Mercurial > repos > lecorguille > xcms_group

annotate lib.r @ 45:99852755ea5c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 10:29:38 +0000
parents 6f3567245d0c
children d9de831270a1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
3
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
4 #@author G. Le Corguille
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
6 parseCommandArgs <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
7 args <- batch::parseCommandArgs(...)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
8 for (key in names(args)) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
9 if (args[key] %in% c("TRUE", "FALSE"))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
10 args[key] <- as.logical(args[key])
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
11 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
12 return(args)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
13 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
14
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
15 #@author G. Le Corguille
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
16 # This function will
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
17 # - load the packages
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
18 # - display the sessionInfo
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
19 loadAndDisplayPackages <- function(pkgs) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
20 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
21
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
22 sessioninfo <- sessionInfo()
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
23 cat(sessioninfo$R.version$version.string, "\n")
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
24 cat("Main packages:\n")
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
25 for (pkg in names(sessioninfo$otherPkgs)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
26 cat(paste(pkg, packageVersion(pkg)), "\t")
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
27 }
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
28 cat("\n")
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
29 cat("Other loaded packages:\n")
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
30 for (pkg in names(sessioninfo$loadedOnly)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
31 cat(paste(pkg, packageVersion(pkg)), "\t")
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
32 }
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
33 cat("\n")
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
34 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
35
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
36 #@author G. Le Corguille
33
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
diff changeset
37 # This function merge several chromBPI or chromTIC into one.
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
38 mergeChrom <- function(chrom_merged, chrom) {
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
39 if (is.null(chrom_merged)) return(NULL)
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
41 return(chrom_merged)
33
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
diff changeset
42 }
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
diff changeset
43
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
diff changeset
44 #@author G. Le Corguille
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
45 # This function merge several xdata into one.
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
46 mergeXData <- function(args) {
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
47 chromTIC <- NULL
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
48 chromBPI <- NULL
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
49 chromTIC_adjusted <- NULL
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
50 chromBPI_adjusted <- NULL
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
51 md5sumList <- NULL
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
52 for (image in args$images) {
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
53
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
54 load(image)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
55 # Handle infiles
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
56 if (!exists("singlefile")) singlefile <- NULL
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
57 if (!exists("zipfile")) zipfile <- NULL
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
59 zipfile <- rawFilePath$zipfile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
60 singlefile <- rawFilePath$singlefile
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
61
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
62 if (exists("raw_data")) xdata <- raw_data
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
64
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
65 cat(sampleNamesList$sampleNamesOrigin, "\n")
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
66
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
67 if (!exists("xdata_merged")) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
68 xdata_merged <- xdata
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
69 singlefile_merged <- singlefile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
70 md5sumList_merged <- md5sumList
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
71 sampleNamesList_merged <- sampleNamesList
33
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
diff changeset
72 chromTIC_merged <- chromTIC
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
diff changeset
73 chromBPI_merged <- chromBPI
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
74 chromTIC_adjusted_merged <- chromTIC_adjusted
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
75 chromBPI_adjusted_merged <- chromBPI_adjusted
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
76 } else {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
80
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
81 singlefile_merged <- c(singlefile_merged, singlefile)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
89 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
90 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
91 rm(image)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
92 xdata <- xdata_merged; rm(xdata_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
93 singlefile <- singlefile_merged; rm(singlefile_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
94 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
95 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
96
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
97 if (!is.null(args$sampleMetadata)) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
98 cat("\tXSET PHENODATA SETTING...\n")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
99 sampleMetadataFile <- args$sampleMetadata
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
100 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = F)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
101 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
102
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
103 if (any(is.na(pData(xdata)$sample_group))) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
104 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
105 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
106 print(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
107 stop(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
108 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
109 }
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
110
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
111 if (!is.null(chromTIC_merged)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
112 chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
113 }
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
114 if (!is.null(chromBPI_merged)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
115 chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
116 }
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
117 if (!is.null(chromTIC_adjusted_merged)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
118 chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
119 }
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
120 if (!is.null(chromBPI_adjusted_merged)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
121 chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
122 }
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
123
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
124 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
125 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
126
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
127 #@author G. Le Corguille
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
128 # This function convert if it is required the Retention Time in minutes
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
129 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
130 if (convertRTMinute) {
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
131 #converting the retention times (seconds) into minutes
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
132 print("converting the retention times into minutes in the variableMetadata")
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
133 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
134 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
135 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
136 }
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
137 return(variableMetadata)
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
138 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
139
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
140 #@author G. Le Corguille
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
141 # This function format ions identifiers
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
142 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
143 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
144 idsDeco <- sapply(splitDeco,
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
145 function(x) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
146 deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
147 }
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
148 )
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
149 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
150 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
17
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 16
diff changeset
151 return(variableMetadata)
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
152 }
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
153
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
154 #@author G. Le Corguille
36
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
155 # This function convert the remain NA to 0 in the dataMatrix
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
156 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
157 if (naTOzero) {
36
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
158 dataMatrix[is.na(dataMatrix)] <- 0
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
159 }
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
160 return(dataMatrix)
