Mercurial > repos > pieterlukasse > prims_metabolomics

comparison xcms_differential_analysis.r @ 55:543958f75e83

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
small fix
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 14:45:28 +0100
parents 10f3cb998c4e
children
comparison
equal deleted inserted replaced
54:10f3cb998c4e 55:543958f75e83
48 48
49 49
50 # info: levels(xcmsSet@phenoData$class) also gives access to the class names 50 # info: levels(xcmsSet@phenoData$class) also gives access to the class names
51 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE) 51 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
52 # set cairo as default for png plots: 52 # set cairo as default for png plots:
53 x11 = function (...) grDevices::x11(...,type='cairo') 53 png = function (...) grDevices::png(...,type='cairo')
54 # run diffreport 54 # run diffreport
55 reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640) 55 reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
56 56
57 # write out tsv table: 57 # write out tsv table:
58 write.table(reporttab, args.outTable, sep="\t", row.names=FALSE) 58 write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)