Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.r @ 6:e0b5c547925d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:57:13 -0400
parents 954499828c1d
children a4a1143a202a
comparison
equal deleted inserted replaced
5:a5ba342e72e0 6:e0b5c547925d
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2
3 # ----- LOG FILE -----
4 log_file=file("log.txt", open = "wt")
5 sink(log_file)
6 sink(log_file, type = "output")
7 2
8 3
9 # ----- PACKAGE ----- 4 # ----- PACKAGE -----
10 cat("\tSESSION INFO\n") 5 cat("\tSESSION INFO\n")
11 6
39 singlefile <- mergeXDataReturn$singlefile 34 singlefile <- mergeXDataReturn$singlefile
40 md5sumList <- mergeXDataReturn$md5sumList 35 md5sumList <- mergeXDataReturn$md5sumList
41 sampleNamesList <- mergeXDataReturn$sampleNamesList 36 sampleNamesList <- mergeXDataReturn$sampleNamesList
42 chromTIC <- mergeXDataReturn$chromTIC 37 chromTIC <- mergeXDataReturn$chromTIC
43 chromBPI <- mergeXDataReturn$chromBPI 38 chromBPI <- mergeXDataReturn$chromBPI
39 chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted
40 chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted
44 41
45 cat("\n\n") 42 cat("\n\n")
46 43
47 44
48 # ----- MAIN PROCESSING INFO ----- 45 # ----- MAIN PROCESSING INFO -----
49 cat("\tMAIN PROCESSING INFO\n") 46 cat("\tMAIN PROCESSING INFO\n")
50 47
51 48
52 cat("\t\tDRAW GRAPHICS\n") 49 cat("\t\tDRAW GRAPHICS\n")
53 50
54 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } 51 if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
55 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } 52 if (!is.null(chromBPI) || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
56 53
57 if (exists("chromTIC_adjusted")) chromTIC <- chromTIC_adjusted 54 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
58 if (exists("chromBPI_adjusted")) chromBPI <- chromBPI_adjusted 55 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
59 56
60 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") 57 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
61 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max") 58 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")
62 59
63 cat("\n\n") 60 cat("\n\n")