Mercurial > repos > lecorguille > xcms_retcor

annotate lib.r @ 34:9714270678a7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:39:48 -0400
parents 69b5a006fca1
children 2b0a4c7a4a48
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
3
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
4 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
6 parseCommandArgs <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
7 args <- batch::parseCommandArgs(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
8 for (key in names(args)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
9 if (args[key] %in% c("TRUE","FALSE"))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
10 args[key] = as.logical(args[key])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
11 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
12 return(args)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
13 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
14
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
15 #@author G. Le Corguille
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
16 # This function will
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
17 # - load the packages
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
18 # - display the sessionInfo
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
19 loadAndDisplayPackages <- function(pkgs) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
21
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
22 sessioninfo = sessionInfo()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
23 cat(sessioninfo$R.version$version.string,"\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
24 cat("Main packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
26 cat("Other loaded packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
28 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
29
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
30 #@author G. Le Corguille
34
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
31 # This function merge several xdata into one.
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
32 mergeXData <- function(args) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
33 for(image in args$images) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
34 load(image)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
35 # Handle infiles
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
36 if (!exists("singlefile")) singlefile <- NULL
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
37 if (!exists("zipfile")) zipfile <- NULL
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
38 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
39 zipfile <- rawFilePath$zipfile
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
40 singlefile <- rawFilePath$singlefile
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
41 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
42 if (exists("raw_data")) xdata <- raw_data
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
43 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
44 cat(sampleNamesList$sampleNamesOrigin,"\n")
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
45 if (!exists("xdata_merged")) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
46 xdata_merged <- xdata
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
47 singlefile_merged <- singlefile
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
48 md5sumList_merged <- md5sumList
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
49 sampleNamesList_merged <- sampleNamesList
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
50 } else {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
51 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
52 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
53 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
54 singlefile_merged <- c(singlefile_merged,singlefile)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
55 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
56 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
57 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
58 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
59 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
60 rm(image)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
61 xdata <- xdata_merged; rm(xdata_merged)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
62 singlefile <- singlefile_merged; rm(singlefile_merged)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
63 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
64 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
65
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
66 if (!is.null(args$sampleMetadata)) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
67 cat("\tXSET PHENODATA SETTING...\n")
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
68 sampleMetadataFile <- args$sampleMetadata
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
69 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
70 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
71
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
72 if (any(is.na(pData(xdata)$sample_group))) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
73 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
74 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
75 print(error_message)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
76 stop(error_message)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
77 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
78 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
79 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
80 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
81
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
82 #@author G. Le Corguille
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
83 # This function convert if it is required the Retention Time in minutes
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
84 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
85 if (convertRTMinute){
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
86 #converting the retention times (seconds) into minutes
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
87 print("converting the retention times into minutes in the variableMetadata")
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
88 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
89 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
90 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
91 }
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
92 return (variableMetadata)
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
93 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
94
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
95 #@author G. Le Corguille
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
96 # This function format ions identifiers
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
97 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
98 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
99 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
100 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
101 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
102 return(variableMetadata)
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
103 }
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
104
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
105 #@author G. Le Corguille
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
106 # Draw the plotChromPeakDensity 3 per page in a pdf file
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
107 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
108 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
109
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
110 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
111
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
112 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
113 names(group_colors) <- unique(xdata$sample_group)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
114
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
115 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
116 for (i in 1:nrow(featureDefinitions(xdata))) {
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
117 mzmin = featureDefinitions(xdata)[i,]$mzmin
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
118 mzmax = featureDefinitions(xdata)[i,]$mzmax
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
119 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
120 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
121 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
122
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
123 dev.off()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
124 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
125
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
126 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
127 # Draw the plotChromPeakDensity 3 per page in a pdf file
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
128 getPlotAdjustedRtime <- function(xdata) {
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
129
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
130 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
131
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
132 # Color by group
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
133 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
34
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
134 if (length(group_colors) > 1) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
135 names(group_colors) <- unique(xdata$sample_group)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
136 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
137 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
138 }
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
139
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
140 # Color by sample
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
141 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
142 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
143
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
144 dev.off()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
145 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
146
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
147 #@author G. Le Corguille
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
148 # value: intensity values to be used into, maxo or intb
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
149 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
150 dataMatrix <- featureValues(xdata, method="medret", value=intval)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
151 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
152 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
153 variableMetadata <- featureDefinitions(xdata)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
154 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
155 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
156
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
157 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
158 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
159
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
160 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
161 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
162
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
163 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
164
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
