Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.r @ 10:dbd877060ac3 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:30:06 -0500
parents 271c9d5f0d10
children 024974037c4e
comparison
equal deleted inserted replaced
9:271c9d5f0d10 10:dbd877060ac3
47 47
48 48
49 cat("\t\tDRAW GRAPHICS\n") 49 cat("\t\tDRAW GRAPHICS\n")
50 50
51 register(SerialParam()) 51 register(SerialParam())
52 if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } 52 if (!exists("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") } 53 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
54 54
55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted 55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted
56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted 56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted
57 57
58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") 58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
64 64
65 cat("\tXCMSnExp OBJECT INFO\n") 65 cat("\tXCMSnExp OBJECT INFO\n")
66 print(xdata) 66 print(xdata)
67 cat("\n\n") 67 cat("\n\n")
68 68
69 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")
70 # Get the legacy xcmsSet object 71 # Get the legacy xcmsSet object
71 xset <- getxcmsSetObject(xdata) 72 #xset <- getxcmsSetObject(xdata)
72 print(xset) 73 #print(xset)
73 cat("\n\n") 74 #cat("\n\n")
74 75
75 76
76 cat("\tDONE\n") 77 cat("\tDONE\n")