Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate lib.r @ 18:4631c19a75ff draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:40:09 +0000
parents 9fff8c8ab4a3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
1 # @authors ABiMS TEAM, Y. Guitton
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
3
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
4 # @author G. Le Corguille
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
6 parseCommandArgs <- function(...) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
7 args <- batch::parseCommandArgs(...)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
8 for (key in names(args)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
9 if (args[key] %in% c("TRUE", "FALSE")) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
10 args[key] <- as.logical(args[key])
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
11 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
12 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
13 return(args)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
14 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
15
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
16 # @author G. Le Corguille
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
17 # This function will
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
18 # - load the packages
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
19 # - display the sessionInfo
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
20 loadAndDisplayPackages <- function(pkgs) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
21 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
22
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
23 sessioninfo <- sessionInfo()
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
24 cat(sessioninfo$R.version$version.string, "\n")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
25 cat("Main packages:\n")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
26 for (pkg in names(sessioninfo$otherPkgs)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
27 cat(paste(pkg, packageVersion(pkg)), "\t")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
28 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
29 cat("\n")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
30 cat("Other loaded packages:\n")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
31 for (pkg in names(sessioninfo$loadedOnly)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
32 cat(paste(pkg, packageVersion(pkg)), "\t")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
33 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
34 cat("\n")
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
35 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
36
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
37 # @author G. Le Corguille
3
60b156e58529 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 2
diff changeset
38 # This function merge several chromBPI or chromTIC into one.
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
39 mergeChrom <- function(chrom_merged, chrom) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
40 if (is.null(chrom_merged)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
41 return(NULL)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
42 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
43 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
44 return(chrom_merged)
3
60b156e58529 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 2
diff changeset
45 }
60b156e58529 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 2
diff changeset
46
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
47 # @author G. Le Corguille
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
48 # This function merge several xdata into one.
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
49 mergeXData <- function(args) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
50 chromTIC <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
51 chromBPI <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
52 chromTIC_adjusted <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
53 chromBPI_adjusted <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
54 md5sumList <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
55 for (image in args$images) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
56 load(image)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
57 # Handle infiles
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
58 if (!exists("singlefile")) singlefile <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
59 if (!exists("zipfile")) zipfile <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
60 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
61 zipfile <- rawFilePath$zipfile
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
62 singlefile <- rawFilePath$singlefile
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
63
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
64 if (exists("raw_data")) xdata <- raw_data
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
65 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
66
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
67 cat(sampleNamesList$sampleNamesOrigin, "\n")
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
68
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
69 if (!exists("xdata_merged")) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
70 xdata_merged <- xdata
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
71 singlefile_merged <- singlefile
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
72 md5sumList_merged <- md5sumList
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
73 sampleNamesList_merged <- sampleNamesList
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
74 chromTIC_merged <- chromTIC
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
75 chromBPI_merged <- chromBPI
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
76 chromTIC_adjusted_merged <- chromTIC_adjusted
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
77 chromBPI_adjusted_merged <- chromBPI_adjusted
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
78 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
79 if (is(xdata, "XCMSnExp")) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
80 xdata_merged <- c(xdata_merged, xdata)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
81 } else if (is(xdata, "OnDiskMSnExp")) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
82 xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
83 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
84 stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
85 }
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
86
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
87 singlefile_merged <- c(singlefile_merged, singlefile)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
88 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
89 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
90 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
91 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
92 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
93 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
94 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
95 }
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
96 }
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
97 rm(image)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
98 xdata <- xdata_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
99 rm(xdata_merged)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
100 singlefile <- singlefile_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
101 rm(singlefile_merged)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
102 md5sumList <- md5sumList_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
103 rm(md5sumList_merged)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
104 sampleNamesList <- sampleNamesList_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
105 rm(sampleNamesList_merged)
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
106
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
107 if (!is.null(args$sampleMetadata)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
108 cat("\tXSET PHENODATA SETTING...\n")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
109 sampleMetadataFile <- args$sampleMetadata
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
110 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
111 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
112
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
113 if (any(is.na(pData(xdata)$sample_group))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
114 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
115 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
116 print(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
117 stop(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
118 }
16
bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 15
diff changeset
119 }
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
120
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
121 if (!is.null(chromTIC_merged)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
122 chromTIC <- chromTIC_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
123 chromTIC@phenoData <- xdata@phenoData
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
124 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
125 if (!is.null(chromBPI_merged)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
126 chromBPI <- chromBPI_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
127 chromBPI@phenoData <- xdata@phenoData
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
128 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
129 if (!is.null(chromTIC_adjusted_merged)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
130 chromTIC_adjusted <- chromTIC_adjusted_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
131 chromTIC_adjusted@phenoData <- xdata@phenoData
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
132 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
133 if (!is.null(chromBPI_adjusted_merged)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
134 chromBPI_adjusted <- chromBPI_adjusted_merged
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
135 chromBPI_adjusted@phenoData <- xdata@phenoData
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
136 }
17
9fff8c8ab4a3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 16
diff changeset
137
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
138 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
139 }
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
140
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
141 # @author G. Le Corguille
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
142 # This function convert if it is required the Retention Time in minutes
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
143 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
144 if (convertRTMinute) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
145 # converting the retention times (seconds) into minutes
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
146 print("converting the retention times into minutes in the variableMetadata")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
147 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
148 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
149 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
150 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
151 return(variableMetadata)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
152 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
153
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
154 # @author G. Le Corguille
