Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.r @ 13:9a5b4a1b9880 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 13:26:21 +0000
parents 5f0327d6f474
children bf87ce10267e
comparison
equal deleted inserted replaced
12:10315a095169 13:9a5b4a1b9880
46 cat("\tMAIN PROCESSING INFO\n") 46 cat("\tMAIN PROCESSING INFO\n")
47 47
48 48
49 cat("\t\tDRAW GRAPHICS\n") 49 cat("\t\tDRAW GRAPHICS\n")
50 50
51 if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } 51 register(SerialParam())
52 if (!is.null(chromBPI) || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } 52 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") }
53 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
53 54
54 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted 55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
55 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted 56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
56 57
57 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") 58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
63 64
64 cat("\tXCMSnExp OBJECT INFO\n") 65 cat("\tXCMSnExp OBJECT INFO\n")
65 print(xdata) 66 print(xdata)
66 cat("\n\n") 67 cat("\n\n")
67 68
68 cat("\txcmsSet OBJECT INFO\n") 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")
69 # Get the legacy xcmsSet object 71 # Get the legacy xcmsSet object
70 xset <- getxcmsSetObject(xdata) 72 #xset <- getxcmsSetObject(xdata)
71 print(xset) 73 #print(xset)
72 cat("\n\n") 74 #cat("\n\n")
73 75
74 76
75 cat("\tDONE\n") 77 cat("\tDONE\n")