Mercurial > repos > pieterlukasse > prims_metabolomics2

comparison metaMS/metaMS_cmd_pick_and_group.r @ 6:4393f982d18f

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reorganized sources
author pieter.lukasse@wur.nl
date Thu, 19 Mar 2015 12:22:23 +0100
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5:41f122255d14 6:4393f982d18f
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 )