camera_combinexsannos: lib.r annotate

author	workflow4metabolomics
date	Fri, 26 Jul 2019 16:49:18 -0400
parents
children	ea15115a5b3f

rev	line source
0 139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	1 # lib.r
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	2
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	3 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	4 # solve an issue with batch if arguments are logical TRUE/FALSE
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	5 parseCommandArgs <- function(...) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	6 args <- batch::parseCommandArgs(...)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	7 for (key in names(args)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	8 if (args[key] %in% c("TRUE","FALSE"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	9 args[key] = as.logical(args[key])
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	10 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	11 return(args)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	12 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	13
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	14 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	15 # This function will
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	16 # - load the packages
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	17 # - display the sessionInfo
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	18 loadAndDisplayPackages <- function(pkgs) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	19 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	20
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	21 sessioninfo = sessionInfo()
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	22 cat(sessioninfo$R.version$version.string,"\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	23 cat("Main packages:\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	24 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	25 cat("Other loaded packages:\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	26 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	27 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	28
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	29 # This function retrieve a xset like object
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	30 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	31 getxcmsSetObject <- function(xobject) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	32 # XCMS 1.x
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	33 if (class(xobject) == "xcmsSet")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	34 return (xobject)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	35 # XCMS 3.x
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	36 if (class(xobject) == "XCMSnExp") {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	37 # Get the legacy xcmsSet object
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	38 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	39 if (is.null(xset@phenoData$sample_group))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	40 sampclass(xset) = "."
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	41 else
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	42 sampclass(xset) <- xset@phenoData$sample_group
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	43 if (!is.null(xset@phenoData$sample_name))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	44 rownames(xset@phenoData) = xset@phenoData$sample_name
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	45 return (xset)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	46 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	47 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	48
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	49 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	50 #The function create a pdf from the different png generated by diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	51 diffreport_png2pdf <- function(filebase) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	52 dir.create("pdf")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	53
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	54 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	55 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	56
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	57 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	58 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	59
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	60 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	61
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	62 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	63 #The function create a zip archive from the different png generated by diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	64 diffreport_png2zip <- function() {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	65 zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	66 zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	67 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	68
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	69 #The function create a zip archive from the different tabular generated by diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	70 diffreport_tabular2zip <- function() {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	71 zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	72 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	73
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	74 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	75 #This function convert if it is required the Retention Time in minutes
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	76 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	77 if (convertRTMinute){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	78 #converting the retention times (seconds) into minutes
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	79 print("converting the retention times into minutes in the variableMetadata")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	80 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	81 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	82 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	83 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	84 return (variableMetadata)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	85 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	86
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	87 #@author G. Le Corguille
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	88 #This function format ions identifiers
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	89 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	90 splitDeco = strsplit(as.character(variableMetadata$name),"_")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	91 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	92 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	93 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	94 return(variableMetadata)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	95 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	96
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	97 #The function annotateDiffreport without the corr function which bugs
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	98 annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	99 # Resolve the bug with x11, with the function png
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	100 options(bitmapType='cairo')
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	101
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	102 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	103 res=try(is.null(xset@filled))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	104
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	105 # ------ annot -------
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	106 args$calcCiS=as.logical(args$calcCiS)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	107 args$calcIso=as.logical(args$calcIso)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	108 args$calcCaS=as.logical(args$calcCaS)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	109
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	110 # common parameters
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	111 args4annotate = list(object=xset,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	112 nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	113 maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	114 ppm=args$ppm,mzabs=args$mzabs,quick=args$quick,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	115 polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	116
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	117 # quick == FALSE
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	118 if(args$quick==FALSE) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	119 args4annotate = append(args4annotate,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	120 list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	121 calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	122 # no ruleset
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	123 if (!is.null(args$multiplier)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	124 args4annotate = append(args4annotate,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	125 list(multiplier=args$multiplier))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	126 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	127 # ruleset
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	128 else {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	129 rulset=read.table(args$rules, h=T, sep=";")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	130 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	131 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	132 if (ncol(rulset) < 4) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	133 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	134 print(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	135 stop(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	136 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	137
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	138 args4annotate = append(args4annotate,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	139 list(rules=rulset))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	140 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	141 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	142
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	143
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	144 # launch annotate
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	145 xa = do.call("annotate", args4annotate)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	146 peakList=getPeaklist(xa,intval=args$intval)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	147 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	148
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	149 # --- Multi condition : diffreport ---
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	150 diffrepOri=NULL
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	151 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	152 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	153 res=try(is.null(xset@filled))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	154 classes=levels(sampclass(xset))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	155 x=1:(length(classes)-1)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	156 for (i in seq(along=x) ) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	157 y=1:(length(classes))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	158 for (n in seq(along=y)){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	159 if(i+n <= length(classes)){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	160 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	161
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	162 diffrep=diffreport(
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	163 object=xset,class1=classes[i],class2=classes[i+n],
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	164 filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	165 sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	166
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	167 diffrepOri = diffrep
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	168
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	169 # renamming of the column rtmed to rt to fit with camera peaklist function output
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	170 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	171 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	172
