--- /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")