165 #@author G. Le Corguille
34
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
166 # It allow different of field separators
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
167 getDataFrameFromFile <- function(filename, header=T) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
168 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
169 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
170 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
171 if (ncol(myDataFrame) < 2) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
172 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
173 print(error_message)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
174 stop(error_message)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
175 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
176 return(myDataFrame)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
177 }
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
178
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
179 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
180
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
181 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
182 if (aggregationFun == "sum")
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
183 type="Total Ion Chromatograms"
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
184 else
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
185 type="Base Peak Intensity Chromatograms"
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
186
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
187 adjusted="Raw"
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
188 if (hasAdjustedRtime(xdata))
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
189 adjusted="Adjusted"
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
190
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
191 main <- paste(type,":",adjusted,"data")
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
192
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
193 pdf(pdfname, width=16, height=10)
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
194
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
195 # Color by group
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
196 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
34
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
197 if (length(group_colors) > 1) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
198 names(group_colors) <- unique(xdata$sample_group)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
199 plot(chrom, col = group_colors[chrom$sample_group], main=main)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
200 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
201 }
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
202
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
203 # Color by sample
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
204 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
205 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
206
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
207 dev.off()
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
208 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
209
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
210 #@author G. Le Corguille
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
211 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
212 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
213 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
214
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
215 #@author G. Le Corguille
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
216 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
217 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
218 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
219
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
220
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
221 # Get the polarities from all the samples of a condition
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
222 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
223 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
224 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
225 cat("Creating the sampleMetadata file...\n")
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
226
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
227 #Create the sampleMetada dataframe
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
228 sampleMetadata <- xdata@phenoData@data
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
229 rownames(sampleMetadata) <- NULL
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
230 colnames(sampleMetadata) <- c("sampleMetadata", "class")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
231
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
232 sampleNamesOrigin <- sampleMetadata$sampleMetadata
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
233 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
234
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
235 if (any(duplicated(sampleNamesMakeNames))) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
236 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
237 for (sampleName in sampleNamesOrigin) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
238 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
239 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
240 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
241 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
242
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
243 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
244 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
245 for (sampleName in sampleNamesOrigin) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
246 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
247 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
248 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
249
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
250 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
251
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
252
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
253 #For each sample file, the following actions are done
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
254 for (fileIdx in 1:length(fileNames(xdata))) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
255 #Check if the file is in the CDF format
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
256 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
257
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
258 # If the column isn't exist, with add one filled with NA
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
259 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
260
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
261 #Extract the polarity (a list of polarities)
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
262 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
263 #Verify if all the scans have the same polarity
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
264 uniq_list <- unique(polarity)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
265 if (length(uniq_list)>1){
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
266 polarity <- "mixed"
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
267 } else {
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
268 polarity <- as.character(uniq_list)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
269 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
270
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
271 #Set the polarity attribute
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
272 sampleMetadata$polarity[fileIdx] <- polarity
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
273 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
274
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
275 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
276
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
277 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
278
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
279 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
280
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
281 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
282
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
283
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
284 # This function check if xcms will found all the files
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
285 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
286 checkFilesCompatibilityWithXcms <- function(directory) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
287 cat("Checking files filenames compatibilities with xmcs...\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
288 # WHAT XCMS WILL FIND
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
289 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
290 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
291 info <- file.info(directory)
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
292 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
293 files <- c(directory[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
294 files_abs <- file.path(getwd(), files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
295 exists <- file.exists(files_abs)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
296 files[exists] <- files_abs[exists]
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
297 files[exists] <- sub("//","/",files[exists])
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
298
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
299 # WHAT IS ON THE FILESYSTEM
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
300 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
301 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
302
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
303 # COMPARISON
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
304 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
305 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
306 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
307 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
308 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
309 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
310
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
311
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
312 #This function list the compatible files within the directory as xcms did
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
313 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
314 getMSFiles <- function (directory) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
315 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
316 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
317 info <- file.info(directory)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
318 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
319 files <- c(directory[!info$isdir], listed)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
320 exists <- file.exists(files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
321 files <- files[exists]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
322 return(files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
323 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
324
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
325 # This function check if XML contains special caracters. It also checks integrity and completness.
