Mercurial > repos > pieterlukasse > prims_metabolomics
diff metaMS_cmd_interface.r @ 41:e67149fbff20
small changes/improvements;
new metams and xcms tools
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 06 Nov 2014 16:14:44 +0100 |
| parents | |
| children | 664ccd5f7cf8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaMS_cmd_interface.r Thu Nov 06 16:14:44 2014 +0100 @@ -0,0 +1,99 @@ +## read args: +args <- commandArgs(TRUE) +## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData" +args.constructedDB <- args[1] +## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/" +args.dataZip <- args[2] +args.zipExtrDir <- paste(args[2],"dir/") +## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings" +args.settings <- args[3] + +## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt" +args.outAnnotationTable <- args[4] +args.outLogFile <- args[5] +args.xsetOut <- args[6] + +## report files +args.htmlReportFile <- args[7] +args.htmlReportFile.files_path <- args[8] + +# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 +msg <- file(args.outLogFile, open="wt") +sink(msg, type="message") +sink(msg, type="output") + +cat("\nSettings used===============:\n") +cat(readChar(args.settings, 1e5)) + + +tryCatch( + { + library(metaMS) + + ## load the constructed DB : + tempEnv <- new.env() + testDB <- load(args.constructedDB, envir=tempEnv) + + ## load the data files from a zip file + files <- unzip(args.dataZip, exdir=args.zipExtrDir) + + ## load settings "script" into "customMetaMSsettings" + source(args.settings, local=tempEnv) + message(paste(" loaded : ", args.settings)) + + # Just to highlight: if you want to use more than one + # trigger runLC: + LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE) + + # write out runLC annotation results: + write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t", row.names=FALSE) + + # the used constructed DB (write to log): + cat("\nConstructed DB info===============:\n") + str(tempEnv[[testDB[1]]]$Info) + cat("\nConstructed DB table===============:\n") + write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE) + write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE) + # save xset as rdata: + xsetData <- LC$xset@xcmsSet + saveRDS(xsetData, file=args.xsetOut) + + message("\nGenerating report.........") + # report + dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) + setwd(file.path(args.htmlReportFile.files_path)) + html <- "<html><body><h1>Extracted Ion Chromatograms of groups with more than 3 peaks</h1>" + + LC$xset@xcmsSet + gt <- groups(LC$xset@xcmsSet) + colnames(gt) + groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3) + if (length(groupidx1) > 0) + { + eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1)) + eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw") + for (i in 1:length(groupidx1)) + { + figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="") + html <- paste(html,"<img src='", "figure", i,".png' />", sep="") + png( figureName ) + plot(eiccor, LC$xset@xcmsSet, groupidx = i) + devname = dev.off() + } + } + + + html <- paste(html,"</body><html>") + message("finished generating report") + write(html,file=args.htmlReportFile) + # unlink(args.htmlReportFile) + cat("\nWarnings================:\n") + str( warnings() ) + }, + error=function(cond) { + sink(NULL, type="message") # default setting + sink(stderr(), type="output") + message("\nERROR: ===========\n") + print(cond) + } + )