xcms_retcor: lib.r annotate

annotate lib.r @ 30:4d6f4cd7c3ef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e

author	lecorguille
date	Thu, 01 Mar 2018 04:16:45 -0500
parents	c013ed353a2f
children	281786a7b9a2

rev	line source
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	3
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	4 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	6 parseCommandArgs <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	7 args <- batch::parseCommandArgs(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	8 for (key in names(args)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	10 args[key] = as.logical(args[key])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	11 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	12 return(args)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	13 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	14
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	15 #@author G. Le Corguille
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	16 # This function will
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	17 # - load the packages
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	18 # - display the sessionInfo
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	21
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	22 sessioninfo = sessionInfo()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	24 cat("Main packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	26 cat("Other loaded packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	28 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	29
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	30 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	31 # This function convert if it is required the Retention Time in minutes
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	33 if (convertRTMinute){
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	34 #converting the retention times (seconds) into minutes
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	35 print("converting the retention times into minutes in the variableMetadata")
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	39 }
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	40 return (variableMetadata)
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	41 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	42
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	43 #@author G. Le Corguille
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	44 # This function format ions identifiers
19 2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 18 diff changeset	45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
19 2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 18 diff changeset	50 return(variableMetadata)
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	51 }
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	52
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	53 #@author G. Le Corguille
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	54 # Draw the plotChromPeakDensity 3 per page in a pdf file
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	55 getPlotChromPeakDensity <- function(xdata) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	57
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	59
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	61 names(group_colors) <- unique(xdata$sample_group)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	62
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	64 for (i in 1:nrow(featureDefinitions(xdata))) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	65 plotChromPeakDensity(xdata, mz=c(featureDefinitions(xdata)[i,]$mzmin,featureDefinitions(xdata)[i,]$mzmax), col=group_colors, pch=16, xlim=xlim)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	66 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	67 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	68
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	69 dev.off()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	70 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	71
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	72 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	73 # Draw the plotChromPeakDensity 3 per page in a pdf file
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	74 getPlotAdjustedRtime <- function(xdata) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	75 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	76 # Color by group
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	77 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	78 names(group_colors) <- unique(xdata$sample_group)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	79 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	80 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	81 # Color by sample
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	82 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	83 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	84 dev.off()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	85 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	86
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	87 #@author G. Le Corguille
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	88 # value: intensity values to be used into, maxo or intb
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	89 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	90 dataMatrix <- featureValues(xdata, method="medret", value=intval)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	91 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	92 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	93 variableMetadata <- featureDefinitions(xdata)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	94 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	95 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	96
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	97 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	98 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	99
19 2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 18 diff changeset	100 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 18 diff changeset	101 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	102
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	103 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	104
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	105 #@author Y. Guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	106 getBPC <- function(file,rtcor=NULL, ...) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	107 object <- xcmsRaw(file)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	108 sel <- profRange(object, ...)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	109 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	110 #plotChrom(xcmsRaw(file), base=T)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	111 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	112
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	113 #@author Y. Guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	114 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	115 cat("Creating BIC pdf...\n")
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	116
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	117 if (is.null(xcmsSet)) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	118 cat("Enter an xcmsSet \n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	119 stop()
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	120 } else {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	121 files <- filepaths(xcmsSet)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	122 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	123
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	124 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	125
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	126 classnames <- vector("list",length(phenoDataClass))
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	127 for (i in 1:length(phenoDataClass)){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	128 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	129 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	130
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	131 N <- dim(phenoData(xcmsSet))[1]
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	132
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	133 TIC <- vector("list",N)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	134
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	135
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	136 for (j in 1:N) {
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	137
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	138 TIC[[j]] <- getBPC(files[j])
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	139 #good for raw
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	140 # seems strange for corrected
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	141 #errors if scanrange used in xcmsSetgeneration
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	142 if (!is.null(xcmsSet) && rt == "corrected")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	143 rtcor <- xcmsSet@rt$corrected[[j]]
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	144 else
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	145 rtcor <- NULL
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	146
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	147 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	148 # TIC[[j]][,1]<-rtcor
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	149 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	150
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	151
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	152
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	153 pdf(pdfname,w=16,h=10)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	154 cols <- rainbow(N)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	155 lty <- 1:N
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	156 pch <- 1:N
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	157 #search for max x and max y in BPCs
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	158 xlim <- range(sapply(TIC, function(x) range(x[,1])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	159 ylim <- range(sapply(TIC, function(x) range(x[,2])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	160 ylim <- c(-ylim[2], ylim[2])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	161
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	162
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	163 ##plot start
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	164
