Mercurial > repos > lecorguille > xcms_plot_chromatogram
comparison xcms_plot_chromatogram.r @ 13:024974037c4e draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
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date | Wed, 07 Apr 2021 12:07:49 +0000 |
parents | dbd877060ac3 |
children | 8846a03995d3 |
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12:0cab69429e1e | 13:024974037c4e |
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3 | 3 |
4 # ----- PACKAGE ----- | 4 # ----- PACKAGE ----- |
5 cat("\tSESSION INFO\n") | 5 cat("\tSESSION INFO\n") |
6 | 6 |
7 #Import the different functions | 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="/")) } | 8 source_local <- function(fname) { |
9 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) | |
10 } | |
9 source_local("lib.r") | 11 source_local("lib.r") |
10 | 12 |
11 pkgs <- c("xcms","batch","RColorBrewer") | 13 pkgs <- c("xcms", "batch", "RColorBrewer") |
12 loadAndDisplayPackages(pkgs) | 14 loadAndDisplayPackages(pkgs) |
13 cat("\n\n"); | 15 cat("\n\n"); |
14 | 16 |
15 | 17 |
16 # ----- ARGUMENTS ----- | 18 # ----- ARGUMENTS ----- |
17 cat("\tARGUMENTS INFO\n") | 19 cat("\tARGUMENTS INFO\n") |
18 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects | 20 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
19 write.table(as.matrix(args), col.names=F, quote=F, sep='\t') | 21 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") |
20 | 22 |
21 cat("\n\n") | 23 cat("\n\n") |
22 | 24 |
23 # ----- PROCESSING INFILE ----- | 25 # ----- PROCESSING INFILE ----- |
24 cat("\tARGUMENTS PROCESSING INFO\n") | 26 cat("\tARGUMENTS PROCESSING INFO\n") |
47 | 49 |
48 | 50 |
49 cat("\t\tDRAW GRAPHICS\n") | 51 cat("\t\tDRAW GRAPHICS\n") |
50 | 52 |
51 register(SerialParam()) | 53 register(SerialParam()) |
52 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } | 54 if (!exists("chromTIC") || is.null(chromTIC)) { |
53 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } | 55 cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") |
56 } | |
57 if (!exists("chromBPI") || is.null(chromBPI)) { | |
58 cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") | |
59 } | |
54 | 60 |
55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted | 61 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted |
56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted | 62 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted |
57 | 63 |
58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") | 64 getPlotChromatogram(chromTIC, xdata, pdfname = "TICs.pdf", aggregationFun = "sum") |
59 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max") | 65 getPlotChromatogram(chromBPI, xdata, pdfname = "BPIs.pdf", aggregationFun = "max") |
60 | 66 |
61 cat("\n\n") | 67 cat("\n\n") |
62 | 68 |
63 # ----- EXPORT ----- | 69 # ----- EXPORT ----- |
64 | 70 |
65 cat("\tXCMSnExp OBJECT INFO\n") | 71 cat("\tXCMSnExp OBJECT INFO\n") |
66 print(xdata) | 72 print(xdata) |
67 cat("\n\n") | 73 cat("\n\n") |
68 | 74 |
69 # 2020-01-17 - disable because xcms 3.4.4 raises an error with xdata build with xcms 3.6.1 | |
70 #cat("\txcmsSet OBJECT INFO\n") | |
71 # Get the legacy xcmsSet object | |
72 #xset <- getxcmsSetObject(xdata) | |
73 #print(xset) | |
74 #cat("\n\n") | |
75 | |
76 | 75 |
77 cat("\tDONE\n") | 76 cat("\tDONE\n") |