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	173 # combines results and reorder columns
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	174 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	175 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	176
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	177 diffrep = RTSecondToMinute(diffrep, args$convertRTMinute)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	178 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	179
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	180 if(args$sortpval){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	181 diffrep=diffrep[order(diffrep$pvalue), ]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	182 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	183
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	184 dir.create("tabular", showWarnings = FALSE)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	185 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	186
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	187 if (args$eicmax != 0) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	188 if (args$png2 == "pdf")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	189 diffreport_png2pdf(filebase)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	190 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	191 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	192 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	193 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	194 if (args$png2 == "zip")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	195 diffreport_png2zip()
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	196 if (args$tabular2 == "zip")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	197 diffreport_tabular2zip()
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	198 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	199
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	200 # --- variableMetadata ---
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	201 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	202 variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	203 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	204 # if we have 2 conditions, we keep stat of diffrep
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	205 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	206 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	207 if(exists("args[[\"sortpval\"]]")){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	208 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	209 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	210 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	211
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	212 variableMetadataOri=variableMetadata
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	213 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	214
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	215 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	216
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	217 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	218
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	219
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	220 combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	221 pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	222 numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	223
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	224 #Load the two Rdata to extract the xset objects from positive and negative mode
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	225 cat("\tObject xset from positive mode\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	226 print(xaP)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	227 cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	228
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	229 cat("\tObject xset from negative mode\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	230 print(xaN)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	231 cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	232
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	233 cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	234 cat("\tCombining...\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	235 #Convert the string to numeric for creating matrix
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	236 row=as.numeric(strsplit(ruleset,",")[[1]][1])
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	237 column=as.numeric(strsplit(ruleset,",")[[1]][2])
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	238 ruleset=cbind(row,column)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	239 #Test if the file comes from an older version tool
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	240 if ((!is.null(xaP)) & (!is.null(xaN))) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	241 #Launch the combinexsannos function from CAMERA
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	242 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	243 } else {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	244 stop("You must relauch the CAMERA.annotate step with the lastest version.")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	245 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	246
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	247 if(pos){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	248 xa=xaP
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	249 mode="neg. Mode"
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	250 } else {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	251 xa=xaN
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	252 mode="pos. Mode"
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	253 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	254
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	255 peakList=getPeaklist(xa)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	256 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	257 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	258 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	259
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	260 #Test if there are more than two classes (conditions)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	261 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	262 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	263 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	264
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	265 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	266 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	267 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	268
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	269 rownames(variableMetadata) = NULL
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	270 #TODO: checker
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	271 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	272
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	273 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	274 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	275
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	276 #If the user want to keep only the metabolites which match a difference
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	277 if(keep_meta){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	278 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	279 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	280
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	281 #Write the output into a tsv file
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	282 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	283 return(variableMetadata);
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	284
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	285 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	286
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	287 # This function get the raw file path from the arguments
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	288 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	289 if (!is.null(args$zipfile)) zipfile = args$zipfile
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	290 if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	291 if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	292
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	293 if (!is.null(args$singlefile_galaxyPath)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	294 singlefile_galaxyPaths = args$singlefile_galaxyPath;
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	295 singlefile_sampleNames = args$singlefile_sampleName
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	296 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	297 if (!is.null(args$singlefile_galaxyPathPositive)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	298 singlefile_galaxyPaths = args$singlefile_galaxyPathPositive;
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	299 singlefile_sampleNames = args$singlefile_sampleNamePositive
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	300 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	301 if (!is.null(args$singlefile_galaxyPathNegative)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	302 singlefile_galaxyPaths = args$singlefile_galaxyPathNegative;
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	303 singlefile_sampleNames = args$singlefile_sampleNameNegative
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	304 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	305 if (exists("singlefile_galaxyPaths")){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	306 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	307 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	308
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	309 singlefile=NULL
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	310 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	311 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	312 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	313 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	314 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	315 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	316 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	317 "singlefile_galaxyPath", "singlefile_sampleName",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	318 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	319 "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	320 args[[argument]]=NULL
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	321 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	322 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	323 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	324
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	325
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	326 # This function retrieve the raw file in the working directory
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	327 # - if zipfile: unzip the file with its directory tree
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	328 # - if singlefiles: set symlink with the good filename
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	329 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	330 if(!is.null(singlefile) && (length("singlefile")>0)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	331 for (singlefile_sampleName in names(singlefile)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	332 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	333 if(!file.exists(singlefile_galaxyPath)){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	334 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	335 print(error_message); stop(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	336 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	337
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	338 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	339 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	340 directory = "."
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	341
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	342 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	343 if(!is.null(zipfile) && (zipfile!="")) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	344 if(!file.exists(zipfile)){
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	345 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	346 print(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	347 stop(error_message)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	348 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	349
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	350 #list all file in the zip file
