Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.r @ 0:fe1f0f16d9e6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
author lecorguille
date Thu, 08 Mar 2018 02:48:44 -0500
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children e6fdadaf039e
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1 #!/usr/bin/env Rscript
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3 # ----- LOG FILE -----
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4 log_file=file("log.txt", open = "wt")
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5 sink(log_file)
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6 sink(log_file, type = "output")
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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12 #Import the different functions
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13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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14 source_local("lib.r")
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16 pkgs <- c("xcms","batch","RColorBrewer")
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17 loadAndDisplayPackages(pkgs)
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18 cat("\n\n");
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21 # ----- ARGUMENTS -----
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22 cat("\tARGUMENTS INFO\n")
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23 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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26 cat("\n\n")
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28 # ----- PROCESSING INFILE -----
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29 cat("\tARGUMENTS PROCESSING INFO\n")
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31 #saving the specific parameters
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32 method <- args$method; args$method <- NULL
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34 cat("\n\n")
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37 # ----- ARGUMENTS PROCESSING -----
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38 cat("\tINFILE PROCESSING INFO\n")
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39
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40 #image is an .RData file necessary to use xset variable given by previous tools
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41 load(args$image); args$image=NULL
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42 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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44 # Handle infiles
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45 if (!exists("singlefile")) singlefile <- NULL
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46 if (!exists("zipfile")) zipfile <- NULL
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47 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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48 zipfile <- rawFilePath$zipfile
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49 singlefile <- rawFilePath$singlefile
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50 args <- rawFilePath$args
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51 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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54 cat("\n\n")
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57 # ----- MAIN PROCESSING INFO -----
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58 cat("\tMAIN PROCESSING INFO\n")
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61 cat("\t\tDRAW GRAPHICS\n")
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63 #@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
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64 getPlotTICs(xdata, pdfname="TICs.pdf")
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65 getPlotBPIs(xdata, pdfname="BPIs.pdf")
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67 cat("\n\n")
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69 # ----- EXPORT -----
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71 cat("\tXCMSnExp OBJECT INFO\n")
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72 print(xdata)
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73 cat("\n\n")
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75 cat("\txcmsSet OBJECT INFO\n")
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76 # Get the legacy xcmsSet object
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77 xset <- getxcmsSetObject(xdata)
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78 print(xset)
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79 cat("\n\n")
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82 cat("\tDONE\n")