xcms_fillpeaks: lib.r annotate

annotate lib.r @ 45:1a711c1b8b1f draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"

author	workflow4metabolomics
date	Wed, 07 Apr 2021 10:28:50 +0000
parents	1b5fb5a27f5e
children	871ffc15a6da

rev	line source
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	3
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	4 #@author G. Le Corguille
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	6 parseCommandArgs <- function(...) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	7 args <- batch::parseCommandArgs(...)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	8 for (key in names(args)) {
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	9 if (args[key] %in% c("TRUE", "FALSE"))
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	10 args[key] <- as.logical(args[key])
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	11 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	12 return(args)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	13 }
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	14
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	15 #@author G. Le Corguille
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	16 # This function will
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	17 # - load the packages
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	18 # - display the sessionInfo
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
45 1a711c1b8b1f "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)))
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	21
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	22 sessioninfo <- sessionInfo()
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	23 cat(sessioninfo$R.version$version.string, "\n")
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	24 cat("Main packages:\n")
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	26 cat(paste(pkg, packageVersion(pkg)), "\t")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	27 }
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	28 cat("\n")
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	29 cat("Other loaded packages:\n")
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	30 for (pkg in names(sessioninfo$loadedOnly)) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	31 cat(paste(pkg, packageVersion(pkg)), "\t")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	32 }
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	33 cat("\n")
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	34 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	35
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	36 #@author G. Le Corguille
35 e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 34 diff changeset	37 # This function merge several chromBPI or chromTIC into one.
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	38 mergeChrom <- function(chrom_merged, chrom) {
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	39 if (is.null(chrom_merged)) return(NULL)
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	41 return(chrom_merged)
35 e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 34 diff changeset	42 }
e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 34 diff changeset	43
e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 34 diff changeset	44 #@author G. Le Corguille
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	45 # This function merge several xdata into one.
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	46 mergeXData <- function(args) {
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	47 chromTIC <- NULL
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	48 chromBPI <- NULL
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	49 chromTIC_adjusted <- NULL
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	50 chromBPI_adjusted <- NULL
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	51 md5sumList <- NULL
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	52 for (image in args$images) {
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	53
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	54 load(image)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	55 # Handle infiles
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	56 if (!exists("singlefile")) singlefile <- NULL
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	57 if (!exists("zipfile")) zipfile <- NULL
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	59 zipfile <- rawFilePath$zipfile
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	60 singlefile <- rawFilePath$singlefile
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	61
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	62 if (exists("raw_data")) xdata <- raw_data
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	64
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	65 cat(sampleNamesList$sampleNamesOrigin, "\n")
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	66
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	67 if (!exists("xdata_merged")) {
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	68 xdata_merged <- xdata
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	69 singlefile_merged <- singlefile
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	70 md5sumList_merged <- md5sumList
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	71 sampleNamesList_merged <- sampleNamesList
35 e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 34 diff changeset	72 chromTIC_merged <- chromTIC
e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 34 diff changeset	73 chromBPI_merged <- chromBPI
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	74 chromTIC_adjusted_merged <- chromTIC_adjusted
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	75 chromBPI_adjusted_merged <- chromBPI_adjusted
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	76 } else {
45 1a711c1b8b1f "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)
1a711c1b8b1f "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)
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	80
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	81 singlefile_merged <- c(singlefile_merged, singlefile)
1a711c1b8b1f "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$origin)
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
1a711c1b8b1f "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)
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	89 }
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	90 }
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	91 rm(image)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	92 xdata <- xdata_merged; rm(xdata_merged)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	93 singlefile <- singlefile_merged; rm(singlefile_merged)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	94 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	95 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	96
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	97 if (!is.null(args$sampleMetadata)) {
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	98 cat("\tXSET PHENODATA SETTING...\n")
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	99 sampleMetadataFile <- args$sampleMetadata
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	100 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = F)
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	101 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	102
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	103 if (any(is.na(pData(xdata)$sample_group))) {
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	104 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
45 1a711c1b8b1f "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 = " "))
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	106 print(error_message)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	107 stop(error_message)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	108 }
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	109 }
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	110
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	111 if (!is.null(chromTIC_merged)) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	112 chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	113 }
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	114 if (!is.null(chromBPI_merged)) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	115 chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	116 }
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	117 if (!is.null(chromTIC_adjusted_merged)) {
1a711c1b8b1f "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
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	119 }
