Mercurial > repos > pieterlukasse > prims_metabolomics
view metaMS_cmd_interface.r @ 42:664ccd5f7cf8
small fix for png method
author | pieter.lukasse@wur.nl |
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date | Fri, 07 Nov 2014 11:45:16 +0100 |
parents | e67149fbff20 |
children |
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## 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$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw") for (i in 1:length(groupidx1)) { figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="") html <- paste(html,"<img src='", "figure", i,".png' />", sep="") png( figureName, type="cairo" ) plot(eiccor, LC$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) } )