Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.r @ 0:c749bfd3410e draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:06:05 -0400
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children 7c0cc7a3c3db
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-1:000000000000 0:c749bfd3410e
1 #!/usr/bin/env Rscript
2
3
4 # ----- PACKAGE -----
5 cat("\tSESSION INFO\n")
6
7 #Import the different functions
8 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
9 source_local("lib.r")
10 source_local("lib-xcms3.x.x.r")
11
12 pkgs <- c("xcms","batch","RColorBrewer")
13 loadAndDisplayPackages(pkgs)
14 cat("\n\n");
15
16
17 # ----- ARGUMENTS -----
18 cat("\tARGUMENTS INFO\n")
19 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
20 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
21
22 cat("\n\n")
23
24 # ----- PROCESSING INFILE -----
25 cat("\tARGUMENTS PROCESSING INFO\n")
26
27 cat("\n\n")
28
29
30 # ----- ARGUMENTS PROCESSING -----
31 cat("\tINFILE PROCESSING INFO\n")
32
33 mergeXDataReturn <- mergeXData(args)
34 xdata <- mergeXDataReturn$xdata
35 singlefile <- mergeXDataReturn$singlefile
36 md5sumList <- mergeXDataReturn$md5sumList
37 sampleNamesList <- mergeXDataReturn$sampleNamesList
38 chromTIC <- mergeXDataReturn$chromTIC
39 chromBPI <- mergeXDataReturn$chromBPI
40 chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted
41 chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted
42
43 cat("\n\n")
44
45
46 # ----- MAIN PROCESSING INFO -----
47 cat("\tMAIN PROCESSING INFO\n")
48
49
50 cat("\t\tDRAW GRAPHICS\n")
51
52 if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
53 if (!is.null(chromBPI) || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
54
55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
57
58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
59 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")
60
61 cat("\n\n")
62
63 # ----- EXPORT -----
64
65 cat("\tXCMSnExp OBJECT INFO\n")
66 print(xdata)
67 cat("\n\n")
68
69 cat("\txcmsSet OBJECT INFO\n")
70 # Get the legacy xcmsSet object
71 xset <- getxcmsSetObject(xdata)
72 print(xset)
73 cat("\n\n")
74
75
76 cat("\tDONE\n")