Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.r @ 3:60b156e58529 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
author lecorguille
date Thu, 05 Apr 2018 18:06:32 -0400
parents e6fdadaf039e
children 954499828c1d
comparison
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2:e6fdadaf039e 3:60b156e58529
37 mergeXDataReturn <- mergeXData(args) 37 mergeXDataReturn <- mergeXData(args)
38 xdata <- mergeXDataReturn$xdata 38 xdata <- mergeXDataReturn$xdata
39 singlefile <- mergeXDataReturn$singlefile 39 singlefile <- mergeXDataReturn$singlefile
40 md5sumList <- mergeXDataReturn$md5sumList 40 md5sumList <- mergeXDataReturn$md5sumList
41 sampleNamesList <- mergeXDataReturn$sampleNamesList 41 sampleNamesList <- mergeXDataReturn$sampleNamesList
42 chromTIC <- mergeXDataReturn$chromTIC
43 chromBPI <- mergeXDataReturn$chromBPI
42 44
43 cat("\n\n") 45 cat("\n\n")
44 46
45 47
46 # ----- MAIN PROCESSING INFO ----- 48 # ----- MAIN PROCESSING INFO -----
47 cat("\tMAIN PROCESSING INFO\n") 49 cat("\tMAIN PROCESSING INFO\n")
48 50
49 51
50 cat("\t\tDRAW GRAPHICS\n") 52 cat("\t\tDRAW GRAPHICS\n")
51 53
52 getPlotTICs(xdata, pdfname="TICs.pdf") 54 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
53 getPlotBPIs(xdata, pdfname="BPIs.pdf") 55 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
56
57 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
58 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")
54 59
55 cat("\n\n") 60 cat("\n\n")
56 61
57 # ----- EXPORT ----- 62 # ----- EXPORT -----
58 63