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	165 if (length(phenoDataClass)>2){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	166 for (k in 1:(length(phenoDataClass)-1)){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	167 for (l in (k+1):length(phenoDataClass)){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	168 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	169 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	170 colvect <- NULL
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	171 for (j in 1:length(classnames[[k]])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	172 tic <- TIC[[classnames[[k]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	173 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	174 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	175 colvect <- append(colvect,cols[classnames[[k]][j]])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	176 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	177 for (j in 1:length(classnames[[l]])) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	178 # i <- class2names[j]
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	179 tic <- TIC[[classnames[[l]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	180 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	181 colvect <- append(colvect,cols[classnames[[l]][j]])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	182 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	183 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	184 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	185 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	186 }#end if length >2
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	187
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	188 if (length(phenoDataClass)==2){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	189 k <- 1
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	190 l <- 2
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	191 colvect <- NULL
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	192 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	193
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	194 for (j in 1:length(classnames[[k]])) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	195
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	196 tic <- TIC[[classnames[[k]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	197 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	198 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	199 colvect<-append(colvect,cols[classnames[[k]][j]])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	200 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	201 for (j in 1:length(classnames[[l]])) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	202 # i <- class2names[j]
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	203 tic <- TIC[[classnames[[l]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	204 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	205 colvect <- append(colvect,cols[classnames[[l]][j]])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	206 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	207 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	208
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	209 }#end length ==2
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	210
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	211 #case where only one class
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	212 if (length(phenoDataClass)==1){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	213 k <- 1
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	214 ylim <- range(sapply(TIC, function(x) range(x[,2])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	215 colvect <- NULL
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	216 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="BPC")
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	217
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	218 for (j in 1:length(classnames[[k]])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	219 tic <- TIC[[classnames[[k]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	220 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	221 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	222 colvect <- append(colvect,cols[classnames[[k]][j]])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	223 }
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	224
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	225 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	226
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	227 }#end length ==1
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	228
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	229 dev.off() #pdf(pdfname,w=16,h=10)
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	230
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	231 invisible(TIC)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	232 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	233
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	234
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	235
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	236 #@author Y. Guitton
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	237 getTIC <- function(file, rtcor=NULL) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	238 object <- xcmsRaw(file)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	239 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	240 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	241
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	242 #overlay TIC from all files in current folder or from xcmsSet, create pdf
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	243 #@author Y. Guitton
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	244 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	245 cat("Creating TIC pdf...\n")
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	246
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	247 if (is.null(xcmsSet)) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	248 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	249 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="\|")
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	250 if (is.null(files))
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	251 files <- getwd()
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	252 info <- file.info(files)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	253 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	254 files <- c(files[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	255 } else {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	256 files <- filepaths(xcmsSet)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	257 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	258
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	259 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	260 classnames <- vector("list",length(phenoDataClass))
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	261 for (i in 1:length(phenoDataClass)){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	262 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	263 }
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	264
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	265 N <- length(files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	266 TIC <- vector("list",N)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	267
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	268 for (i in 1:N) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	269 if (!is.null(xcmsSet) && rt == "corrected")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	270 rtcor <- xcmsSet@rt$corrected[[i]] else
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	271 rtcor <- NULL
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	272 TIC[[i]] <- getTIC(files[i], rtcor=rtcor)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	273 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	274
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	275 pdf(pdfname, w=16, h=10)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	276 cols <- rainbow(N)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	277 lty <- 1:N
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	278 pch <- 1:N
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	279 #search for max x and max y in TICs
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	280 xlim <- range(sapply(TIC, function(x) range(x[,1])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	281 ylim <- range(sapply(TIC, function(x) range(x[,2])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	282 ylim <- c(-ylim[2], ylim[2])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	283
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	284
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	285 ##plot start
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	286 if (length(phenoDataClass)>2){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	287 for (k in 1:(length(phenoDataClass)-1)){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	288 for (l in (k+1):length(phenoDataClass)){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	289 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	290 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	291 colvect <- NULL
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	292 for (j in 1:length(classnames[[k]])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	293 tic <- TIC[[classnames[[k]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	294 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	295 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	296 colvect <- append(colvect,cols[classnames[[k]][j]])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	297 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	298 for (j in 1:length(classnames[[l]])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	299 # i=class2names[j]
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	300 tic <- TIC[[classnames[[l]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	301 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	302 colvect <- append(colvect,cols[classnames[[l]][j]])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	303 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	304 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	305 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	306 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	307 }#end if length >2
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	308 if (length(phenoDataClass)==2){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	309 k <- 1
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	310 l <- 2
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	311
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	312 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	313 colvect <- NULL
