Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.r @ 4:954499828c1d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d6c70bb63fd89932c9f95010d6f2c9297df96155
author lecorguille
date Fri, 06 Apr 2018 11:12:44 -0400
parents 60b156e58529
children e0b5c547925d
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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 cat("\n\n")
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34 # ----- ARGUMENTS PROCESSING -----
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35 cat("\tINFILE PROCESSING INFO\n")
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37 mergeXDataReturn <- mergeXData(args)
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38 xdata <- mergeXDataReturn$xdata
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39 singlefile <- mergeXDataReturn$singlefile
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40 md5sumList <- mergeXDataReturn$md5sumList
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41 sampleNamesList <- mergeXDataReturn$sampleNamesList
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42 chromTIC <- mergeXDataReturn$chromTIC
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43 chromBPI <- mergeXDataReturn$chromBPI
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45 cat("\n\n")
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48 # ----- MAIN PROCESSING INFO -----
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49 cat("\tMAIN PROCESSING INFO\n")
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52 cat("\t\tDRAW GRAPHICS\n")
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54 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
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55 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
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57 if (exists("chromTIC_adjusted")) chromTIC <- chromTIC_adjusted
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58 if (exists("chromBPI_adjusted")) chromBPI <- chromBPI_adjusted
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60 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
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61 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")
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63 cat("\n\n")
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65 # ----- EXPORT -----
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67 cat("\tXCMSnExp OBJECT INFO\n")
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68 print(xdata)
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69 cat("\n\n")
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71 cat("\txcmsSet OBJECT INFO\n")
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72 # Get the legacy xcmsSet object
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73 xset <- getxcmsSetObject(xdata)
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74 print(xset)
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75 cat("\n\n")
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78 cat("\tDONE\n")