Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.r @ 14:8846a03995d3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:18:38 +0000
parents 024974037c4e
children 9291271ec4d9
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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 -----
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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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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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 #Import the different functions
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8 source_local <- function(fname) {
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workflow4metabolomics
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9 argv <- commandArgs(trailingOnly = FALSE)
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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10 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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11 source(paste(base_dir, fname, sep = "/"))
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12 }
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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13 source_local("lib.r")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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14
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workflow4metabolomics
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15 pkgs <- c("xcms", "batch", "RColorBrewer")
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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16 loadAndDisplayPackages(pkgs)
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17 cat("\n\n")
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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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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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20 # ----- ARGUMENTS -----
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21 cat("\tARGUMENTS INFO\n")
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22 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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23 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
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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
lecorguille
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25 cat("\n\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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27 # ----- PROCESSING INFILE -----
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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28 cat("\tARGUMENTS PROCESSING INFO\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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30 cat("\n\n")
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33 # ----- ARGUMENTS PROCESSING -----
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 cat("\tINFILE PROCESSING INFO\n")
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 mergeXDataReturn <- mergeXData(args)
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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37 xdata <- mergeXDataReturn$xdata
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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38 singlefile <- mergeXDataReturn$singlefile
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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39 md5sumList <- mergeXDataReturn$md5sumList
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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40 sampleNamesList <- mergeXDataReturn$sampleNamesList
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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41 chromTIC <- mergeXDataReturn$chromTIC
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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42 chromBPI <- mergeXDataReturn$chromBPI
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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43 chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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44 chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46 cat("\n\n")
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49 # ----- MAIN PROCESSING INFO -----
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50 cat("\tMAIN PROCESSING INFO\n")
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53 cat("\t\tDRAW GRAPHICS\n")
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55 register(SerialParam())
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56 if (!exists("chromTIC") || is.null(chromTIC)) {
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57 cat("\t\t\tCompute TIC\n")
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58 chromTIC <- chromatogram(xdata, aggregationFun = "sum")
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59 }
024974037c4e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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60 if (!exists("chromBPI") || is.null(chromBPI)) {
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61 cat("\t\t\tCompute BPI\n")
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62 chromBPI <- chromatogram(xdata, aggregationFun = "max")
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63 }
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65 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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66 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
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67
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68 getPlotChromatogram(chromTIC, xdata, pdfname = "TICs.pdf", aggregationFun = "sum")
024974037c4e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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69 getPlotChromatogram(chromBPI, xdata, pdfname = "BPIs.pdf", aggregationFun = "max")
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71 cat("\n\n")
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73 # ----- EXPORT -----
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75 cat("\tXCMSnExp OBJECT INFO\n")
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76 print(xdata)
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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77 cat("\n\n")
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80 cat("\tDONE\n")