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	314 for (j in 1:length(classnames[[k]])) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	315 tic <- TIC[[classnames[[k]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	316 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	317 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	318 colvect <- append(colvect,cols[classnames[[k]][j]])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	319 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	320 for (j in 1:length(classnames[[l]])) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	321 # i <- class2names[j]
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	322 tic <- TIC[[classnames[[l]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	323 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	324 colvect <- append(colvect,cols[classnames[[l]][j]])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	325 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	326 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	327
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	328 }#end length ==2
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	329
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	330 #case where only one class
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	331 if (length(phenoDataClass)==1){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	332 k <- 1
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	333 ylim <- range(sapply(TIC, function(x) range(x[,2])))
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	334
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	335 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="TIC")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	336 colvect <- NULL
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	337 for (j in 1:length(classnames[[k]])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	338 tic <- TIC[[classnames[[k]][j]]]
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	339 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	340 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	341 colvect <- append(colvect,cols[classnames[[k]][j]])
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	342 }
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	343
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	344 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	345
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	346 }#end length ==1
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	347
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	348 dev.off() #pdf(pdfname,w=16,h=10)
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	349
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	350 invisible(TIC)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	351 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	352
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	353
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	354
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	355 # Get the polarities from all the samples of a condition
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	356 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	357 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	358 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	359 cat("Creating the sampleMetadata file...\n")
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	360
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	361 #Create the sampleMetada dataframe
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	362 sampleMetadata <- xdata@phenoData@data
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	363 rownames(sampleMetadata) <- NULL
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	364 colnames(sampleMetadata) <- c("sampleMetadata", "class")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	365
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	366 sampleNamesOrigin <- sampleMetadata$sampleMetadata
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	367 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	368
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	369 if (any(duplicated(sampleNamesMakeNames))) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	370 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	371 for (sampleName in sampleNamesOrigin) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	372 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	373 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	374 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	375 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	376
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	377 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	378 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	379 for (sampleName in sampleNamesOrigin) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	380 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	381 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	382 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	383
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	384 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	385
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	386
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	387 #For each sample file, the following actions are done
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	388 for (fileIdx in 1:length(fileNames(xdata))) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	389 #Check if the file is in the CDF format
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	390 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	391
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	392 # If the column isn't exist, with add one filled with NA
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	393 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	394
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	395 #Extract the polarity (a list of polarities)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	396 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	397 #Verify if all the scans have the same polarity
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	398 uniq_list <- unique(polarity)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	399 if (length(uniq_list)>1){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	400 polarity <- "mixed"
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	401 } else {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	402 polarity <- as.character(uniq_list)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	403 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	404
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	405 #Set the polarity attribute
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	406 sampleMetadata$polarity[fileIdx] <- polarity
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	407 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	408
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	409 }
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	410
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	411 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	412
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	413 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	414
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	415 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	416
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	417
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	418 # This function check if xcms will found all the files
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	419 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	420 checkFilesCompatibilityWithXcms <- function(directory) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	421 cat("Checking files filenames compatibilities with xmcs...\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	422 # WHAT XCMS WILL FIND
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	423 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	424 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	425 info <- file.info(directory)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	426 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	427 files <- c(directory[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	428 files_abs <- file.path(getwd(), files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	429 exists <- file.exists(files_abs)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	430 files[exists] <- files_abs[exists]
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	431 files[exists] <- sub("//","/",files[exists])
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	432
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	433 # WHAT IS ON THE FILESYSTEM
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	434 filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.' -not -path 'conda-env' -type f -name \"\"", sep=""), intern=T)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	435 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	436
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	437 # COMPARISON
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	438 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	439 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	440 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	441 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	442 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	443 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	444
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	445
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	446 #This function list the compatible files within the directory as xcms did
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	447 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	448 getMSFiles <- function (directory) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	449 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	450 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	451 info <- file.info(directory)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	452 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	453 files <- c(directory[!info$isdir], listed)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	454 exists <- file.exists(files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	455 files <- files[exists]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	456 return(files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	457 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	458
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	459 # This function check if XML contains special caracters. It also checks integrity and completness.
