Mercurial > repos > pieterlukasse > prims_metabolomics2

comparison xcms_differential_analysis.r @ 0:dffc38727496

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
initial commit
author pieter.lukasse@wur.nl
date Sat, 07 Feb 2015 22:02:00 +0100
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dffc38727496
1 ## read args:
2 args <- commandArgs(TRUE)
3 #cat("args <- \"\"\n")
4 ## a xcms xset saved as .RData
5 args.xsetData <- args[1]
6 #cat(paste("args.xsetData <- \"", args[1], "\"\n", sep=""))
7
8 args.class1 <- args[2]
9 args.class2 <- args[3]
10 #cat(paste("args.class1 <- \"", args[2], "\"\n", sep=""))
11 #cat(paste("args.class2 <- \"", args[3], "\"\n", sep=""))
12
13 args.topcount <- strtoi(args[4])
14 #cat(paste("args.topcount <- ", args[4], "\n", sep=""))
15
16 args.outTable <- args[5]
17
18 ## report files
19 args.htmlReportFile <- args[6]
20 args.htmlReportFile.files_path <- args[7]
21 #cat(paste("args.htmlReportFile <- \"", args[6], "\"\n", sep=""))
22 #cat(paste("args.htmlReportFile.files_path <- \"", args[7], "\"\n", sep=""))
23
24
25 if (length(args) == 8)
26 {
27 args.outLogFile <- args[8]
28 # suppress messages:
29 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
30 msg <- file(args.outLogFile, open="wt")
31 sink(msg, type="message")
32 sink(msg, type="output")
33 }
34
35 tryCatch(
36 {
37 library(metaMS)
38 library(xcms)
39 #library("R2HTML")
40
41 # load the xset data :
42 xsetData <- readRDS(args.xsetData)
43 # if here to support both scenarios:
44 if ("xcmsSet" %in% slotNames(xsetData) )
45 {
46 xsetData <- xsetData@xcmsSet
47 }
48
49
50 # info: levels(xcmsSet@phenoData$class) also gives access to the class names
51 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
52 # set cairo as default for png plots:
53 png = function (...) grDevices::png(...,type='cairo')
54 # run diffreport
55 reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
56
57 # write out tsv table:
58 write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)
59
60 message("\nGenerating report.........")
61
62 cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile)
63 #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile)
64 figuresPath <- paste(args.htmlReportFile.files_path, "/fig_eic", sep="")
65 message(figuresPath)
66 listOfFiles <- list.files(path = figuresPath)
67 for (i in 1:length(listOfFiles))
68 {
69 figureName <- listOfFiles[i]
70 # maybe we still need to copy the figures to the args.htmlReportFile.files_path
71 cat(paste("<img src='fig_eic/", figureName,"' />", sep=""), file= args.htmlReportFile, append=TRUE)
72 cat(paste("<img src='fig_box/", figureName,"' />", sep=""), file= args.htmlReportFile, append=TRUE)
73 }
74
75 message("finished generating report")
76 cat("\nWarnings================:\n")
77 str( warnings() )
78 },
79 error=function(cond) {
80 sink(NULL, type="message") # default setting
81 sink(stderr(), type="output")
82 message("\nERROR: ===========\n")
83 print(cond)
84 }
85 )