Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.r @ 13:024974037c4e draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 12:07:49 +0000
parents dbd877060ac3
children 8846a03995d3
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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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4 # ----- PACKAGE -----
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lecorguille
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5 cat("\tSESSION INFO\n")
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7 #Import the different functions
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8 source_local <- function(fname) {
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9 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
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10 }
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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11 source_local("lib.r")
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12
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13 pkgs <- c("xcms", "batch", "RColorBrewer")
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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14 loadAndDisplayPackages(pkgs)
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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15 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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18 # ----- ARGUMENTS -----
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19 cat("\tARGUMENTS INFO\n")
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20 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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21 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 cat("\n\n")
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25 # ----- PROCESSING INFILE -----
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26 cat("\tARGUMENTS PROCESSING INFO\n")
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28 cat("\n\n")
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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31 # ----- ARGUMENTS PROCESSING -----
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32 cat("\tINFILE PROCESSING INFO\n")
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34 mergeXDataReturn <- mergeXData(args)
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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35 xdata <- mergeXDataReturn$xdata
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 singlefile <- mergeXDataReturn$singlefile
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37 md5sumList <- mergeXDataReturn$md5sumList
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38 sampleNamesList <- mergeXDataReturn$sampleNamesList
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39 chromTIC <- mergeXDataReturn$chromTIC
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40 chromBPI <- mergeXDataReturn$chromBPI
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41 chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted
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42 chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted
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44 cat("\n\n")
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47 # ----- MAIN PROCESSING INFO -----
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48 cat("\tMAIN PROCESSING INFO\n")
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51 cat("\t\tDRAW GRAPHICS\n")
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53 register(SerialParam())
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54 if (!exists("chromTIC") || is.null(chromTIC)) {
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55 cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum")
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56 }
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57 if (!exists("chromBPI") || is.null(chromBPI)) {
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58 cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max")
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59 }
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61 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
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62 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
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63
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64 getPlotChromatogram(chromTIC, xdata, pdfname = "TICs.pdf", aggregationFun = "sum")
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65 getPlotChromatogram(chromBPI, xdata, pdfname = "BPIs.pdf", aggregationFun = "max")
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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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76 cat("\tDONE\n")