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	460 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	461 checkXmlStructure <- function (directory) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	462 cat("Checking XML structure...\n")
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	463
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	464 cmd <- paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	465 capture <- system(cmd, intern=TRUE)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	466
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	467 if (length(capture)>0){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	468 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	469 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	470 write(capture, stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	471 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	472 }
15 c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 14 diff changeset	473
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	474 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	475
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	476
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	477 # This function check if XML contain special characters
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	478 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	479 deleteXmlBadCharacters<- function (directory) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	480 cat("Checking Non ASCII characters in the XML...\n")
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	481
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	482 processed <- F
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	483 l <- system( paste("find",directory, "-not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	484 for (i in l){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	485 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	486 capture <- suppressWarnings(system(cmd, intern=TRUE))
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	487 if (length(capture)>0){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	488 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	489 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	490 c <- system(cmd, intern=TRUE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	491 capture <- ""
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	492 processed <- T
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	493 }
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	494 }
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	495 if (processed) cat("\n\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	496 return(processed)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	497 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	498
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	499
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	500 # This function will compute MD5 checksum to check the data integrity
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	501 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	502 getMd5sum <- function (directory) {
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	503 cat("Compute md5 checksum...\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	504 # WHAT XCMS WILL FIND
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	505 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	506 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	507 info <- file.info(directory)
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	508 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	509 files <- c(directory[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	510 exists <- file.exists(files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	511 files <- files[exists]
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	512
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	513 library(tools)
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	514
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	515 #cat("\n\n")
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	516
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	517 return(as.matrix(md5sum(files)))
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	518 }
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	519
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	520
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	521 # This function get the raw file path from the arguments
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	522 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	523 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	524 if (!is.null(args$zipfile)) zipfile <- args$zipfile
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	525 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	526 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	527
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	528 if (!is.null(args$singlefile_galaxyPath)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	529 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	530 singlefile_sampleNames <- args$singlefile_sampleName
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	531 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	532 if (!is.null(args$singlefile_galaxyPathPositive)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	533 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	534 singlefile_sampleNames <- args$singlefile_sampleNamePositive
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	535 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	536 if (!is.null(args$singlefile_galaxyPathNegative)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	537 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	538 singlefile_sampleNames <- args$singlefile_sampleNameNegative
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	539 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	540 if (exists("singlefile_galaxyPaths")){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	541 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,","))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	542 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,","))
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	543
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	544 singlefile <- NULL
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	545 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	546 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	547 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	548 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	549 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	550 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	551 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	552 args[[argument]] <- NULL
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	553 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	554 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	555 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	556
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	557
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	558 # This function retrieve the raw file in the working directory
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	559 # - if zipfile: unzip the file with its directory tree
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	560 # - if singlefiles: set symlink with the good filename
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	561 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	562 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	563 if(!is.null(singlefile) && (length("singlefile")>0)) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	564 for (singlefile_sampleName in names(singlefile)) {
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	565 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	566 if(!file.exists(singlefile_galaxyPath)){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	567 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	568 print(error_message); stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	569 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	570
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	571 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	572 file.copy(singlefile_galaxyPath, singlefile_sampleName)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	573
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	574 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	575 directory <- "."
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	576
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	577 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	578 if(!is.null(zipfile) && (zipfile != "")) {
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	579 if(!file.exists(zipfile)){
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	580 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	581 print(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	582 stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	583 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	584
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	585 #list all file in the zip file
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	586 #zip_files <- unzip(zipfile,list=T)[,"Name"]
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	587
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	588 #unzip
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	589 suppressWarnings(unzip(zipfile, unzip="unzip"))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	590
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	591 #get the directory name
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	592 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	593 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	594 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	595 directory <- "."
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	596 if (length(directories) == 1) directory <- directories
22 411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	597
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	598 cat("files_root_directory\t",directory,"\n")
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	599
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	600 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	601 return (directory)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 19 diff changeset	602 }
30 4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	603
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	604
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	605 # This function retrieve a xset like object
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	606 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	607 getxcmsSetObject <- function(xobject) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	608 # XCMS 1.x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	609 if (class(xobject) == "xcmsSet")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	610 return (xobject)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	611 # XCMS 3.x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	612 if (class(xobject) == "XCMSnExp") {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	613 # Get the legacy xcmsSet object
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	614 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	615 sampclass(xset) <- xset@phenoData$sample_group
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	616 return (xset)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	617 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	618 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	619
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	620
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	621 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	622 # https://github.com/sneumann/xcms/issues/250
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	623 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	624 mzfmt <- paste("%.", mzdec, "f", sep = "")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	625 rtfmt <- paste("%.", rtdec, "f", sep = "")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	626
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	627 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	628 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	629
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	630 if (any(dup <- duplicated(gnames)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	631 for (dupname in unique(gnames[dup])) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	632 dupidx <- which(gnames == dupname)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	633 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	634 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	635
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	636 return (gnames)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	637 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	638
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	639 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	640 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	641 .concatenate_XCMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	642 x <- list(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	643 if (length(x) == 0)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	644 return(NULL)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	645 if (length(x) == 1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	646 return(x[[1]])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	647 ## Check that all are XCMSnExp objects.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	648 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	649 stop("All passed objects should be 'XCMSnExp' objects")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	650 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	651 ## If any of the XCMSnExp has alignment results or detected features drop
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	652 ## them!
