6
+ − 1 ## read args:
+ − 2 args <- commandArgs(TRUE)
+ − 3 ## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
+ − 4 args.dataZip <- args[1]
+ − 5 args.zipExtrDir <- sub("\\.","_",paste(args[1],"dir", sep=""))
+ − 6 dir.create(file.path(args.zipExtrDir), showWarnings = FALSE, recursive = TRUE)
+ − 7 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
+ − 8 args.settings <- args[2]
+ − 9
+ − 10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
+ − 11 args.outPeakTable <- args[3]
+ − 12 args.xsetOut <- args[4]
+ − 13
+ − 14 # polarity as explicit parameter:
+ − 15 args.runLC_polarity <- args[5]
+ − 16
+ − 17 ## report files
+ − 18 args.htmlReportFile <- args[6]
+ − 19 args.htmlReportFile.files_path <- args[7]
+ − 20
+ − 21
+ − 22 if (length(args) == 8)
+ − 23 {
+ − 24 args.outLogFile <- args[8]
+ − 25 # suppress messages:
+ − 26 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+ − 27 msg <- file(args.outLogFile, open="wt")
+ − 28 sink(msg, type="message")
+ − 29 sink(msg, type="output")
+ − 30 }
+ − 31
+ − 32 cat("\nSettings used===============:\n")
+ − 33 cat(readChar(args.settings, 1e5))
+ − 34
+ − 35
+ − 36 tryCatch(
+ − 37 {
+ − 38 library(metaMS)
+ − 39
+ − 40 ## load the data files from a zip file
+ − 41 files <- unzip(args.dataZip, exdir=args.zipExtrDir)
+ − 42
+ − 43 ## load settings "script" into "customMetaMSsettings"
+ − 44 tempEnv <- new.env()
+ − 45 source(args.settings, local=tempEnv)
+ − 46 message(paste(" loaded : ", args.settings))
+ − 47 allSettings <- tempEnv[["customMetaMSsettings"]]
+ − 48
+ − 49 # trigger runLC:
+ − 50 LC <- runLC(files, settings = allSettings, polarity=args.runLC_polarity, nSlaves=20, returnXset = TRUE)
+ − 51
+ − 52 # write out runLC annotation results:
+ − 53 write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE)
+ − 54
+ − 55 # save xset as rdata:
+ − 56 xsAnnotatePreparedData <- LC$xset
+ − 57 saveRDS(xsAnnotatePreparedData, file=args.xsetOut)
+ − 58
+ − 59 message("\nGenerating report.........")
+ − 60 # report
+ − 61 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
+ − 62 html <- "<html><body><h1>Info on alignment quality </h1>"
+ − 63 # TODO add (nr and mass error) and group size
+ − 64
+ − 65 message("\nPlotting figures... ")
+ − 66 figureName <- paste(args.htmlReportFile.files_path, "/figure_retcor.png", sep="")
+ − 67 html <- paste(html,"<img src='figure_retcor.png' /><br/>", sep="")
+ − 68 png( figureName, type="cairo", width=1100,height=600 )
+ − 69 retcor(LC$xset@xcmsSet, method="peakgroups", plottype = "mdevden")
+ − 70 html <- paste(html,"<a>*NB: retention time correction plot based on 'peakgroups' option with default settings. This is not the plot matching the exact settings used in the run,
+ − 71 but just intended to give a rough estimate of the retention time shifts present in the data. A more accurate plot will be available once
+ − 72 this option is added in metaMS API. </a><br/>", sep="")
+ − 73 devname = dev.off()
+ − 74
+ − 75
+ − 76 gt <- groups(LC$xset@xcmsSet)
+ − 77 groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
+ − 78
+ − 79 html <- paste(html,"</body><html>")
+ − 80 message("finished generating report")
+ − 81 write(html,file=args.htmlReportFile)
+ − 82 # unlink(args.htmlReportFile)
+ − 83 cat("\nWarnings================:\n")
+ − 84 str( warnings() )
+ − 85 },
+ − 86 error=function(cond) {
+ − 87 sink(NULL, type="message") # default setting
+ − 88 sink(stderr(), type="output")
+ − 89 message("\nERROR: ===========\n")
+ − 90 print(cond)
+ − 91 }
+ − 92 )
