") +# Get the legacy xcmsSet object +xset <- getxcmsSetObject(xdata) +print(xset) +cat("\n\n") + + +cat("\tDONE\n")