Mercurial > repos > rlegendre > ving
changeset 5:0cec66d7f637 draft
Uploaded
| author | rlegendre |
|---|---|
| date | Tue, 28 Jul 2015 05:44:48 -0400 |
| parents | 5ed41b948030 |
| children | 97ae4ee7a6a2 |
| files | COPYING.txt README.txt ving.R ving_wrapper.xml |
| diffstat | 4 files changed, 1853 insertions(+), 1002 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING.txt Tue Jul 28 05:44:48 2015 -0400 @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. 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Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Tue Jul 28 05:44:48 2015 -0400 @@ -0,0 +1,152 @@ +Authors' notes and preface +------------------------ +The script in this package was designed by Marc Descrimes. +The current implementation was written by Marc Descrimes and Yousra Ben Zouari. + +Software: Ving +Title: Representation and manipulation of RNA seq data. +Description: Tool for efficient visualization and analysis + of high-throughput sequencing data (a.k.a. NGS data). + +Version: beta 1.0 + +Prerequisites +------------- +The script runs with R(>= 3.0.2). +R packages GenomicRanges and Rsamtools should be installed. + +Samtools should be up and running in order to create bam file indexes. +Index files must be in the same directory as bam files, with the default +file name given by samtools. +Samtools are in the repositories of many distros. Go here for the freshest version: + + http://samtools.sourceforge.net/ + +If everything goes well you can now get started using real data! :) + +How to use the Ving.R script +---------------------------- + +To get more help, just run: Rscript ving.R + +Visualization requires at least a bam file and coordinates of a genome region to visualize: chromosome name, start and end. + Rscript ving.R [options] <input> [<input2> <input3> ...] +For example: + Rscript ving.R WT1.bam -c chr15 -S 210400 -E 224400 + +This produces an "output.png" image with the default parameters. + +You can also chmod +x ving.R and run ving like this: ./ving.R +Just check the shebang in the first line of ving.R, it has to match the PATH of your Rscript. + +Options +------- + +-o/--output <string> + Sets file name for Ving output. Default is "output.png" + +-v/--typeVisu <string> + Changes visualization type. Default is "classic". Can be "heatmap" or "lines". + +-t/--description-data <string> + Describes each data set with a name. Default is the filename. + Example for multiple bam files : + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam -t "wild type rep1" WT2.bam -t "wild type rep2" + If two (or more) bam files have exactly the same name, ving will pool these bam files + to generate only one signal. + Example : + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam -t "wild type" WT2.bam -t "wild type" + +-n/--normalization-coefficient <number,number,...> + Each bam file is multiplied by a coefficient. + By default no normalization is performed. + You have to specify as many coefficient as there are bam files. + Example for multiple bam files : + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam WT2.bam -n 0.5,1.5 + +-i/--inverseStrand + Use this if library type is fr-first-strand. + All bam files are treated the same way. + +-u/--unstranded + Use for an non-strand-specific visualization + Default is strand-specific. + +-l/--scale-log + Use this if you want a logarithmic scale. + Don't use this if you don't want a logarithmic scale. + +-y/--symetric-scale + This option is for a symetric scale with the same maximum and minimum + for both strand in the "classic" and "lines" visualization. + +-a/--annotation <string> + Specifies an annotation file (GFF file). + Annotation features will be displayed on output image. + More than one file can be provided: + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam -a saccharomyces_cerevisiae.gff -a cryptics.gff + +-r/--typeTranscript <string> + Use this option to select annotation features for visualization. + Separate multiple transcripts by commas. Example : + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam -a saccharomyces_cerevisiae.gff -r gene,XUT + +-C/--annotation-colors <string> + Sets the different colors for annoatation features. Any color name accepted by R. + Hexadecimal color code is allowed, but do not use "#" character. + Use