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41
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1 ## read args:
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2 args <- commandArgs(TRUE)
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3 ## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
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4 args.constructedDB <- args[1]
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5 ## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
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6 args.dataZip <- args[2]
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7 args.zipExtrDir <- paste(args[2],"dir/")
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8 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
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9 args.settings <- args[3]
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10
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11 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
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12 args.outAnnotationTable <- args[4]
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13 args.outLogFile <- args[5]
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14 args.xsetOut <- args[6]
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15
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16 ## report files
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17 args.htmlReportFile <- args[7]
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18 args.htmlReportFile.files_path <- args[8]
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19
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20 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
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21 msg <- file(args.outLogFile, open="wt")
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22 sink(msg, type="message")
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23 sink(msg, type="output")
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24
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25 cat("\nSettings used===============:\n")
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26 cat(readChar(args.settings, 1e5))
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27
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28
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29 tryCatch(
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30 {
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31 library(metaMS)
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32
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33 ## load the constructed DB :
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34 tempEnv <- new.env()
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35 testDB <- load(args.constructedDB, envir=tempEnv)
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36
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37 ## load the data files from a zip file
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38 files <- unzip(args.dataZip, exdir=args.zipExtrDir)
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39
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40 ## load settings "script" into "customMetaMSsettings"
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41 source(args.settings, local=tempEnv)
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42 message(paste(" loaded : ", args.settings))
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43
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44 # Just to highlight: if you want to use more than one
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45 # trigger runLC:
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46 LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
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47
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48 # write out runLC annotation results:
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49 write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t", row.names=FALSE)
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50
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51 # the used constructed DB (write to log):
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52 cat("\nConstructed DB info===============:\n")
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53 str(tempEnv[[testDB[1]]]$Info)
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54 cat("\nConstructed DB table===============:\n")
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55 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
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56 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
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57 # save xset as rdata:
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58 xsetData <- LC$xset@xcmsSet
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59 saveRDS(xsetData, file=args.xsetOut)
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60
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61 message("\nGenerating report.........")
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62 # report
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63 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
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64 setwd(file.path(args.htmlReportFile.files_path))
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65 html <- "<html><body><h1>Extracted Ion Chromatograms of groups with more than 3 peaks</h1>"
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66
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67 LC$xset@xcmsSet
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68 gt <- groups(LC$xset@xcmsSet)
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69 colnames(gt)
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70 groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
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71 if (length(groupidx1) > 0)
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72 {
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73 eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1))
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74 eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw")
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75 for (i in 1:length(groupidx1))
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76 {
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77 figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
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78 html <- paste(html,"<img src='", "figure", i,".png' />", sep="")
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42
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79 png( figureName, type="cairo" )
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41
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80 plot(eiccor, LC$xset@xcmsSet, groupidx = i)
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81 devname = dev.off()
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82 }
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83 }
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84
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85
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86 html <- paste(html,"</body><html>")
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87 message("finished generating report")
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88 write(html,file=args.htmlReportFile)
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89 # unlink(args.htmlReportFile)
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90 cat("\nWarnings================:\n")
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91 str( warnings() )
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92 },
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93 error=function(cond) {
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94 sink(NULL, type="message") # default setting
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95 sink(stderr(), type="output")
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96 message("\nERROR: ===========\n")
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97 print(cond)
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98 }
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99 )
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