camera_combinexsannos: lib.r annotate

annotate lib.r @ 1:ea15115a5b3f draft

"planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429"

author	workflow4metabolomics
date	Thu, 13 Feb 2020 17:23:27 -0500
parents	139ff66b0b5d
children	c4c13745e797

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

Mercurial > repos > workflow4metabolomics > camera_combinexsannos

annotate lib.r @ 1:ea15115a5b3f draft