comma-separated list. Number of colors and number of features should be the same. + Example : + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam -a saccharomyces_cerevisiae.gff -a cryptics.gff -r gene,XUT,SUT -C blue,salmon,649B88 + +--annotation-color-by-strand + Use this if you want the transcripts to be colored according to the strand. + +-s/--annotation-shapes <string> + Sets the shape used for annotation (Comma-separated list). + Four shapes are available: box,rectangle,arrow,line. Default is box. + Numbers of shapes and features should be the same. + For organisms with few or no introns (e.g. yeast), we suggest to use "box" for every type of feature. + Otherwise, we suggest to use "rectangle" for exons and "arrow" for introns. + +--classic-plus-color <string> + Sets the color of plus strand for the classic visualization. + +--classic-minus-color <string> + Sets the color of minus strand for the classic visualization. + Example : + Rscript ving.R -c chr15 -S 210400 -E 224400 WT1.bam WT2.bam -n 0.5,1.5 --classic-plus-color=darkred --classic-minus-color=gold + +--heatmap-max-color <string> + Sets the maximum color of the palette for heatmap visualization. + +--heatmap-min-color <string> + Sets the minimum color of the palette for heatmap visualization. + +--heatmap-palette-method <string> + Sets the method of the palette for the heatmap visualization. + Two settings : + - hsv : varies the hues + - rgb : varies the shades + Example : + Rscript ving.R -v heatmap -c chr15 -S 210400 -E 224400 WT1.bam WT2.bam --heatmap-min-color=lavenderblush --heatmap-max-color=darksalmon + Rscript ving.R -v heatmap -c chr15 -S 210400 -E 224400 WT1.bam WT2.bam --heatmap-min-color=white --heatmap-max-color=black --heatmap-palette-method=rgb + +--lines-samples-colors <string,string,...> + Sets the colors for lines visualization (comma-separated list). + You have to specify as many colors as there are bam files. + +--lines-samples-type-line <integer,integer,...> + Sets the type of lines for lines visualization (comma-separated list). + You have to specify as many line types as there are bam files. + Example :axs + Rscript ving.R -v lines -c chr15 -S 210400 -E 224400 WT1.bam WT2.bam mut1.bam mut2.bam -l --lines-samples-colors=1,1,2,2 --lines-samples-type-line=1,2,1,2 + +-L/--smoothLength <number> + Sets the length of the sliding window smoothing. The default is NA and allows ving to compute + an optimal length, according to the length of the asked genomic region. + If you don't want any smoothing, set this to zero. + +Examples : + Rscript ving.R -o classic.png -c chr15 -S 210400 -E 224400 WT1.bam -t "wild type rep1" WT2.bam -t "wild type rep2" mut1.bam -t "mutant rep1" mut2.bam -t "mutant rep2" -a saccharomyces_cerevisiae.gff -a cryptics.gff -r gene,XUT,SUT -C blue,salmon,649B88 + Rscript ving.R -v heatmap -o heatmap.png -c chr15 -S 210400 -E 224400 WT1.bam -t "wild type rep1" WT2.bam -t "wild type rep2" mut1.bam -t "mutant rep1" mut2.bam -t "mutant rep2" -l -a saccharomyces_cerevisiae.gff -a cryptics.gff -r gene,XUT,SUT -C blue,salmon,649B88 + Rscript ving.R -v lines -o lines.png -c chr15 -S 210400 -E 224400 WT1.bam -t "wild type rep1" WT2.bam -t "wild type rep2" mut1.bam -t "mutant rep1" mut2.bam -t "mutant rep2" -l -a saccharomyces_cerevisiae.gff -a cryptics.gff -r gene,XUT,SUT -C blue,salmon,649B88 --lines-samples-colors=black,black,green,green --lines-samples-type-line=1,2,1,2
--- a/ving.R Tue Jul 29 09:47:47 2014 -0400 +++ b/ving.R Tue Jul 28 05:44:48 2015 -0400 @@ -1,211 +1,186 @@ #! /usr/bin/Rscript -RetreiveAndDestroy=function(opt,root,stem,regexp,SearchNames,Out,isValue,NbFound,StockNames){ - Bool=lapply(paste(root,SearchNames,stem,sep=""),grepl,opt) - names(Bool)=StockNames - Pos=lapply(Bool,which) - names(Pos)=StockNames - disable=c() - for (i in StockNames){ - nbmatch=length(Pos[[i]]) - if(nbmatch>0){ - NbFound[[i]]=NbFound[[i]]+nbmatch - disable=c(disable,-1*Pos[[i]]) - if(is.null(Out[[i]])){ - if(isValue[[i]]!=0){ - if(regexp=="next"){ - Out[[i]]=opt[Pos[[i]]+1] - disable=c(disable,-1*(Pos[[i]]+1)) - }else{ - Out[[i]]=sub(regexp,"\\1",opt[Pos[[i]]]) - } - }else{ - Out[[i]]=TRUE - } - }else{ - if(isValue[[i]]!