36
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
161 }
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
162
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
163 #@author G. Le Corguille
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
164 # Draw the plotChromPeakDensity 3 per page in a pdf file
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
165 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
166 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
167
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
168 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
169
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
170 if (length(unique(xdata$sample_group)) < 10) {
44
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
171 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
172 }else{
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
173 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
44
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
174 }
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
175 names(group_colors) <- unique(xdata$sample_group)
43
053e81c58b11 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 42
diff changeset
176 col_per_samp <- as.character(xdata$sample_group)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
177 for (i in seq_len(length(group_colors))) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
178 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
179 }
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
180
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
181 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
182 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
183 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
184 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
185 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
186 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
187 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
188
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
189 dev.off()
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
190 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
191
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
192 #@author G. Le Corguille
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
193 # Draw the plotChromPeakDensity 3 per page in a pdf file
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
194 getPlotAdjustedRtime <- function(xdata) {
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
195
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
196 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
197
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
198 # Color by group
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
199 if (length(unique(xdata$sample_group)) < 10) {
44
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
200 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
201 } else {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
202 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
44
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
203 }
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
204 if (length(group_colors) > 1) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
205 names(group_colors) <- unique(xdata$sample_group)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
206 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
207 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
208 }
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
209
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
210 # Color by sample
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
211 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
212 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
213
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
214 dev.off()
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
215 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
216
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
217 #@author G. Le Corguille
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
218 # value: intensity values to be used into, maxo or intb
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
219 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = F, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
220 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
38
fef2dd87fb80 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
lecorguille
parents: 36
diff changeset
221 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
222 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
223 variableMetadata <- featureDefinitions(xdata)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
224 colnames(variableMetadata)[1] <- "mz"; colnames(variableMetadata)[4] <- "rt"
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
225 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
226
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
227 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
228 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
36
eddc995c6df1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 35
diff changeset
229 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
230
39
af8da7f83ff7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 38
diff changeset
231 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
232 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
39
af8da7f83ff7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 38
diff changeset
233
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
234 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = F, row.names = F)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
235 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = F, row.names = F)
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
236
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
237 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
238
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
239 #@author G. Le Corguille
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
240 # It allow different of field separators
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
241 getDataFrameFromFile <- function(filename, header = T) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
242 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = F)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
243 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = F)
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
244 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = F)
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
245 if (ncol(myDataFrame) < 2) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
246 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
247 print(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
248 stop(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
249 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
250 return(myDataFrame)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
251 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
252
35
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
253 #@author G. Le Corguille
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
254 # Draw the BPI and TIC graphics
aeba79c716b1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 34
diff changeset
255 # colored by sample names or class names
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
256 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
257
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
258 if (aggregationFun == "sum")
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
259 type <- "Total Ion Chromatograms"
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
260 else
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
261 type <- "Base Peak Intensity Chromatograms"
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
262
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
263 adjusted <- "Raw"
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
264 if (hasAdjustedRtime(xdata))
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
265 adjusted <- "Adjusted"
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
266
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
267 main <- paste(type, ":", adjusted, "data")
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
268
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
269 pdf(pdfname, width = 16, height = 10)
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
270
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
271 # Color by group
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
272 if (length(unique(xdata$sample_group)) < 10) {
44
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
273 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
274 }else{
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
275 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
44
6f3567245d0c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
workflow4metabolomics
parents: 43
diff changeset
276 }
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
277 if (length(group_colors) > 1) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
278 names(group_colors) <- unique(xdata$sample_group)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
279 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
280 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
diff changeset
281 }
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
282
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
283 # Color by sample
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
284 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
285 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
31
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
286
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 30
diff changeset
287 dev.off()
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
288 }
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
289
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
290
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
291 # Get the polarities from all the samples of a condition
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
292 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
293 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
294 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
295 cat("Creating the sampleMetadata file...\n")
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
296
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
297 #Create the sampleMetada dataframe
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
298 sampleMetadata <- xdata@phenoData@data
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
299 rownames(sampleMetadata) <- NULL
39
af8da7f83ff7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 38
diff changeset
300 colnames(sampleMetadata) <- c("sample_name", "class")
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
301
39
af8da7f83ff7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 38
diff changeset
302 sampleNamesOrigin <- sampleMetadata$sample_name
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
303 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
304
