Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.r @ 4:954499828c1d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d6c70bb63fd89932c9f95010d6f2c9297df96155
author lecorguille
date Fri, 06 Apr 2018 11:12:44 -0400
parents 60b156e58529
children e0b5c547925d
comparison
equal deleted inserted replaced
3:60b156e58529 4:954499828c1d
52 cat("\t\tDRAW GRAPHICS\n") 52 cat("\t\tDRAW GRAPHICS\n")
53 53
54 if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } 54 if (!exists("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") } 55 if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") }
56 56
57 if (exists("chromTIC_adjusted")) chromTIC <- chromTIC_adjusted
58 if (exists("chromBPI_adjusted")) chromBPI <- chromBPI_adjusted
59
57 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") 60 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum")
58 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max") 61 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")
59 62
60 cat("\n\n") 63 cat("\n\n")
61 64