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
155 # This function format ions identifiers
16
bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 15
diff changeset
156 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
157 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
158 idsDeco <- sapply(
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
159 splitDeco,
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
160 function(x) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
161 deco <- unlist(x)[2]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
162 if (is.na(deco)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
163 return("")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
164 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
165 return(paste0("_", deco))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
166 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
167 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
168 )
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
169 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
170 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
171 return(variableMetadata)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
172 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
173
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
174 # @author G. Le Corguille
7
a4a1143a202a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 6
diff changeset
175 # This function convert the remain NA to 0 in the dataMatrix
a4a1143a202a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 6
diff changeset
176 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
177 if (naTOzero) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
178 dataMatrix[is.na(dataMatrix)] <- 0
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
179 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
180 return(dataMatrix)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
181 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
182
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
183 # @author G. Le Corguille
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
184 # Draw the plotChromPeakDensity 3 per page in a pdf file
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
185 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
186 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
187
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
188 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
189
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
190 if (length(unique(xdata$sample_group)) < 10) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
191 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
192 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
193 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
194 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
195 names(group_colors) <- unique(xdata$sample_group)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
196 col_per_samp <- as.character(xdata$sample_group)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
197 for (i in seq_len(length(group_colors))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
198 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
199 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
200
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
201 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
202 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
203 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
204 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
205 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
206 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
207 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
208
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
209 dev.off()
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
210 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
211
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
212 # @author G. Le Corguille
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
213 # Draw the plotChromPeakDensity 3 per page in a pdf file
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
214 getPlotAdjustedRtime <- function(xdata) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
215 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
216
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
217 # Color by group
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
218 if (length(unique(xdata$sample_group)) < 10) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
219 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
220 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
221 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
222 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
223 if (length(group_colors) > 1) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
224 names(group_colors) <- unique(xdata$sample_group)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
225 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
226 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
227 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
228
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
229 # Color by sample
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
230 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
231 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
232
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
233 dev.off()
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
234 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
235
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
236 # @author G. Le Corguille
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
237 # value: intensity values to be used into, maxo or intb
17
9fff8c8ab4a3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 16
diff changeset
238 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
239 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
240 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
241 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
242 variableMetadata <- featureDefinitions(xdata)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
243 colnames(variableMetadata)[1] <- "mz"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
244 colnames(variableMetadata)[4] <- "rt"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
245 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
246
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
247 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
248 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
249 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
250
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
251 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
252 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
10
a92c1d4f0173 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 9
diff changeset
253
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
254 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
255 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
256 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
257
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
258 # @author G. Le Corguille
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
259 # It allow different of field separators
17
9fff8c8ab4a3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 16
diff changeset
260 getDataFrameFromFile <- function(filename, header = TRUE) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
261 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
262 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
263 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
264 if (ncol(myDataFrame) < 2) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
265 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
266 print(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
267 stop(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
268 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
269 return(myDataFrame)
2
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
270 }
e6fdadaf039e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 0
diff changeset
271
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
272 # @author G. Le Corguille
6
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
273 # Draw the BPI and TIC graphics
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 5
diff changeset
274 # colored by sample names or class names
16
bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 15
diff changeset
275 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
276 if (aggregationFun == "sum") {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
277 type <- "Total Ion Chromatograms"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
278 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
279 type <- "Base Peak Intensity Chromatograms"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
280 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
281
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
282 adjusted <- "Raw"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
283 if (hasAdjustedRtime(xdata)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
284 adjusted <- "Adjusted"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
285 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
286
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
287 main <- paste(type, ":", adjusted, "data")
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
288
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
289 pdf(pdfname, width = 16, height = 10)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
290
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
291 # Color by group
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
292 if (length(unique(xdata$sample_group)) < 10) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
293 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
294 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
295 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
296 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
297 if (length(group_colors) > 1) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
298 names(group_colors) <- unique(xdata$sample_group)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
299 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
300 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
301 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
302
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
303 # Color by sample
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
304 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
305 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
306
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
307 dev.off()
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
308 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
309
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
310
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
311 # Get the polarities from all the samples of a condition
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
312 # @author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
313 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
16
bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 15
diff changeset
314 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
315 cat("Creating the sampleMetadata file...\n")
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
316
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
317 # Create the sampleMetada dataframe
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
318 sampleMetadata <- xdata@phenoData@data
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
