Mercurial > repos > lecorguille > xcms_plot_chromatogram
diff xcms_plot_chromatogram.r @ 6:e0b5c547925d draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author | lecorguille |
---|---|
date | Wed, 05 Sep 2018 05:57:13 -0400 |
parents | 954499828c1d |
children | a4a1143a202a |
line wrap: on
line diff
--- a/xcms_plot_chromatogram.r Fri Aug 31 08:59:44 2018 -0400 +++ b/xcms_plot_chromatogram.r Wed Sep 05 05:57:13 2018 -0400 @@ -1,10 +1,5 @@ #!/usr/bin/env Rscript -# ----- LOG FILE ----- -log_file=file("log.txt", open = "wt") -sink(log_file) -sink(log_file, type = "output") - # ----- PACKAGE ----- cat("\tSESSION INFO\n") @@ -41,6 +36,8 @@ sampleNamesList <- mergeXDataReturn$sampleNamesList chromTIC <- mergeXDataReturn$chromTIC chromBPI <- mergeXDataReturn$chromBPI +chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted +chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted cat("\n\n") @@ -51,11 +48,11 @@ cat("\t\tDRAW GRAPHICS\n") -if (!exists("chromTIC") || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } -if (!exists("chromBPI") || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } +if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } +if (!is.null(chromBPI) || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } -if (exists("chromTIC_adjusted")) chromTIC <- chromTIC_adjusted -if (exists("chromBPI_adjusted")) chromBPI <- chromBPI_adjusted +if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted +if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max")