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
305 if (any(duplicated(sampleNamesMakeNames))) {
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
306 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())
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
307 for (sampleName in sampleNamesOrigin) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
308 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
309 }
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
310 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
311 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
312
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
313 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
314 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")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
315 for (sampleName in sampleNamesOrigin) {
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
316 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
317 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
318 }
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
319
39
af8da7f83ff7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 38
diff changeset
320 sampleMetadata$sample_name <- sampleNamesMakeNames
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
321
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
322
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
323 #For each sample file, the following actions are done
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
324 for (fileIdx in seq_len(length(fileNames(xdata)))) {
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
325 #Check if the file is in the CDF format
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
326 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
327
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
328 # If the column isn't exist, with add one filled with NA
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
329 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
330
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
331 #Extract the polarity (a list of polarities)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
332 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
333 #Verify if all the scans have the same polarity
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
334 uniq_list <- unique(polarity)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
335 if (length(uniq_list) > 1) {
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
336 polarity <- "mixed"
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
337 } else {
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
338 polarity <- as.character(uniq_list)
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
339 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
340
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
341 #Set the polarity attribute
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
342 sampleMetadata$polarity[fileIdx] <- polarity
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
343 }
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
344
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
345 }
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
346
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
347 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
348
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
349 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
350
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
351 }
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
352
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
353
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
354 # This function will compute MD5 checksum to check the data integrity
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
355 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
356 getMd5sum <- function(files) {
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
357 cat("Compute md5 checksum...\n")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
358 library(tools)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
359 return(as.matrix(md5sum(files)))
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
360 }
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
361
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
362 # This function retrieve the raw file in the working directory
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
363 # - if zipfile: unzip the file with its directory tree
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
364 # - if singlefiles: set symlink with the good filename
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
366 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
367
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
368 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
369
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
370 # single - if the file are passed in the command arguments -> refresh singlefile
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
371 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
372 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
373 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
374
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
375 singlefile <- NULL
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
376 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
377 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
378 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
379 # In case, an url is used to import data within Galaxy
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
380 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
381 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
382 }
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
383 }
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
384 # zipfile - if the file are passed in the command arguments -> refresh zipfile
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
385 if (!is.null(args[[paste0("zipfile", prefix)]]))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
386 zipfile <- args[[paste0("zipfile", prefix)]]
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
387
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
388 # single
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
389 if (!is.null(singlefile) && (length("singlefile") > 0)) {
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
390 files <- vector()
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
391 for (singlefile_sampleName in names(singlefile)) {
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
392 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
393 if (!file.exists(singlefile_galaxyPath)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
394 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
395 print(error_message); stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
396 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
397
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
398 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
399 file.copy(singlefile_galaxyPath, singlefile_sampleName)
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
400 files <- c(files, singlefile_sampleName)
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
401 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
402 }
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
403 # zipfile
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
404 if (!is.null(zipfile) && (zipfile != "")) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
405 if (!file.exists(zipfile)) {
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
406 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
407 print(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
408 stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
409 }
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
410 suppressWarnings(unzip(zipfile, unzip = "unzip"))
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
411
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
412 #get the directory name
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
413 suppressWarnings(filesInZip <- unzip(zipfile, list = T))
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
414 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
415 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
416 directory <- "."
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
417 if (length(directories) == 1) directory <- directories
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
418
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
419 cat("files_root_directory\t", directory, "\n")
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
420
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
421 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
422 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
423 info <- file.info(directory)
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
424 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
425 files <- c(directory[!info$isdir], listed)
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
426 exists <- file.exists(files)
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
427 files <- files[exists]
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
428
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
429 }
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
430 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
42
9a9d91ddbe75 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 41
diff changeset
431
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
432 }
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
433
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
434
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
435 # This function retrieve a xset like object
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
436 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
437 getxcmsSetObject <- function(xobject) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
438 # XCMS 1.x
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
439 if (class(xobject) == "xcmsSet")
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
440 return(xobject)
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
441 # XCMS 3.x
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
442 if (class(xobject) == "XCMSnExp") {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
443 # Get the legacy xcmsSet object
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
444 suppressWarnings(xset <- as(xobject, "xcmsSet"))
34
89233250f4b0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 33
diff changeset
445 if (!is.null(xset@phenoData$sample_group))
89233250f4b0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 33
diff changeset
446 sampclass(xset) <- xset@phenoData$sample_group
89233250f4b0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 33
diff changeset
447 else
89233250f4b0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 33
diff changeset
448 sampclass(xset) <- "."
45
99852755ea5c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 44
diff changeset
449 return(xset)
29
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
450 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
451 }