Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.r @ 10:dbd877060ac3 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:30:06 -0500
parents 271c9d5f0d10
children 024974037c4e
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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1 #!/usr/bin/env Rscript
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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4 # ----- PACKAGE -----
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5 cat("\tSESSION INFO\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 #Import the different functions
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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8 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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9 source_local("lib.r")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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11 pkgs <- c("xcms","batch","RColorBrewer")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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12 loadAndDisplayPackages(pkgs)
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 cat("\n\n");
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # ----- ARGUMENTS -----
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17 cat("\tARGUMENTS INFO\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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19 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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21 cat("\n\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 # ----- PROCESSING INFILE -----
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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24 cat("\tARGUMENTS PROCESSING INFO\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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26 cat("\n\n")
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29 # ----- ARGUMENTS PROCESSING -----
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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30 cat("\tINFILE PROCESSING INFO\n")
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32 mergeXDataReturn <- mergeXData(args)
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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33 xdata <- mergeXDataReturn$xdata
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 singlefile <- mergeXDataReturn$singlefile
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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35 md5sumList <- mergeXDataReturn$md5sumList
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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36 sampleNamesList <- mergeXDataReturn$sampleNamesList
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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37 chromTIC <- mergeXDataReturn$chromTIC
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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38 chromBPI <- mergeXDataReturn$chromBPI
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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39 chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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40 chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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42 cat("\n\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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45 # ----- MAIN PROCESSING INFO -----
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46 cat("\tMAIN PROCESSING INFO\n")
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49 cat("\t\tDRAW GRAPHICS\n")
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51 register(SerialParam())
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52 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
dbd877060ac3 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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53 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
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55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
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56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
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58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
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59 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")
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61 cat("\n\n")
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63 # ----- EXPORT -----
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65 cat("\tXCMSnExp OBJECT INFO\n")
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66 print(xdata)
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67 cat("\n\n")
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68
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69 # 2020-01-17 - disable because xcms 3.4.4 raises an error with xdata build with xcms 3.6.1
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70 #cat("\txcmsSet OBJECT INFO\n")
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71 # Get the legacy xcmsSet object
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72 #xset <- getxcmsSetObject(xdata)
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73 #print(xset)
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74 #cat("\n\n")
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77 cat("\tDONE\n")