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	351 #zip_files=unzip(zipfile,list=T)[,"Name"]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	352
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	353 #unzip
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	354 suppressWarnings(unzip(zipfile, unzip="unzip"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	355
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	356 #get the directory name
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	357 filesInZip=unzip(zipfile, list=T);
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	358 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	359 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	360 directory = "."
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	361 if (length(directories) == 1) directory = directories
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	362
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	363 cat("files_root_directory\t",directory,"\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	364
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	365 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	366 return (directory)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	367 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	368
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	369 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	370 # https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	371 # https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	372 ############################################################
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	373 ## getEIC
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	374 getEIC <- function(object, mzrange, rtrange = 200,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	375 groupidx, sampleidx = sampnames(object),
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	376 rt = c("corrected", "raw")) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	377
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	378 files <- filepaths(object)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	379 grp <- groups(object)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	380 samp <- sampnames(object)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	381 prof <- profinfo(object)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	382
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	383 rt <- match.arg(rt)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	384
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	385 if (is.numeric(sampleidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	386 sampleidx <- sampnames(object)[sampleidx]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	387 sampidx <- match(sampleidx, sampnames(object))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	388
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	389 if (!missing(groupidx)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	390 if (is.numeric(groupidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	391 groupidx <- groupnames(object)[unique(as.integer(groupidx))]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	392 grpidx <- match(groupidx, groupnames(object, template = groupidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	393 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	394
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	395 if (missing(mzrange)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	396 if (missing(groupidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	397 stop("No m/z range or groups specified")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	398 if (any(is.na(groupval(object, value = "mz"))))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	399 warning(
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	400 "`NA` values in xcmsSet. Use fillPeaks() on the object to fill",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	401 "-in missing peak values. Note however that this will also ",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	402 "insert intensities of 0 for peaks that can not be filled in.")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	403 mzmin <- apply(groupval(object, value = "mzmin"), 1, min, na.rm = TRUE)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	404 mzmax <- apply(groupval(object, value = "mzmax"), 1, max, na.rm = TRUE)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	405 mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	406 ## if (any(is.na(groupval(object, value = "mz"))))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	407 ## stop('Please use fillPeaks() to fill up NA values !')
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	408 ## mzmin <- -rowMax(-groupval(object, value = "mzmin"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	409 ## mzmax <- rowMax(groupval(object, value = "mzmax"))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	410 ## mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	411 } else if (all(c("mzmin","mzmax") %in% colnames(mzrange)))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	412 mzrange <- mzrange[,c("mzmin", "mzmax"),drop=FALSE]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	413 else if (is.null(dim(mzrange)))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	414 stop("mzrange must be a matrix")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	415 colnames(mzrange) <- c("mzmin", "mzmax")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	416
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	417 if (length(rtrange) == 1) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	418 if (missing(groupidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	419 rtrange <- matrix(rep(range(object@rt[[rt]][sampidx]), nrow(mzrange)),
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	420 ncol = 2, byrow = TRUE)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	421 else {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	422 rtrange <- retexp(grp[grpidx,c("rtmin","rtmax"),drop=FALSE], rtrange)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	423 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	424 } else if (is.null(dim(rtrange)))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	425 stop("rtrange must be a matrix or single number")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	426 colnames(rtrange) <- c("rtmin", "rtmax")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	427
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	428 ## Ensure that we've got corrected retention time if requested.
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	429 if (is.null(object@rt[[rt]]))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	430 stop(rt, " retention times not present in 'object'!")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	431
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	432 ## Ensure that the defined retention time range is within the rtrange of the
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	433 ## object: we're using the max minimal rt of all files and the min maximal rt
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	434 rtrs <- lapply(object@rt[[rt]], range)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	435 rtr <- c(max(unlist(lapply(rtrs, "[", 1))),
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	436 min(unlist(lapply(rtrs, "[", 2))))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	437 ## Check if we've got a range which is completely off:
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	438 if (any(rtrange[, "rtmin"] >= rtr[2] \| rtrange[, "rtmax"] <= rtr[1])) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	439 outs <- which(rtrange[, "rtmin"] >= rtr[2] \|
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	440 rtrange[, "rtmax"] <= rtr[1])
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	441 stop(length(outs), " of the specified 'rtrange' are completely outside ",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	442 "of the retention time range of 'object' which is (", rtr[1], ", ",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	443 rtr[2], "). The first was: (", rtrange[outs[1], "rtmin"], ", ",
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	444 rtrange[outs[1], "rtmax"], "!")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	445 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	446 lower_rt_outside <- rtrange[, "rtmin"] < rtr[1]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	447 upper_rt_outside <- rtrange[, "rtmax"] > rtr[2]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	448 if (any(lower_rt_outside) \| any(upper_rt_outside)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	449 ## Silently fix these ranges.
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	450 rtrange[lower_rt_outside, "rtmin"] <- rtr[1]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	451 rtrange[upper_rt_outside, "rtmax"] <- rtr[2]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	452 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	453
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	454 if (missing(groupidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	455 gnames <- character(0)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	456 else
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	457 gnames <- groupidx
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	458
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	459 eic <- vector("list", length(sampleidx))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	460 names(eic) <- sampleidx
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	461
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	462 for (i in seq(along = sampidx)) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	463
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	464 ## cat(sampleidx[i], "")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	465 flush.console()
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	466 ## getXcmsRaw takes care of rt correction, susetting to scanrage and other
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	467 ## stuff.
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	468 lcraw <- getXcmsRaw(object, sampleidx = sampidx[i], rt=rt)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	469 currenteic <- xcms::getEIC(lcraw, mzrange, rtrange, step = prof$step)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	470 eic[[i]] <- currenteic@eic[[1]]
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	471 rm(lcraw)
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	472 gc()
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	473 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	474 ## cat("\n")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	475
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	476 invisible(new("xcmsEIC", eic = eic, mzrange = mzrange, rtrange = rtrange,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	477 rt = rt, groupnames = gnames))
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	478 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	479
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	480 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	481 # https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	482 # https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	483 ############################################################
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	484 ## diffreport
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	485 diffreport = function(object,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	486 class1 = levels(sampclass(object))[1],
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	487 class2 = levels(sampclass(object))[2],
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	488 filebase = character(),
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	489 eicmax = 0, eicwidth = 200,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	490 sortpval = TRUE,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	491 classeic = c(class1,class2),
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	492 value = c("into","maxo","intb"),
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	493 metlin = FALSE,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	494 h = 480, w = 640, mzdec=2,
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	495 missing = numeric(), ...) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	496
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	497 if ( nrow(object@groups)<1 \|\| length(object@groupidx) <1) {
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	498 stop("No group information. Use group().")
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	499 }
139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464 workflow4metabolomics parents: diff changeset	500