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
326 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
327 checkXmlStructure <- function (directory) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
328 cat("Checking XML structure...\n")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
329
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
330 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
331 capture <- system(cmd, intern=TRUE)
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
332
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
333 if (length(capture)>0){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
334 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
335 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
336 write(capture, stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
337 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
338 }
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
diff changeset
339
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
340 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
341
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
342
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
343 # This function check if XML contain special characters
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
344 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
345 deleteXmlBadCharacters<- function (directory) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
346 cat("Checking Non ASCII characters in the XML...\n")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
347
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
348 processed <- F
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
349 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
350 for (i in l){
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
351 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
352 capture <- suppressWarnings(system(cmd, intern=TRUE))
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
353 if (length(capture)>0){
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
354 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
355 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
356 c <- system(cmd, intern=TRUE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
357 capture <- ""
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
358 processed <- T
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
359 }
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
360 }
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
361 if (processed) cat("\n\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
362 return(processed)
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
363 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
364
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
365
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
366 # This function will compute MD5 checksum to check the data integrity
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
367 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
368 getMd5sum <- function (directory) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
369 cat("Compute md5 checksum...\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
370 # WHAT XCMS WILL FIND
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
371 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
372 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
373 info <- file.info(directory)
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
374 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
375 files <- c(directory[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
376 exists <- file.exists(files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
377 files <- files[exists]
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
378
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
379 library(tools)
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
380
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
381 #cat("\n\n")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
382
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
383 return(as.matrix(md5sum(files)))
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
384 }
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
385
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
386
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
387 # This function get the raw file path from the arguments
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
388 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
389 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
390 if (!is.null(args$zipfile)) zipfile <- args$zipfile
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
391 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
392 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
393
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
394 if (!is.null(args$singlefile_galaxyPath)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
395 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
396 singlefile_sampleNames <- args$singlefile_sampleName
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
397 }
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
398 if (!is.null(args$singlefile_galaxyPathPositive)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
399 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
400 singlefile_sampleNames <- args$singlefile_sampleNamePositive
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
401 }
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
402 if (!is.null(args$singlefile_galaxyPathNegative)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
403 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
404 singlefile_sampleNames <- args$singlefile_sampleNameNegative
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
405 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
406 if (exists("singlefile_galaxyPaths")){
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
407 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
408 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
409
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
410 singlefile <- NULL
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
411 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
412 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
413 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
414 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
415 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
416 }
34
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
417 return(list(zipfile=zipfile, singlefile=singlefile))
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
418 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
419
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
420
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
421 # This function retrieve the raw file in the working directory
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
422 # - if zipfile: unzip the file with its directory tree
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
423 # - if singlefiles: set symlink with the good filename
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
425 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
426 if(!is.null(singlefile) && (length("singlefile")>0)) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
427 for (singlefile_sampleName in names(singlefile)) {
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
428 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
429 if(!file.exists(singlefile_galaxyPath)){
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
430 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
431 print(error_message); stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
432 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
433
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
434 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
435 file.copy(singlefile_galaxyPath, singlefile_sampleName)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
436
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
437 }
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
438 directory <- "."
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
439
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
440 }
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
441 if(!is.null(zipfile) && (zipfile != "")) {
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
442 if(!file.exists(zipfile)){
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
443 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
444 print(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
445 stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
446 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
447
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
448 #list all file in the zip file
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
449 #zip_files <- unzip(zipfile,list=T)[,"Name"]
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
450
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
451 #unzip
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
452 suppressWarnings(unzip(zipfile, unzip="unzip"))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
453
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
454 #get the directory name
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
455 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
456 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
457 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
458 directory <- "."
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
459 if (length(directories) == 1) directory <- directories
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
460
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
461 cat("files_root_directory\t",directory,"\n")
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
462
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
463 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
464 return (directory)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
465 }
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
466
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
467
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
468 # This function retrieve a xset like object
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
469 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
470 getxcmsSetObject <- function(xobject) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
471 # XCMS 1.x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
472 if (class(xobject) == "xcmsSet")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
473 return (xobject)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
474 # XCMS 3.x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
475 if (class(xobject) == "XCMSnExp") {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
476 # Get the legacy xcmsSet object
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
477 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
478 sampclass(xset) <- xset@phenoData$sample_group
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
479 return (xset)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
480 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
481 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
482
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
483
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
484 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
485 # https://github.com/sneumann/xcms/issues/250
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
486 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
487 mzfmt <- paste("%.", mzdec, "f", sep = "")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
488 rtfmt <- paste("%.", rtdec, "f", sep = "")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
489
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
490 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
491 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
492
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
493 if (any(dup <- duplicated(gnames)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
494 for (dupname in unique(gnames[dup])) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
495 dupidx <- which(gnames == dupname)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
496 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
497 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
498
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
499 return (gnames)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
500 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
501
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
502 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
503 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
504 .concatenate_XCMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
505 x <- list(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
506 if (length(x) == 0)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
507 return(NULL)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
508 if (length(x) == 1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
509 return(x[[1]])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
510 ## Check that all are XCMSnExp objects.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
511 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
512 stop("All passed objects should be 'XCMSnExp' objects")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
513 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
514 ## If any of the XCMSnExp has alignment results or detected features drop
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
515 ## them!