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	120 if (!is.null(chromBPI_adjusted_merged)) {
1a711c1b8b1f "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
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	122 }
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	123
45 1a711c1b8b1f "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))
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	125 }
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	126
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	127 #@author G. Le Corguille
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	128 # This function convert if it is required the Retention Time in minutes
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	129 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	130 if (convertRTMinute) {
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	131 #converting the retention times (seconds) into minutes
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	132 print("converting the retention times into minutes in the variableMetadata")
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	133 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	134 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	135 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	136 }
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	137 return(variableMetadata)
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	138 }
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	139
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	140 #@author G. Le Corguille
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	141 # This function format ions identifiers
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	142 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	143 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	144 idsDeco <- sapply(splitDeco,
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	145 function(x) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	146 deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	147 }
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	148 )
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	149 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	150 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
20 02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	151 return(variableMetadata)
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	152 }
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	153
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	154 #@author G. Le Corguille
38 a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	155 # This function convert the remain NA to 0 in the dataMatrix
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	156 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	157 if (naTOzero) {
38 a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	158 dataMatrix[is.na(dataMatrix)] <- 0
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	159 }
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	160 return(dataMatrix)
38 a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	161 }
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	162
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	163 #@author G. Le Corguille
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	164 # Draw the plotChromPeakDensity 3 per page in a pdf file
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	165 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
1a711c1b8b1f "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)
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	167
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	168 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	169
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	170 if (length(unique(xdata$sample_group)) < 10) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	171 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	172 }else{
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	173 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	174 }
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	175 names(group_colors) <- unique(xdata$sample_group)
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	176 col_per_samp <- as.character(xdata$sample_group)
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	177 for (i in seq_len(length(group_colors))) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	178 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	179 }
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	180
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	181 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	182 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	183 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	184 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
1a711c1b8b1f "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)))
1a711c1b8b1f "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)
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	187 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	188
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	189 dev.off()
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	190 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	191
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	192 #@author G. Le Corguille
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	193 # Draw the plotChromPeakDensity 3 per page in a pdf file
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	194 getPlotAdjustedRtime <- function(xdata) {
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	195
45 1a711c1b8b1f "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)
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	197
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	198 # Color by group
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	199 if (length(unique(xdata$sample_group)) < 10) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	200 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	201 } else {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	202 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	203 }
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	204 if (length(group_colors) > 1) {
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	205 names(group_colors) <- unique(xdata$sample_group)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	206 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
45 1a711c1b8b1f "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)
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	208 }
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	209
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	210 # Color by sample
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	211 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	212 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	213
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	214 dev.off()
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	215 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	216
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	217 #@author G. Le Corguille
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	218 # value: intensity values to be used into, maxo or intb
45 1a711c1b8b1f "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) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	220 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
40 beebef001d7d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty lecorguille parents: 38 diff changeset	221 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	222 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	223 variableMetadata <- featureDefinitions(xdata)
45 1a711c1b8b1f "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"
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	225 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	226
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	227 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	228 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
38 a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513 lecorguille parents: 37 diff changeset	229 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	230
41 dbe526f13ff3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 40 diff changeset	231 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
45 1a711c1b8b1f "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 = ",")
41 dbe526f13ff3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 40 diff changeset	233
45 1a711c1b8b1f "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)