0

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

1 # lib.r

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

2

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

3 #@author G. Le Corguille

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

4 # solve an issue with batch if arguments are logical TRUE/FALSE

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

5 parseCommandArgs <- function(...) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

6 args <- batch::parseCommandArgs(...)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

7 for (key in names(args)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

8 if (args[key] %in% c("TRUE","FALSE"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

9 args[key] = as.logical(args[key])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

10 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

11 return(args)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

12 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

13

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

14 #@author G. Le Corguille

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

15 # This function will

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

16 # - load the packages

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

17 # - display the sessionInfo

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

18 loadAndDisplayPackages <- function(pkgs) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

19 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

20

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

21 sessioninfo = sessionInfo()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

22 cat(sessioninfo$R.version$version.string,"\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

23 cat("Main packages:\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

24 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

25 cat("Other loaded packages:\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

26 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

27 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

28

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

29 # This function retrieve a xset like object

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

30 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

31 getxcmsSetObject <- function(xobject) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

32 # XCMS 1.x

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

33 if (class(xobject) == "xcmsSet")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

34 return (xobject)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

35 # XCMS 3.x

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

36 if (class(xobject) == "XCMSnExp") {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

37 # Get the legacy xcmsSet object

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

38 suppressWarnings(xset <- as(xobject, 'xcmsSet'))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

39 if (is.null(xset@phenoData$sample_group))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

40 sampclass(xset) = "."

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

41 else

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

42 sampclass(xset) <- xset@phenoData$sample_group

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

43 if (!is.null(xset@phenoData$sample_name))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

44 rownames(xset@phenoData) = xset@phenoData$sample_name

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

45 return (xset)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

46 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

47 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

48

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

49 #@author G. Le Corguille

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

50 #The function create a pdf from the different png generated by diffreport

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

51 diffreport_png2pdf <- function(filebase) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

52 dir.create("pdf")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

53

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

54 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

55 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

56

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

57 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

58 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

59

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

60 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

61

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

62 #@author G. Le Corguille

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

63 #The function create a zip archive from the different png generated by diffreport

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

64 diffreport_png2zip <- function() {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

65 zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

66 zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

67 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

68

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

69 #The function create a zip archive from the different tabular generated by diffreport

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

70 diffreport_tabular2zip <- function() {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

71 zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

72 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

73

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

74 #@author G. Le Corguille

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

75 #This function convert if it is required the Retention Time in minutes

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

76 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

77 if (convertRTMinute){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

78 #converting the retention times (seconds) into minutes

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

79 print("converting the retention times into minutes in the variableMetadata")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

80 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

81 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

82 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

83 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

84 return (variableMetadata)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

85 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

86

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

87 #@author G. Le Corguille

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

88 #This function format ions identifiers

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

89 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

90 splitDeco = strsplit(as.character(variableMetadata$name),"_")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

91 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

92 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

93 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

94 return(variableMetadata)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

95 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

96

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

97 #The function annotateDiffreport without the corr function which bugs

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

98 annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

99 # Resolve the bug with x11, with the function png

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

100 options(bitmapType='cairo')

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

101

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

102 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

103 res=try(is.null(xset@filled))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

104

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

105 # ------ annot -------

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

106 args$calcCiS=as.logical(args$calcCiS)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

107 args$calcIso=as.logical(args$calcIso)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

108 args$calcCaS=as.logical(args$calcCaS)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

109

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

110 # common parameters

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

111 args4annotate = list(object=xset,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

112 nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

113 maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

114 ppm=args$ppm,mzabs=args$mzabs,quick=args$quick,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

115 polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

116

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

117 # quick == FALSE

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

118 if(args$quick==FALSE) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

119 args4annotate = append(args4annotate,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

120 list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

121 calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

122 # no ruleset

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

123 if (!is.null(args$multiplier)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

