Mercurial > repos > pieterlukasse > prims_metabolomics
diff xcms_differential_analysis.r @ 8:ddef5534c294
new tool diffreport
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 06 Nov 2014 13:06:25 +0100 |
| parents | 627ddbd15823 |
| children |
line wrap: on
line diff
--- a/xcms_differential_analysis.r Thu Nov 06 11:32:16 2014 +0100 +++ b/xcms_differential_analysis.r Thu Nov 06 13:06:25 2014 +0100 @@ -38,22 +38,17 @@ xcmsSet <- readRDS(args.xsetData) # info: levels(xcmsSet@phenoData$class) also gives access to the class names - - reporttab <- diffreport(xcmsSet, args.class1, args.class2, args.htmlReportFile.files_path, args.topcount, metlin = 0.15, h=480, w=640) + dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) + reporttab <- diffreport(xcmsSet, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640) # write out tsv table: write.table(reporttab, args.outTable, sep="\t", row.names=FALSE) message("\nGenerating report.........") - # report - dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) - # setwd(file.path(args.htmlReportFile.files_path)) - file.rename("fig_eic", paste(args.htmlReportFile.files_path, "/fig_eic")) - cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile) #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile) - figuresPath <- paste(args.htmlReportFile.files_path, "_eic", sep="") + figuresPath <- paste(args.htmlReportFile.files_path, "/fig_eic", sep="") message(figuresPath) listOfFiles <- list.files(path = figuresPath) for (i in 1:length(listOfFiles))