1a711c1b8b1f "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)
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	236
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	237 }
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	238
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	239 #@author G. Le Corguille
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	240 # It allow different of field separators
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	241 getDataFrameFromFile <- function(filename, header = T) {
1a711c1b8b1f "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)
1a711c1b8b1f "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)
1a711c1b8b1f "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)
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	245 if (ncol(myDataFrame) < 2) {
45 1a711c1b8b1f "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"
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	247 print(error_message)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	248 stop(error_message)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	249 }
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	250 return(myDataFrame)
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	251 }
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	252
37 9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	253 #@author G. Le Corguille
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	254 # Draw the BPI and TIC graphics
9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8 lecorguille parents: 36 diff changeset	255 # colored by sample names or class names
45 1a711c1b8b1f "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") {
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	257
ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	258 if (aggregationFun == "sum")
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	259 type <- "Total Ion Chromatograms"
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	260 else
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	261 type <- "Base Peak Intensity Chromatograms"
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	262
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	263 adjusted <- "Raw"
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	264 if (hasAdjustedRtime(xdata))
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	265 adjusted <- "Adjusted"
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	266
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	267 main <- paste(type, ":", adjusted, "data")
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	268
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	269 pdf(pdfname, width = 16, height = 10)
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	270
ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	271 # Color by group
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	272 if (length(unique(xdata$sample_group)) < 10) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	273 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	274 }else{
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	275 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	276 }
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	277 if (length(group_colors) > 1) {
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	278 names(group_colors) <- unique(xdata$sample_group)
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	279 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
1a711c1b8b1f "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)
34 d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: 33 diff changeset	281 }
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	282
ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	283 # Color by sample
45 1a711c1b8b1f "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$sample_name)), main = main, peakType = "none")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	285 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
33 ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	286
ea611367e1da planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 32 diff changeset	287 dev.off()
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	288 }
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	289
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	290
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	291 # Get the polarities from all the samples of a condition
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	292 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	293 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	294 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	295 cat("Creating the sampleMetadata file...\n")
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	296
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	297 #Create the sampleMetada dataframe
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	298 sampleMetadata <- xdata@phenoData@data
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	299 rownames(sampleMetadata) <- NULL
41 dbe526f13ff3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 40 diff changeset	300 colnames(sampleMetadata) <- c("sample_name", "class")
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	301
41 dbe526f13ff3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 40 diff changeset	302 sampleNamesOrigin <- sampleMetadata$sample_name
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	303 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	304
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	305 if (any(duplicated(sampleNamesMakeNames))) {
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 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())
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	307 for (sampleName in sampleNamesOrigin) {
45 1a711c1b8b1f "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())
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	309 }
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 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.")
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	311 }
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	312
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	313 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 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")
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	315 for (sampleName in sampleNamesOrigin) {
45 1a711c1b8b1f "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"))
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	317 }
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	318 }
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	319
41 dbe526f13ff3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 40 diff changeset	320 sampleMetadata$sample_name <- sampleNamesMakeNames
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	321
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	322
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	323 #For each sample file, the following actions are done
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	324 for (fileIdx in seq_len(length(fileNames(xdata)))) {
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	325 #Check if the file is in the CDF format
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	326 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	327
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	328 # If the column isn't exist, with add one filled with NA
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	329 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	330
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	331 #Extract the polarity (a list of polarities)
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	332 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	333 #Verify if all the scans have the same polarity
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	334 uniq_list <- unique(polarity)
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	335 if (length(uniq_list) > 1) {
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	336 polarity <- "mixed"
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	337 } else {
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	338 polarity <- as.character(uniq_list)
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	339 }
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	340
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	341 #Set the polarity attribute
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	342 sampleMetadata$polarity[fileIdx] <- polarity
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	343 }
