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comparison metaMS_cmd_interface.r @ 41:e67149fbff20

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small changes/improvements; new metams and xcms tools
author pieter.lukasse@wur.nl
date Thu, 06 Nov 2014 16:14:44 +0100
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children 664ccd5f7cf8
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40:a7b609941846 41:e67149fbff20
1 ## read args:
2 args <- commandArgs(TRUE)
3 ## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
4 args.constructedDB <- args[1]
5 ## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
6 args.dataZip <- args[2]
7 args.zipExtrDir <- paste(args[2],"dir/")
8 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
9 args.settings <- args[3]
10
11 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
12 args.outAnnotationTable <- args[4]
13 args.outLogFile <- args[5]
14 args.xsetOut <- args[6]
15
16 ## report files
17 args.htmlReportFile <- args[7]
18 args.htmlReportFile.files_path <- args[8]
19
20 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
21 msg <- file(args.outLogFile, open="wt")
22 sink(msg, type="message")
23 sink(msg, type="output")
24
25 cat("\nSettings used===============:\n")
26 cat(readChar(args.settings, 1e5))
27
28
29 tryCatch(
30 {
31 library(metaMS)
32
33 ## load the constructed DB :
34 tempEnv <- new.env()
35 testDB <- load(args.constructedDB, envir=tempEnv)
36
37 ## load the data files from a zip file
38 files <- unzip(args.dataZip, exdir=args.zipExtrDir)
39
40 ## load settings "script" into "customMetaMSsettings"
41 source(args.settings, local=tempEnv)
42 message(paste(" loaded : ", args.settings))
43
44 # Just to highlight: if you want to use more than one
45 # trigger runLC:
46 LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
47
48 # write out runLC annotation results:
49 write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t", row.names=FALSE)
50
51 # the used constructed DB (write to log):
52 cat("\nConstructed DB info===============:\n")
53 str(tempEnv[[testDB[1]]]$Info)
54 cat("\nConstructed DB table===============:\n")
55 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
56 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
57 # save xset as rdata:
58 xsetData <- LC$xset@xcmsSet
59 saveRDS(xsetData, file=args.xsetOut)
60
61 message("\nGenerating report.........")
62 # report
63 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
64 setwd(file.path(args.htmlReportFile.files_path))
65 html <- "<html><body><h1>Extracted Ion Chromatograms of groups with more than 3 peaks</h1>"
66
67 LC$xset@xcmsSet
68 gt <- groups(LC$xset@xcmsSet)
69 colnames(gt)
70 groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
71 if (length(groupidx1) > 0)
72 {
73 eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1))
74 eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw")
75 for (i in 1:length(groupidx1))
76 {
77 figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
78 html <- paste(html,"<img src='", "figure", i,".png' />", sep="")
79 png( figureName )
80 plot(eiccor, LC$xset@xcmsSet, groupidx = i)
81 devname = dev.off()
82 }
83 }
84
85
86 html <- paste(html,"</body><html>")
87 message("finished generating report")
88 write(html,file=args.htmlReportFile)
89 # unlink(args.htmlReportFile)
90 cat("\nWarnings================:\n")
91 str( warnings() )
92 },
93 error=function(cond) {
94 sink(NULL, type="message") # default setting
95 sink(stderr(), type="output")
96 message("\nERROR: ===========\n")
97 print(cond)
98 }
99 )