Mercurial > repos > lecorguille > xcms_group

diff xcms_group.r @ 40:87c082612887 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Fri, 08 Feb 2019 09:59:46 -0500
parents eddc995c6df1
children a031435293aa
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--- a/xcms_group.r	Fri Nov 09 15:28:19 2018 -0500
+++ b/xcms_group.r	Fri Feb 08 09:59:46 2019 -0500
@@ -12,7 +12,6 @@
 #Import the different functions
 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
 source_local("lib.r")
-source_local("lib-xcms3.x.x.r")
 
 pkgs <- c("xcms","batch","RColorBrewer")
 loadAndDisplayPackages(pkgs)
@@ -84,7 +83,7 @@
 
 
 cat("\t\tDRAW GRAPHICS\n")
-getPlotChromPeakDensity(xdata)
+getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
 
 if (exists("intval")) {
     getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")