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	653 x <- lapply(x, function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	654 if (hasAdjustedRtime(z)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	655 z <- dropAdjustedRtime(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	656 warning("Adjusted retention times found, had to drop them.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	657 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	658 if (hasFeatures(z)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	659 z <- dropFeatureDefinitions(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	660 warning("Feature definitions found, had to drop them.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	661 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	662 z
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	663 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	664 ## Combine peaks
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	665 fls <- lapply(x, fileNames)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	666 startidx <- cumsum(lengths(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	667 pks <- lapply(x, chromPeaks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	668 procH <- lapply(x, processHistory)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	669 for (i in 2:length(fls)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	670 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	671 procH[[i]] <- lapply(procH[[i]], function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	672 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	673 z
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	674 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	675 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	676 pks <- do.call(rbind, pks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	677 new_x@.processHistory <- unlist(procH)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	678 chromPeaks(new_x) <- pks
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	679 if (validObject(new_x))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	680 new_x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	681 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	682
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	683 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	684 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	685 .concatenate_OnDiskMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	686 x <- list(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	687 if (length(x) == 0)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	688 return(NULL)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	689 if (length(x) == 1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	690 return(x[[1]])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	691 ## Check that all are XCMSnExp objects.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	692 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	693 stop("All passed objects should be 'OnDiskMSnExp' objects")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	694 ## Check processingQueue
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	695 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	696 new_procQ <- procQ[[1]]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	697 is_ok <- unlist(lapply(procQ, function(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	698 !is.character(all.equal(new_procQ, z))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	699 ))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	700 if (any(!is_ok)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	701 warning("Processing queues from the submitted objects differ! ",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	702 "Dropping the processing queue.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	703 new_procQ <- list()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	704 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	705 ## processingData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	706 fls <- lapply(x, function(z) z@processingData@files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	707 startidx <- cumsum(lengths(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	708 ## featureData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	709 featd <- lapply(x, fData)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	710 ## Have to update the file index and the spectrum names.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	711 for (i in 2:length(featd)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	712 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	713 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	714 fileIds = featd[[i]]$fileIdx,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	715 spectrumIds = featd[[i]]$spIdx,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	716 nSpectra = nrow(featd[[i]]),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	717 nFiles = length(unlist(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	718 )
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	719 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	720 featd <- do.call(rbind, featd)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	721 featd$spectrum <- 1:nrow(featd)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	722 ## experimentData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	723 expdata <- lapply(x, function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	724 ed <- z@experimentData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	725 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	726 instrumentModel = ed@instrumentModel,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	727 ionSource = ed@ionSource,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	728 analyser = ed@analyser,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	729 detectorType = ed@detectorType,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	730 stringsAsFactors = FALSE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	731 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	732 expdata <- do.call(rbind, expdata)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	733 expdata <- new("MIAPE",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	734 instrumentManufacturer = expdata$instrumentManufacturer,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	735 instrumentModel = expdata$instrumentModel,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	736 ionSource = expdata$ionSource,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	737 analyser = expdata$analyser,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	738 detectorType = expdata$detectorType)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	739
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	740 ## protocolData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	741 protodata <- lapply(x, function(z) z@protocolData)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	742 if (any(unlist(lapply(protodata, nrow)) > 0))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	743 warning("Found non-empty protocol data, but merging protocol data is",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	744 " currently not supported. Skipped.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	745 ## phenoData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	746 pdata <- do.call(rbind, lapply(x, pData))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	747 res <- new(
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	748 "OnDiskMSnExp",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	749 phenoData = new("NAnnotatedDataFrame", data = pdata),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	750 featureData = new("AnnotatedDataFrame", featd),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	751 processingData = new("MSnProcess",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	752 processing = paste0("Concatenated [", date(), "]"),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	753 files = unlist(fls), smoothed = NA),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	754 experimentData = expdata,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	755 spectraProcessingQueue = new_procQ)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	756 if (validObject(res))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	757 res
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	758 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	759
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	760 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	761 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	762 c.XCMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	763 .concatenate_XCMSnExp(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 29 diff changeset	764 }

Mercurial > repos > lecorguille > xcms_retcor

annotate lib.r @ 30:4d6f4cd7c3ef draft