--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib.r	Fri Apr 08 10:38:52 2016 -0400
@@ -0,0 +1,400 @@
+# lib.r version="2.0.1"
+#Authors ABiMS TEAM
+#Lib.r for Galaxy Workflow4Metabo
+#version 2.2
+#Based on lib.r 2.1
+#Modifications made by Guitton Yann 
+#correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
+#Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
+
+
+
+
+#@author Y. Guitton
+getBPC <- function(file,rtcor=NULL, ...) {
+  object <- xcmsRaw(file)
+  sel <- profRange(object, ...)
+  cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
+  #plotChrom(xcmsRaw(file), base=T)
+}
+
+#@author Y. Guitton
+getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
+  cat("Creating BIC pdf...\n")
+
+  if (is.null(xcmsSet)) {
+    cat("Enter an xcmsSet \n")
+    stop()
+  } else {
+    files <- filepaths(xcmsSet)
+  }
+
+  class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
+
+  classnames<-vector("list",length(class))
+  for (i in 1:length(class)){
+    classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
+  }
+
+  N <- dim(phenoData(xcmsSet))[1]
+
+  TIC <- vector("list",N)
+
+
+  for (j in 1:N) {
+
+    TIC[[j]] <- getBPC(files[j])
+    #good for raw 
+    # seems strange for corrected
+    #errors if scanrange used in xcmsSetgeneration
+    if (!is.null(xcmsSet) && rt == "corrected")
+    rtcor <- xcmsSet@rt$corrected[[j]] else
+    rtcor <- NULL
+    
+    TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
+    # TIC[[j]][,1]<-rtcor
+  }
+
+
+
+  pdf(pdfname,w=16,h=10)
+  cols <- rainbow(N)
+  lty = 1:N
+  pch = 1:N
+  #search for max x and max y in BPCs
+  xlim = range(sapply(TIC, function(x) range(x[,1])))
+  ylim = range(sapply(TIC, function(x) range(x[,2])))
+  ylim = c(-ylim[2], ylim[2])
+
+
+  ##plot start
+  
+  if (length(class)>2){
+    for (k in 1:(length(class)-1)){
+      for (l in (k+1):length(class)){
+        #print(paste(class[k],"vs",class[l],sep=" ")) 
+        plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
+        colvect<-NULL
+        for (j in 1:length(classnames[[k]])) {
+          tic <- TIC[[classnames[[k]][j]]]
+          # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+          points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+          colvect<-append(colvect,cols[classnames[[k]][j]])
+        }
+        for (j in 1:length(classnames[[l]])) {
+          # i=class2names[j]
+          tic <- TIC[[classnames[[l]][j]]]
+          points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+          colvect<-append(colvect,cols[classnames[[l]][j]])
+        }
+        legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+      }
+    }
+  }#end if length >2
+
+  if (length(class)==2){
+    k=1
+    l=2
+    colvect<-NULL
+    plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
+
+    for (j in 1:length(classnames[[k]])) {
+
+      tic <- TIC[[classnames[[k]][j]]]
+      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+      points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+      colvect<-append(colvect,cols[classnames[[k]][j]])
+    }
+    for (j in 1:length(classnames[[l]])) {
+      # i=class2names[j]
+      tic <- TIC[[classnames[[l]][j]]]
+      points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+      colvect<-append(colvect,cols[classnames[[l]][j]])
+    }
+    legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+
+  }#end length ==2
+
+  dev.off() #pdf(pdfname,w=16,h=10)
+
+  invisible(TIC)
+}
+
+
+
+#@author Y. Guitton
+getTIC <- function(file,rtcor=NULL) {
+  object <- xcmsRaw(file)
+  cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
+}
+
+##
+##  overlay TIC from all files in current folder or from xcmsSet, create pdf
+##
+#@author Y. Guitton
+getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
+  cat("Creating TIC pdf...\n")
+
+  if (is.null(xcmsSet)) {
+    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+    filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
+    if (is.null(files))
+      files <- getwd()
+    info <- file.info(files)
+    listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
+    files <- c(files[!info$isdir], listed)
+  } else {
+    files <- filepaths(xcmsSet)
+  }
+
+  class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
+
+  classnames<-vector("list",length(class))
+  for (i in 1:length(class)){
+    classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
+  }
+  
+  N <- length(files)
+  TIC <- vector("list",N)
+
+  for (i in 1:N) {
+    if (!is.null(xcmsSet) && rt == "corrected")
+      rtcor <- xcmsSet@rt$corrected[[i]] else
+    rtcor <- NULL
+    TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
+  }
+
+  pdf(pdfname,w=16,h=10)
+  cols <- rainbow(N)
+  lty = 1:N
+  pch = 1:N
+  #search for max x and max y in TICs
+  xlim = range(sapply(TIC, function(x) range(x[,1])))
+  ylim = range(sapply(TIC, function(x) range(x[,2])))
+  ylim = c(-ylim[2], ylim[2])
+
+
+  ##plot start
+  if (length(class)>2){
+    for (k in 1:(length(class)-1)){
+      for (l in (k+1):length(class)){
+        #print(paste(class[k],"vs",class[l],sep=" ")) 
+        plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
+        colvect<-NULL
+        for (j in 1:length(classnames[[k]])) {
+
+          tic <- TIC[[classnames[[k]][j]]]
+          # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+          points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+          colvect<-append(colvect,cols[classnames[[k]][j]])
+        }
+        for (j in 1:length(classnames[[l]])) {
+          # i=class2names[j]
+          tic <- TIC[[classnames[[l]][j]]]
+          points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+          colvect<-append(colvect,cols[classnames[[l]][j]])
+        }
+        legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+      }
+    }
+  }#end if length >2
+  if (length(class)==2){
+    k=1
+    l=2
+
+    plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
+    colvect<-NULL
+    for (j in 1:length(classnames[[k]])) {
+      tic <- TIC[[classnames[[k]][j]]]
