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1 ## =========== This is a copy that can be executed in R environment directly for interactive tests
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2
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3 ## read args:
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4 args <- "test"
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5
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6 ## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
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7 args.constructedDB <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/LCDBtest.RData"
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8 ## 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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9 args.dataZip <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/extdata.zip"
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10 args.zipExtrDir <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/zipOut"
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11 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
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12 args.settings <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/example_settings.txt"
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13
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14 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
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15 args.outAnnotationTable <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/out/annotationTable.txt"
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16 args.outLogFile <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/out/logfile.txt"
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17
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18 library(metaMS)
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19
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20 ## load the constructed DB :
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21 tempEnv <- new.env()
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22 testDB <- load(args.constructedDB, envir=tempEnv)
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23
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24 ## load the data files from a zip file
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25 files <- unzip(args.dataZip, exdir=args.zipExtrDir)
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26
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27 ## load settings "script" into "customMetaMSsettings"
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28 source(args.settings, local=tempEnv)
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29
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30
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31 # Just to highlight: if you want to use more than one
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32 # trigger runLC:
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33 LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
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34
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35 # write out runLC annotation results:
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36 write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t", row.names=FALSE)
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37
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38 # the used constructed DB (write to log):
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39 sink( args.outLogFile )
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40 cat("Constructed DB info===============:")
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41 str(tempEnv[[testDB[1]]]$Info)
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42 cat("Constructed DB table===============:")
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43 sink()
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44 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
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45 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
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46
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47 # report
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48 LC$xset@xcmsSet
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49 gt <- groups(LC$xset@xcmsSet)
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50 colnames(gt)
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51 groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
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52 if (length(groupidx1) > 0)
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53 {
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54 eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1))
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55 eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw")
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56 for (i in 1:length(groupidx1))
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57 {
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58 png( paste("E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/out/outplot", i,".png", sep="") )
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59 plot(eiccor, LC$xset@xcmsSet, groupidx = i)
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60 devname = dev.off()
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61 }
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62
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63 }
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