124 args4annotate = append(args4annotate,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

125 list(multiplier=args$multiplier))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

126 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

127 # ruleset

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

128 else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

129 rulset=read.table(args$rules, h=T, sep=";")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

130 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

131 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

132 if (ncol(rulset) < 4) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

133 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

134 print(error_message)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

135 stop(error_message)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

136 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

137

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

138 args4annotate = append(args4annotate,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

139 list(rules=rulset))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

140 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

141 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

142

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

143

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

144 # launch annotate

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

145 xa = do.call("annotate", args4annotate)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

146 peakList=getPeaklist(xa,intval=args$intval)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

147 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

148

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

149 # --- Multi condition : diffreport ---

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

150 diffrepOri=NULL

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

151 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

152 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

153 res=try(is.null(xset@filled))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

154 classes=levels(sampclass(xset))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

155 x=1:(length(classes)-1)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

156 for (i in seq(along=x) ) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

157 y=1:(length(classes))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

158 for (n in seq(along=y)){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

159 if(i+n <= length(classes)){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

160 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

161

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

162 diffrep=diffreport(

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

163 object=xset,class1=classes[i],class2=classes[i+n],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

164 filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

165 sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

166

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

167 diffrepOri = diffrep

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

168

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

169 # renamming of the column rtmed to rt to fit with camera peaklist function output

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

170 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

171 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

172

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

173 # combines results and reorder columns

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

174 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

175 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

176

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

177 diffrep = RTSecondToMinute(diffrep, args$convertRTMinute)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

178 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

179

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

180 if(args$sortpval){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

181 diffrep=diffrep[order(diffrep$pvalue), ]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

182 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

183

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

184 dir.create("tabular", showWarnings = FALSE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

185 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

186

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

187 if (args$eicmax != 0) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

188 if (args$png2 == "pdf")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

189 diffreport_png2pdf(filebase)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

190 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

191 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

192 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

193 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

194 if (args$png2 == "zip")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

195 diffreport_png2zip()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

196 if (args$tabular2 == "zip")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

197 diffreport_tabular2zip()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

198 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

199

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

200 # --- variableMetadata ---

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

201 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

202 variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

203 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

204 # if we have 2 conditions, we keep stat of diffrep

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

205 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

206 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

207 if(exists("args[[\"sortpval\"]]")){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

208 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

209 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

210 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

211

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

212 variableMetadataOri=variableMetadata

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

213 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

214

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

215 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

216

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

217 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

218

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

219

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

220 combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

221 pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

222 numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

223

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

224 #Load the two Rdata to extract the xset objects from positive and negative mode

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

225 cat("\tObject xset from positive mode\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

226 print(xaP)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

227 cat("\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

228

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

229 cat("\tObject xset from negative mode\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

230 print(xaN)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

231 cat("\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

232

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

233 cat("\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

234 cat("\tCombining...\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

235 #Convert the string to numeric for creating matrix

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

236 row=as.numeric(strsplit(ruleset,",")[[1]][1])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

237 column=as.numeric(strsplit(ruleset,",")[[1]][2])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

238 ruleset=cbind(row,column)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

239 #Test if the file comes from an older version tool

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

240 if ((!is.null(xaP)) & (!is.null(xaN))) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

241 #Launch the combinexsannos function from CAMERA

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

242 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

243 } else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

244 stop("You must relauch the CAMERA.annotate step with the lastest version.")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

245 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

246

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

247 if(pos){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

248 xa=xaP

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

249 mode="neg. Mode"

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

250 } else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

251 xa=xaN

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

252 mode="pos. Mode"

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

253 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

254

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

255 peakList=getPeaklist(xa)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

256 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

257 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

258 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

259

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

260 #Test if there are more than two classes (conditions)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

261 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

262 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

263 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

264

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

265 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

266 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

267 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

268

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

269 rownames(variableMetadata) = NULL

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

270 #TODO: checker

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

271 #colnames(variableMetadata)[1:2] = c("name","mz/rt");

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

272

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

273 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

274 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

275

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

276 #If the user want to keep only the metabolites which match a difference

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

277 if(keep_meta){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

278 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

279 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

280

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

281 #Write the output into a tsv file

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

282 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

283 return(variableMetadata);

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

284

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

285 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

286

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

287 # This function get the raw file path from the arguments

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

288 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

289 if (!is.null(args$zipfile)) zipfile = args$zipfile

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

290 if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

291 if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

292

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

293 if (!is.null(args$singlefile_galaxyPath)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

294 singlefile_galaxyPaths = args$singlefile_galaxyPath;

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

295 singlefile_sampleNames = args$singlefile_sampleName

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

296 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

297 if (!is.null(args$singlefile_galaxyPathPositive)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

298 singlefile_galaxyPaths = args$singlefile_galaxyPathPositive;

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

299 singlefile_sampleNames = args$singlefile_sampleNamePositive

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

300 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

301 if (!is.null(args$singlefile_galaxyPathNegative)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

302 singlefile_galaxyPaths = args$singlefile_galaxyPathNegative;