+      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+      points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+      colvect<-append(colvect,cols[classnames[[k]][j]])
+    }
+    for (j in 1:length(classnames[[l]])) {
+      # i=class2names[j]
+      tic <- TIC[[classnames[[l]][j]]]
+      points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+      colvect<-append(colvect,cols[classnames[[l]][j]])
+    }
+    legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+
+  }#end length ==2
+  dev.off() #pdf(pdfname,w=16,h=10)
+
+  invisible(TIC)
+}
+
+
+
+##
+##  Get the polarities from all the samples of a condition
+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
+getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
+  cat("Creating the sampleMetadata file...\n")
+
+  #Create the sampleMetada dataframe
+  sampleMetadata=xset@phenoData
+  sampleNamesOrigin=rownames(sampleMetadata)
+  sampleNamesMakeNames=make.names(sampleNamesOrigin)
+    
+  if (any(duplicated(sampleNamesMakeNames))) {
+    write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
+    for (sampleName in sampleNamesOrigin) {
+      write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
+    }
+    stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
+  }
+
+  if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
+    cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
+    for (sampleName in sampleNamesOrigin) {
+      cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
+    }
+  }
+
+  sampleMetadata$sampleMetadata=sampleNamesMakeNames
+  sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
+  rownames(sampleMetadata)=NULL
+
+  #Create a list of files name in the current directory
+  list_files=xset@filepaths
+  #For each sample file, the following actions are done
+  for (file in list_files){
+    #Check if the file is in the CDF format
+    if (!mzR:::netCDFIsFile(file)){
+
+      # If the column isn't exist, with add one filled with NA
+      if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
+
+      #Create a simple xcmsRaw object for each sample
+      xcmsRaw=xcmsRaw(file)
+      #Extract the polarity (a list of polarities)
+      polarity=xcmsRaw@polarity
+      #Verify if all the scans have the same polarity
+      uniq_list=unique(polarity)
+      if (length(uniq_list)>1){
+        polarity="mixed"
+      } else {
+        polarity=as.character(uniq_list)
+      }
+      #Transforms the character to obtain only the sample name
+      filename=basename(file)
+      library(tools)
+      samplename=file_path_sans_ext(filename)
+
+      #Set the polarity attribute
+      sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
+      
+      #Delete xcmsRaw object because it creates a bug for the fillpeaks step
+      rm(xcmsRaw)
+    }
+
+  }
+
+  write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
+
+  return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
+
+}
+
+
+##
+## This function check if xcms will found all the files
+##
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
+checkFilesCompatibilityWithXcms <- function(directory) {
+  cat("Checking files filenames compatibilities with xmcs...\n")
+  # WHAT XCMS WILL FIND
+  filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+  filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
+  info <- file.info(directory)
+  listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
+  files <- c(directory[!info$isdir], listed)
+  files_abs <- file.path(getwd(), files)
+  exists <- file.exists(files_abs)
+  files[exists] <- files_abs[exists]
+  files[exists] <- sub("//","/",files[exists])
+
+  # WHAT IS ON THE FILESYSTEM
+  filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
+  filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
+
+  # COMPARISON
+  if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { 
+    write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
+    write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
+    stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
+
+  }
+}
+
+
+
+##
+## This function check if XML contains special caracters. It also checks integrity and completness.
+##
+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
+checkXmlStructure <- function (directory) {
+  cat("Checking XML structure...\n")
+
+  cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
+  capture=system(cmd,intern=TRUE)
+
+  if (length(capture)>0){
+    #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
+    write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
+    write(capture, stderr())
+    stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
+  }
+   
+}
+
+
+##
+## This function check if XML contain special characters
+##
+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
+deleteXmlBadCharacters<- function (directory) {
+  cat("Checking Non ASCII characters in the XML...\n")
+
+  processed=F
+  l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE) 
+  for (i in l){
+    cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
+    capture=suppressWarnings(system(cmd,intern=TRUE))
+    if (length(capture)>0){
+      cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
+      print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
+      c=system(cmd,intern=TRUE)
+      capture=""
+      processed=T 
+    }
+  }
+  if (processed) cat("\n\n")
+  return(processed)
+}
+
+
+## 
+## This function will compute MD5 checksum to check the data integrity
+##
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
+getMd5sum <- function (directory) {
+  cat("Compute md5 checksum...\n")
+  # WHAT XCMS WILL FIND
+  filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+  filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
+  info <- file.info(directory)
+  listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
+  files <- c(directory[!info$isdir], listed)
+  exists <- file.exists(files)
+  files <- files[exists]
+
+  library(tools)
+
+  #cat("\n\n")
+
+  return(as.matrix(md5sum(files)))
+}
+