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
516 x <- lapply(x, function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
517 if (hasAdjustedRtime(z)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
518 z <- dropAdjustedRtime(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
519 warning("Adjusted retention times found, had to drop them.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
520 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
521 if (hasFeatures(z)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
522 z <- dropFeatureDefinitions(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
523 warning("Feature definitions found, had to drop them.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
524 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
525 z
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
526 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
527 ## Combine peaks
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
528 fls <- lapply(x, fileNames)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
529 startidx <- cumsum(lengths(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
530 pks <- lapply(x, chromPeaks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
531 procH <- lapply(x, processHistory)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
532 for (i in 2:length(fls)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
533 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
534 procH[[i]] <- lapply(procH[[i]], function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
535 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
536 z
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
537 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
538 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
539 pks <- do.call(rbind, pks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
540 new_x@.processHistory <- unlist(procH)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
541 chromPeaks(new_x) <- pks
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
542 if (validObject(new_x))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
543 new_x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
544 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
545
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
546 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
547 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
548 .concatenate_OnDiskMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
549 x <- list(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
550 if (length(x) == 0)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
551 return(NULL)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
552 if (length(x) == 1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
553 return(x[[1]])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
554 ## Check that all are XCMSnExp objects.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
555 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
556 stop("All passed objects should be 'OnDiskMSnExp' objects")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
557 ## Check processingQueue
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
558 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
559 new_procQ <- procQ[[1]]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
560 is_ok <- unlist(lapply(procQ, function(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
561 !is.character(all.equal(new_procQ, z))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
562 ))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
563 if (any(!is_ok)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
564 warning("Processing queues from the submitted objects differ! ",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
565 "Dropping the processing queue.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
566 new_procQ <- list()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
567 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
568 ## processingData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
569 fls <- lapply(x, function(z) z@processingData@files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
570 startidx <- cumsum(lengths(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
571 ## featureData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
572 featd <- lapply(x, fData)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
573 ## Have to update the file index and the spectrum names.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
574 for (i in 2:length(featd)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
575 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
576 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
577 fileIds = featd[[i]]$fileIdx,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
578 spectrumIds = featd[[i]]$spIdx,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
579 nSpectra = nrow(featd[[i]]),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
580 nFiles = length(unlist(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
581 )
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
582 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
583 featd <- do.call(rbind, featd)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
584 featd$spectrum <- 1:nrow(featd)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
585 ## experimentData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
586 expdata <- lapply(x, function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
587 ed <- z@experimentData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
588 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
589 instrumentModel = ed@instrumentModel,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
590 ionSource = ed@ionSource,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
591 analyser = ed@analyser,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
592 detectorType = ed@detectorType,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
593 stringsAsFactors = FALSE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
594 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
595 expdata <- do.call(rbind, expdata)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
596 expdata <- new("MIAPE",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
597 instrumentManufacturer = expdata$instrumentManufacturer,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
598 instrumentModel = expdata$instrumentModel,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
599 ionSource = expdata$ionSource,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
600 analyser = expdata$analyser,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
601 detectorType = expdata$detectorType)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
602
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
603 ## protocolData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
604 protodata <- lapply(x, function(z) z@protocolData)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
605 if (any(unlist(lapply(protodata, nrow)) > 0))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
606 warning("Found non-empty protocol data, but merging protocol data is",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
607 " currently not supported. Skipped.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
608 ## phenoData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
609 pdata <- do.call(rbind, lapply(x, pData))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
610 res <- new(
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
611 "OnDiskMSnExp",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
612 phenoData = new("NAnnotatedDataFrame", data = pdata),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
613 featureData = new("AnnotatedDataFrame", featd),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
614 processingData = new("MSnProcess",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
615 processing = paste0("Concatenated [", date(), "]"),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
616 files = unlist(fls), smoothed = NA),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
617 experimentData = expdata,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
618 spectraProcessingQueue = new_procQ)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
619 if (validObject(res))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
620 res
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
621 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
622
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
624 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
625 c.XCMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
626 .concatenate_XCMSnExp(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
627 }
34
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
628
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
629 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
630 # https://github.com/sneumann/xcms/issues/247
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
631 c.MSnbase <- function(...) {
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
632 .concatenate_OnDiskMSnExp(...)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 33
diff changeset
633 }