Mercurial > repos > pieterlukasse > prims_metabolomics

annotate metaMS_cmd_pick_and_group.r @ 49:f772a5caa86a

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Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
parents
children 684d2341968c
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49
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1 ## read args:
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2 args <- commandArgs(TRUE)
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3 ## 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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4 args.dataZip <- args[1]
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5 args.zipExtrDir <- sub("\\.","_",paste(args[1],"dir", sep=""))
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6 dir.create(file.path(args.zipExtrDir), showWarnings = FALSE, recursive = TRUE)
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7 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
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8 args.settings <- args[2]
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9
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10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
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11 args.outPeakTable <- args[3]
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12 args.xsetOut <- args[4]
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13
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14 ## report files
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15 args.htmlReportFile <- args[5]
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16 args.htmlReportFile.files_path <- args[6]
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17
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18
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19 if (length(args) == 7)
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20 {
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21 args.outLogFile <- args[7]
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22 # suppress messages:
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23 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
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24 msg <- file(args.outLogFile, open="wt")
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25 sink(msg, type="message")
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26 sink(msg, type="output")
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27 }
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28
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29 cat("\nSettings used===============:\n")
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30 cat(readChar(args.settings, 1e5))
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31
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32
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33 tryCatch(
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34 {
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35 library(metaMS)
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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 tempEnv <- new.env()
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42 source(args.settings, local=tempEnv)
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43 message(paste(" loaded : ", args.settings))
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44 allSettings <- tempEnv[["customMetaMSsettings"]]
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45
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46 # trigger runLC:
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47 LC <- runLC(files, settings = allSettings, nSlaves=20, returnXset = TRUE)
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48
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49 # write out runLC annotation results:
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50 write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE)
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51
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52 # save xset as rdata:
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53 xsAnnotatePreparedData <- LC$xset
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54 saveRDS(xsAnnotatePreparedData, file=args.xsetOut)
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55
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56 message("\nGenerating report.........")
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57 # report
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58 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
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59 html <- "<html><body><h1>Info on alignment quality </h1>"
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60 # TODO add (nr and mass error) and group size
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61
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62 message("\nPlotting figures... ")
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63 figureName <- paste(args.htmlReportFile.files_path, "/figure_retcor.png", sep="")
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64 html <- paste(html,"<img src='figure_retcor.png' /><br/>", sep="")
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65 png( figureName, type="cairo", width=1100,height=600 )
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66 retcor(LC$xset@xcmsSet, method="peakgroups", plottype = "mdevden")
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67 html <- paste(html,"<a>*NB: retention time correction plot based on 'peakgroups' option with default settings. This is not the plot matching the exact settings used in the run,
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68 but just intended to give a rough estimate of the retention time shifts present in the data. A more accurate plot will be available once
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69 this option is added in metaMS API. </a><br/>", sep="")
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70 devname = dev.off()
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71
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72
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73 gt <- groups(LC$xset@xcmsSet)
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74 groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
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75
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76 html <- paste(html,"</body><html>")
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77 message("finished generating report")
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78 write(html,file=args.htmlReportFile)
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79 # unlink(args.htmlReportFile)
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80 cat("\nWarnings================:\n")
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81 str( warnings() )
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82 },
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83 error=function(cond) {
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84 sink(NULL, type="message") # default setting
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85 sink(stderr(), type="output")
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86 message("\nERROR: ===========\n")
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87 print(cond)
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88 }
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89 )