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

303 singlefile_sampleNames = args$singlefile_sampleNameNegative

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

304 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

305 if (exists("singlefile_galaxyPaths")){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

306 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

307 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

308

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

309 singlefile=NULL

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

310 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

311 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

312 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

313 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

314 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

315 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

316 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

317 "singlefile_galaxyPath", "singlefile_sampleName",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

318 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

319 "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

320 args[[argument]]=NULL

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

321 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

322 return(list(zipfile=zipfile, singlefile=singlefile, args=args))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

323 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

324

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

325

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

326 # This function retrieve the raw file in the working directory

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

327 # - if zipfile: unzip the file with its directory tree

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

328 # - if singlefiles: set symlink with the good filename

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

329 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

330 if(!is.null(singlefile) && (length("singlefile")>0)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

331 for (singlefile_sampleName in names(singlefile)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

332 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

333 if(!file.exists(singlefile_galaxyPath)){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

334 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

335 print(error_message); stop(error_message)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

336 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

337

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

338 file.symlink(singlefile_galaxyPath,singlefile_sampleName)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

339 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

340 directory = "."

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

341

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

342 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

343 if(!is.null(zipfile) && (zipfile!="")) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

344 if(!file.exists(zipfile)){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

345 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

346 print(error_message)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

347 stop(error_message)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

348 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

349

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

350 #list all file in the zip file

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

351 #zip_files=unzip(zipfile,list=T)[,"Name"]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

352

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

353 #unzip

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

354 suppressWarnings(unzip(zipfile, unzip="unzip"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

355

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

356 #get the directory name

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

357 filesInZip=unzip(zipfile, list=T);

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

358 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

359 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

360 directory = "."

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

361 if (length(directories) == 1) directory = directories

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

362

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

363 cat("files_root_directory\t",directory,"\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

364

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

365 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

366 return (directory)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

367 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

368

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

369 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

370 # https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

371 # https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

372 ############################################################

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

373 ## getEIC

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

374 getEIC <- function(object, mzrange, rtrange = 200,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

375 groupidx, sampleidx = sampnames(object),

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

376 rt = c("corrected", "raw")) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

377

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

378 files <- filepaths(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

379 grp <- groups(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

380 samp <- sampnames(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

381 prof <- profinfo(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

382

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

383 rt <- match.arg(rt)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

384

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

385 if (is.numeric(sampleidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

386 sampleidx <- sampnames(object)[sampleidx]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

387 sampidx <- match(sampleidx, sampnames(object))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

388

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

389 if (!missing(groupidx)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

390 if (is.numeric(groupidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

391 groupidx <- groupnames(object)[unique(as.integer(groupidx))]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

392 grpidx <- match(groupidx, groupnames(object, template = groupidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

393 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

394

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

395 if (missing(mzrange)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

396 if (missing(groupidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

397 stop("No m/z range or groups specified")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

398 if (any(is.na(groupval(object, value = "mz"))))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

399 warning(

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

400 "`NA` values in xcmsSet. Use fillPeaks() on the object to fill",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

401 "-in missing peak values. Note however that this will also ",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

402 "insert intensities of 0 for peaks that can not be filled in.")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

403 mzmin <- apply(groupval(object, value = "mzmin"), 1, min, na.rm = TRUE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

404 mzmax <- apply(groupval(object, value = "mzmax"), 1, max, na.rm = TRUE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

405 mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

406 ## if (any(is.na(groupval(object, value = "mz"))))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

407 ## stop('Please use fillPeaks() to fill up NA values !')

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

408 ## mzmin <- -rowMax(-groupval(object, value = "mzmin"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

409 ## mzmax <- rowMax(groupval(object, value = "mzmax"))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

410 ## mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

411 } else if (all(c("mzmin","mzmax") %in% colnames(mzrange)))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

412 mzrange <- mzrange[,c("mzmin", "mzmax"),drop=FALSE]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

413 else if (is.null(dim(mzrange)))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

414 stop("mzrange must be a matrix")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

415 colnames(mzrange) <- c("mzmin", "mzmax")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

416

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

417 if (length(rtrange) == 1) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

418 if (missing(groupidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

419 rtrange <- matrix(rep(range(object@rt[[rt]][sampidx]), nrow(mzrange)),

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

420 ncol = 2, byrow = TRUE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

421 else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

422 rtrange <- retexp(grp[grpidx,c("rtmin","rtmax"),drop=FALSE], rtrange)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

423 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

424 } else if (is.null(dim(rtrange)))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

425 stop("rtrange must be a matrix or single number")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

426 colnames(rtrange) <- c("rtmin", "rtmax")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

427

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

428 ## Ensure that we've got corrected retention time if requested.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

429 if (is.null(object@rt[[rt]]))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

430 stop(rt, " retention times not present in 'object'!")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

431

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

432 ## Ensure that the defined retention time range is within the rtrange of the

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

433 ## object: we're using the max minimal rt of all files and the min maximal rt

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

434 rtrs <- lapply(object@rt[[rt]], range)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

435 rtr <- c(max(unlist(lapply(rtrs, "[", 1))),

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

436 min(unlist(lapply(rtrs, "[", 2))))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