319 rownames(sampleMetadata) <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
320 colnames(sampleMetadata) <- c("sample_name", "class")
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
321
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
322 sampleNamesOrigin <- sampleMetadata$sample_name
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
323 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
324
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
325 if (any(duplicated(sampleNamesMakeNames))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
326 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())
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
327 for (sampleName in sampleNamesOrigin) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
328 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
329 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
330 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
331 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
332
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
333 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
334 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")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
335 for (sampleName in sampleNamesOrigin) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
336 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
337 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
338 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
339
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
340 sampleMetadata$sample_name <- sampleNamesMakeNames
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
341
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
342
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
343 # For each sample file, the following actions are done
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
344 for (fileIdx in seq_len(length(fileNames(xdata)))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
345 # Check if the file is in the CDF format
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
346 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
347 # If the column isn't exist, with add one filled with NA
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
348 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
349
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
350 # Extract the polarity (a list of polarities)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
351 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
352 # Verify if all the scans have the same polarity
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
353 uniq_list <- unique(polarity)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
354 if (length(uniq_list) > 1) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
355 polarity <- "mixed"
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
356 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
357 polarity <- as.character(uniq_list)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
358 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
359
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
360 # Set the polarity attribute
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
361 sampleMetadata$polarity[fileIdx] <- polarity
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
362 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
363 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
364
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
365 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
366
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
367 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
368 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
369
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
370
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
371 # This function will compute MD5 checksum to check the data integrity
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
372 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
16
bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 15
diff changeset
373 getMd5sum <- function(files) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
374 cat("Compute md5 checksum...\n")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
375 library(tools)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
376 return(as.matrix(md5sum(files)))
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
377 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
378
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
379 # This function retrieve the raw file in the working directory
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
380 # - if zipfile: unzip the file with its directory tree
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
381 # - if singlefiles: set symlink with the good filename
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
382 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
16
bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 15
diff changeset
383 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
384 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
13
9a5b4a1b9880 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 12
diff changeset
385
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
386 # single - if the file are passed in the command arguments -> refresh singlefile
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
387 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
388 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
389 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
13
9a5b4a1b9880 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 12
diff changeset
390
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
391 singlefile <- NULL
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
392 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
393 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
394 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
395 # In case, an url is used to import data within Galaxy
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
396 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
397 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
398 }
17
9fff8c8ab4a3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 16
diff changeset
399 }
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
400 # zipfile - if the file are passed in the command arguments -> refresh zipfile
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
401 if (!is.null(args[[paste0("zipfile", prefix)]])) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
402 zipfile <- args[[paste0("zipfile", prefix)]]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
403 }
17
9fff8c8ab4a3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 16
diff changeset
404
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
405 # single
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
406 if (!is.null(singlefile) && (length("singlefile") > 0)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
407 files <- vector()
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
408 for (singlefile_sampleName in names(singlefile)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
409 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
410 if (!file.exists(singlefile_galaxyPath)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
411 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
412 print(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
413 stop(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
414 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
415
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
416 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE))) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
417 file.copy(singlefile_galaxyPath, singlefile_sampleName)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
418 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
419 files <- c(files, singlefile_sampleName)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
420 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
421 }
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
422 # zipfile
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
423 if (!is.null(zipfile) && (zipfile != "")) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
424 if (!file.exists(zipfile)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
425 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
426 print(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
427 stop(error_message)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
428 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
429 suppressWarnings(unzip(zipfile, unzip = "unzip"))
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
430
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
431 # get the directory name
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
432 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
433 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
434 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
435 directory <- "."
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
436 if (length(directories) == 1) directory <- directories
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
437
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
438 cat("files_root_directory\t", directory, "\n")
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
439
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
440 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
441 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
442 info <- file.info(directory)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
443 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
444 files <- c(directory[!info$isdir], listed)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
445 exists <- file.exists(files)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
446 files <- files[exists]
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
447 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
448 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
449 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
450
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
451
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
452 # This function retrieve a xset like object
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
453 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
454 getxcmsSetObject <- function(xobject) {
18
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
455 # XCMS 1.x
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
456 if (class(xobject) == "xcmsSet") {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
457 return(xobject)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
458 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
459 # XCMS 3.x
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
460 if (class(xobject) == "XCMSnExp") {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
461 # Get the legacy xcmsSet object
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
462 suppressWarnings(xset <- as(xobject, "xcmsSet"))
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
463 if (!is.null(xset@phenoData$sample_group)) {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
464 sampclass(xset) <- xset@phenoData$sample_group
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
465 } else {
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
466 sampclass(xset) <- "."
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
467 }
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
468 return(xset)
4631c19a75ff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 17
diff changeset
469 }
0
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
470 }