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	344
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	345 }
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	346
45 1a711c1b8b1f "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)
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	348
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	349 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	350
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	351 }
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	352
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	353
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	354 # This function will compute MD5 checksum to check the data integrity
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	355 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	356 getMd5sum <- function(files) {
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	357 cat("Compute md5 checksum...\n")
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	358 library(tools)
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	359 return(as.matrix(md5sum(files)))
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	360 }
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	361
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	362 # This function retrieve the raw file in the working directory
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	363 # - if zipfile: unzip the file with its directory tree
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	364 # - if singlefiles: set symlink with the good filename
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	366 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	367
45 1a711c1b8b1f "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'")
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	369
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	370 # single - if the file are passed in the command arguments -> refresh singlefile
45 1a711c1b8b1f "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)]])) {
1a711c1b8b1f "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)]], "\\\|"))
1a711c1b8b1f "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)]], "\\\|"))
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	374
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	375 singlefile <- NULL
45 1a711c1b8b1f "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))) {
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	377 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	378 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	379 # In case, an url is used to import data within Galaxy
45 1a711c1b8b1f "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)
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	381 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	382 }
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	383 }
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	384 # zipfile - if the file are passed in the command arguments -> refresh zipfile
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	385 if (!is.null(args[[paste0("zipfile", prefix)]]))
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	386 zipfile <- args[[paste0("zipfile", prefix)]]
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	387
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	388 # single
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	389 if (!is.null(singlefile) && (length("singlefile") > 0)) {
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	390 files <- vector()
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	391 for (singlefile_sampleName in names(singlefile)) {
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	392 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	393 if (!file.exists(singlefile_galaxyPath)) {
1a711c1b8b1f "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!")
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	395 print(error_message); stop(error_message)
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	396 }
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	397
45 1a711c1b8b1f "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)))
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	399 file.copy(singlefile_galaxyPath, singlefile_sampleName)
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	400 files <- c(files, singlefile_sampleName)
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	401 }
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	402 }
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	403 # zipfile
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	404 if (!is.null(zipfile) && (zipfile != "")) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	405 if (!file.exists(zipfile)) {
1a711c1b8b1f "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!")
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	407 print(error_message)
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	408 stop(error_message)
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	409 }
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	410 suppressWarnings(unzip(zipfile, unzip = "unzip"))
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	411
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	412 #get the directory name
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	413 suppressWarnings(filesInZip <- unzip(zipfile, list = T))
1a711c1b8b1f "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])))
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	415 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	416 directory <- "."
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	417 if (length(directories) == 1) directory <- directories
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	418
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	419 cat("files_root_directory\t", directory, "\n")
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	420
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	421 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	422 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "\|")
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	423 info <- file.info(directory)
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	424 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	425 files <- c(directory[!info$isdir], listed)
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	426 exists <- file.exists(files)
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	427 files <- files[exists]
1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	428
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	429 }
45 1a711c1b8b1f "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))
44 1b5fb5a27f5e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 43 diff changeset	431
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 20 diff changeset	432 }
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	433
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	434
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	435 # This function retrieve a xset like object
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	436 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	437 getxcmsSetObject <- function(xobject) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	438 # XCMS 1.x
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	439 if (class(xobject) == "xcmsSet")
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	440 return(xobject)
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	441 # XCMS 3.x
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	442 if (class(xobject) == "XCMSnExp") {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	443 # Get the legacy xcmsSet object
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	444 suppressWarnings(xset <- as(xobject, "xcmsSet"))
36 e3efe78b14c5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e lecorguille parents: 35 diff changeset	445 if (!is.null(xset@phenoData$sample_group))
e3efe78b14c5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e lecorguille parents: 35 diff changeset	446 sampclass(xset) <- xset@phenoData$sample_group
e3efe78b14c5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e lecorguille parents: 35 diff changeset	447 else
e3efe78b14c5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e lecorguille parents: 35 diff changeset	448 sampclass(xset) <- "."
45 1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 44 diff changeset	449 return(xset)
31 8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	450 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 30 diff changeset	451 }

Mercurial > repos > lecorguille > xcms_fillpeaks

annotate lib.r @ 45:1a711c1b8b1f draft