437 ## Check if we've got a range which is completely off:

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

438 if (any(rtrange[, "rtmin"] >= rtr[2] | rtrange[, "rtmax"] <= rtr[1])) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

439 outs <- which(rtrange[, "rtmin"] >= rtr[2] |

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

440 rtrange[, "rtmax"] <= rtr[1])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

441 stop(length(outs), " of the specified 'rtrange' are completely outside ",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

442 "of the retention time range of 'object' which is (", rtr[1], ", ",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

443 rtr[2], "). The first was: (", rtrange[outs[1], "rtmin"], ", ",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

444 rtrange[outs[1], "rtmax"], "!")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

445 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

446 lower_rt_outside <- rtrange[, "rtmin"] < rtr[1]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

447 upper_rt_outside <- rtrange[, "rtmax"] > rtr[2]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

448 if (any(lower_rt_outside) | any(upper_rt_outside)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

449 ## Silently fix these ranges.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

450 rtrange[lower_rt_outside, "rtmin"] <- rtr[1]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

451 rtrange[upper_rt_outside, "rtmax"] <- rtr[2]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

452 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

453

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

454 if (missing(groupidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

455 gnames <- character(0)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

456 else

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

457 gnames <- groupidx

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

458

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

459 eic <- vector("list", length(sampleidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

460 names(eic) <- sampleidx

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

461

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

462 for (i in seq(along = sampidx)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

463

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

464 ## cat(sampleidx[i], "")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

465 flush.console()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

466 ## getXcmsRaw takes care of rt correction, susetting to scanrage and other

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

467 ## stuff.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

468 lcraw <- getXcmsRaw(object, sampleidx = sampidx[i], rt=rt)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

469 currenteic <- xcms::getEIC(lcraw, mzrange, rtrange, step = prof$step)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

470 eic[[i]] <- currenteic@eic[[1]]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

471 rm(lcraw)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

472 gc()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

473 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

474 ## cat("\n")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

475

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

476 invisible(new("xcmsEIC", eic = eic, mzrange = mzrange, rtrange = rtrange,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

477 rt = rt, groupnames = gnames))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

478 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

479

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

480 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

481 # https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

482 # https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

483 ############################################################

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

484 ## diffreport

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

485 diffreport = function(object,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

486 class1 = levels(sampclass(object))[1],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

487 class2 = levels(sampclass(object))[2],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

488 filebase = character(),

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

489 eicmax = 0, eicwidth = 200,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

490 sortpval = TRUE,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

491 classeic = c(class1,class2),

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

492 value = c("into","maxo","intb"),

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

493 metlin = FALSE,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

494 h = 480, w = 640, mzdec=2,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

495 missing = numeric(), ...) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

496

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

497 if ( nrow(object@groups)<1 || length(object@groupidx) <1) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

498 stop("No group information. Use group().")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

499 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

500

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

501 if (!is.numeric(w) || !is.numeric(h))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

502 stop("'h' and 'w' have to be numeric")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

503 ## require(multtest) || stop("Couldn't load multtest")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

504

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

505 value <- match.arg(value)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

506 groupmat <- groups(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

507 if (length(groupmat) == 0)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

508 stop("No group information found")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

509 samples <- sampnames(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

510 n <- length(samples)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

511 classlabel <- sampclass(object)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

512 classlabel <- levels(classlabel)[as.vector(unclass(classlabel))]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

513

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

514 values <- groupval(object, "medret", value=value)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

515 indecies <- groupval(object, "medret", value = "index")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

516

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

517 if (!all(c(class1,class2) %in% classlabel))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

518 stop("Incorrect Class Labels")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

519

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

520 ## c1 and c2 are column indices of class1 and class2 resp.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

521 c1 <- which(classlabel %in% class1)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

522 c2 <- which(classlabel %in% class2)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

523 ceic <- which(classlabel %in% classeic)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

524 if (length(intersect(c1, c2)) > 0)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

525 stop("Intersecting Classes")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

526

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

527 ## Optionally replace NA values with the value provided with missing

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

528 if (length(missing)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

529 if (is.numeric(missing)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

530 ## handles NA, Inf and -Inf

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

531 values[, c(c1, c2)][!is.finite(values[, c(c1, c2)])] <- missing[1]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

532 } else

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

533 stop("'missing' should be numeric")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

534 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

535 ## Check against missing Values

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

536 if (any(is.na(values[, c(c1, c2)])))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

537 warning("`NA` values in xcmsSet. Use fillPeaks() on the object to fill",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

538 "-in missing peak values. Note however that this will also ",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

539 "insert intensities of 0 for peaks that can not be filled in.")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

540

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

541 mean1 <- rowMeans(values[,c1,drop=FALSE], na.rm = TRUE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

542 mean2 <- rowMeans(values[,c2,drop=FALSE], na.rm = TRUE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

543

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

544 ## Calculate fold change.

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

545 ## For foldchange <1 set fold to 1/fold

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

546 ## See tstat to check which was higher

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

547 fold <- mean2 / mean1

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

548 fold[!is.na(fold) & fold < 1] <- 1/fold[!is.na(fold) & fold < 1]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

549

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

550 testval <- values[,c(c1,c2)]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

551 ## Replace eventual infinite values with NA (CAMERA issue #33)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

552 testval[is.infinite(testval)] <- NA

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

553 testclab <- c(rep(0,length(c1)),rep(1,length(c2)))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

554

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

555 if (min(length(c1), length(c2)) >= 2) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

556 tstat <- mt.teststat(testval, testclab, ...)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

557 pvalue <- xcms:::pval(testval, testclab, tstat)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

558 } else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

559 message("Too few samples per class, skipping t-test.")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

560 tstat <- pvalue <- rep(NA,nrow(testval))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

561 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

562 stat <- data.frame(fold = fold, tstat = tstat, pvalue = pvalue)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

563 if (length(levels(sampclass(object))) >2) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

564 pvalAnova<-c()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

565 for(i in 1:nrow(values)){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

566 var<-as.numeric(values[i,])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

567 ano<-summary(aov(var ~ sampclass(object)) )

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

568 pvalAnova<-append(pvalAnova, unlist(ano)["Pr(>F)1"])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

569 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

570 stat<-cbind(stat, anova= pvalAnova)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

571 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

572 if (metlin) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

573 neutralmass <- groupmat[,"mzmed"] + ifelse(metlin < 0, 1, -1)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

574 metlin <- abs(metlin)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

575 digits <- ceiling(-log10(metlin))+1

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

576 metlinurl <-

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

577 paste("http://metlin.scripps.edu/simple_search_result.php?mass_min=",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

578 round(neutralmass - metlin, digits), "&mass_max=",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

579 round(neutralmass + metlin, digits), sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

580 values <- cbind(metlin = metlinurl, values)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

581 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

582 twosamp <- cbind(name = groupnames(object), stat, groupmat, values)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

583 if (sortpval) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

584 tsidx <- order(twosamp[,"pvalue"])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

585 twosamp <- twosamp[tsidx,]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

586 rownames(twosamp) <- 1:nrow(twosamp)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

587 values<-values[tsidx,]

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

588 } else

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

589 tsidx <- 1:nrow(values)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

590

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

591 if (length(filebase))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

592 write.table(twosamp, paste(filebase, ".tsv", sep = ""), quote = FALSE, sep = "\t", col.names = NA)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

593

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

594 if (eicmax > 0) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

595 if (length(unique(peaks(object)[,"rt"])) > 1) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

596 ## This looks like "normal" LC data

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

597

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

598 eicmax <- min(eicmax, length(tsidx))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

599 eics <- getEIC(object, rtrange = eicwidth*1.1, sampleidx = ceic,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

600 groupidx = tsidx[seq(length = eicmax)])

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

601

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

602 if (length(filebase)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

603 eicdir <- paste(filebase, "_eic", sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

604 boxdir <- paste(filebase, "_box", sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

605 dir.create(eicdir)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

606 dir.create(boxdir)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

607 if (capabilities("png")){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

608 xcms:::xcmsBoxPlot(values[seq(length = eicmax),],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

609 sampclass(object), dirpath=boxdir, pic="png", width=w, height=h)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

610 png(file.path(eicdir, "%003d.png"), width = w, height = h)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

611 } else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

612 xcms:::xcmsBoxPlot(values[seq(length = eicmax),],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

613 sampclass(object), dirpath=boxdir, pic="pdf", width=w, height=h)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

614 pdf(file.path(eicdir, "%003d.pdf"), width = w/72,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

615 height = h/72, onefile = FALSE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

616 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

617 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

618 plot(eics, object, rtrange = eicwidth, mzdec=mzdec)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

619

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

620 if (length(filebase))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

621 dev.off()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

622 } else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

623 ## This looks like a direct-infusion single spectrum

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

624 if (length(filebase)) {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

625 eicdir <- paste(filebase, "_eic", sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

626 boxdir <- paste(filebase, "_box", sep="")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

627 dir.create(eicdir)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

628 dir.create(boxdir)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

629 if (capabilities("png")){

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

630 xcmsBoxPlot(values[seq(length = eicmax),],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

631 sampclass(object), dirpath=boxdir, pic="png",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

632 width=w, height=h)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

633 png(file.path(eicdir, "%003d.png"), width = w, height = h,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

634 units = "px")

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

635 } else {

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

636 xcmsBoxPlot(values[seq(length = eicmax),],

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

637 sampclass(object), dirpath=boxdir, pic="pdf",

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

638 width=w, height=h)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

639 pdf(file.path(eicdir, "%003d.pdf"), width = w/72,

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

640 height = h/72, onefile = FALSE)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

641 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

642 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

643

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

644 plotSpecWindow(object, gidxs = tsidx[seq(length = eicmax)], borderwidth=1)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

645

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

646 if (length(filebase))

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

647 dev.off()

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

648 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

649 }

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

650

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

651 invisible(twosamp)

139ff66b0b5d planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464

workflow4metabolomics

parents:

diff changeset

652 }

Mercurial > repos > workflow4metabolomics > camera_combinexsannos

annotate lib.r @ 0:139ff66b0b5d draft