=0){ - if(regexp=="next"){ - Out[[i]]=c(Out[[i]],opt[Pos[[i]]+1]) - disable=c(disable,-1*(Pos[[i]]+1)) - }else{ - Out[[i]]=c(Out[[i]],sub(regexp,"\\1",opt[Pos[[i]]])) - } - }else{ - Out[[i]]=c(Out[[i]],TRUE) - } - } - } +RetreiveAndDestroy=function(opt,root,stem,regexp,SearchNames,Out,isValue,NbFound,StockNames) { + Bool=lapply(paste(root,SearchNames,stem,sep=""),grepl,opt) + names(Bool)=StockNames + Pos=lapply(Bool,which) + names(Pos)=StockNames + disable=c() + for(i in StockNames) { + nbmatch=length(Pos[[i]]) + if(nbmatch>0) { + NbFound[[i]]=NbFound[[i]]+nbmatch + disable=c(disable,-1*Pos[[i]]) + if(is.null(Out[[i]])) { + if(isValue[[i]]!=0) { + if(regexp=="next") { + Out[[i]]=opt[Pos[[i]]+1] + disable=c(disable,-1*(Pos[[i]]+1)) + } + else { + Out[[i]]=sub(regexp,"\\1",opt[Pos[[i]]]) + } + } + else { + Out[[i]]=TRUE } - if(length(disable)>0){ - opt=opt[disable] + } + else { + if(isValue[[i]]!=0) { + if(regexp=="next") { + Out[[i]]=c(Out[[i]],opt[Pos[[i]]+1]) + disable=c(disable,-1*(Pos[[i]]+1)) + } + else { + Out[[i]]=c(Out[[i]],sub(regexp,"\\1",opt[Pos[[i]]])) + } } - Out[["ARGUMENT"]]=list() - Out[["ARGUMENT"]][["opt"]]=opt - Out[["ARGUMENT"]][["NbFound"]]=NbFound - return(Out) + else { + Out[[i]]=c(Out[[i]],TRUE) + } + } + } + } + if(length(disable)>0) { + opt=opt[disable] + } + Out[["ARGUMENT"]]=list() + Out[["ARGUMENT"]][["opt"]]=opt + Out[["ARGUMENT"]][["NbFound"]]=NbFound + return(Out) } -getopt = function (spec=NULL,opt=commandArgs()) { - - FindArgs=which(opt=="--args") - if(length(FindArgs)!=1){ - stop(length(FindArgs)," --args found where 1 expected.",call.=F) - } - ExecName=sub("--file=","",opt[FindArgs-1]) - - if(FindArgs<length(opt)){ - opt=opt[(FindArgs+1):length(opt)] - }else{ - opt="" - } - - - min.columns=5 - colNames=c("LongName","ShortName","Flag","Mod","Default") - max.columns=6 - DimSpec=dim(spec) - if(DimSpec[2]>min.columns){ - colNames=c(colNames,"Description") - } - - if(is.null(spec) | !is.matrix(spec) | (DimSpec[2]<min.columns | DimSpec[2]>max.columns)){ - stop('argument "spec" is required and must be a matrix with 4|5 columns.',call.=F) - } - colnames(spec)=colNames - - spec=as.data.frame(spec,stringsAsFactors=F) - #spec validation - if(length(unique(c(spec$ShortName,"ARGUMENT","args")))!=DimSpec[1]+2 | length(unique(spec$LongName))!=DimSpec[1]){ - stop('Long|Short names for flags must be unique (Long name : "ARGUMENT" and "args" forbidden).', - "\n","List of duplicated :", - "\n","Short: ",paste(spec$ShortName[duplicated(c(spec$ShortName,"ARGUMENT","args"))],collapse=" "), - "\n","Long: ",paste(spec$ShortName[duplicated(spec$LongName)],collapse=" "),call.=F) - } - if(length(which(nchar(spec$ShortName)>1))!=0){ - stop('Short names flags can\'t be longer than 1 character.') - } - - - #initialize - Out=list() - Short2Long=list() - NbFound=list() - isValue=list() - for (i in 1:DimSpec[1]){ - Short2Long[[spec$ShortName[i]]]=spec$LongName[i] - NbFound[[spec$LongName[i]]]=0 - isValue[[spec$LongName[i]]]=spec$Flag[i] - } - - #Map, retreive and suppress ARGUMENTs and arguments - #Value ARGUMENT --example=value - Out=RetreiveAndDestroy(opt,"^--","=.+$",".+=(.+)$",spec$LongName,Out,isValue,NbFound,spec$LongName) - opt=Out[["ARGUMENT"]][["opt"]] - NbFound=Out[["ARGUMENT"]][["NbFound"]] - Out[["ARGUMENT"]]=NULL - #boolean ARGUMENT --example - Out=RetreiveAndDestroy(opt,"^--","$","$",spec$LongName,Out,isValue,NbFound,spec$LongName) - opt=Out[["ARGUMENT"]][["opt"]] - NbFound=Out[["ARGUMENT"]][["NbFound"]] - Out[["ARGUMENT"]]=NULL - #short name ARGUMENT -t value OR boolean -t - Out=RetreiveAndDestroy(opt,"^-","$","next",spec$ShortName,Out,isValue,NbFound,spec$LongName) - opt=Out[["ARGUMENT"]][["opt"]] - NbFound=Out[["ARGUMENT"]][["NbFound"]] - Out[["ARGUMENT"]]=NULL - #Warn about non mapped ARGUMENTs - if(length(opt)>0){ - PosUnkArg=which(grepl("^-",opt)) - if(length(PosUnkArg)){ - message("Error, argument unreconized :","\n",paste(opt[PosUnkArg],collapse="\n"),"\n\n") - } - if(length(PosUnkArg)>0){ - opt=opt[PosUnkArg*-1] - } - } - #Arguments - Out[["ARGUMENT"]]=opt - - #Validation of ARGUMENTs - for(i in 1:DimSpec[1]){ - if(spec$Flag[i]=="0"){#verify boolean arguments - NbValue=length(Out[[spec$LongName[i]]]) - if(NbValue>1){ - message("Warning : ",spec$LongName[i]," found ",NbValue," times") - } - } - if(length(Out[[spec$LongName[i]]])==0){ - Out[[spec$LongName[i]]]=spec$Default[i] - } - library("methods") - Out[[spec$LongName[i]]]=as(Out[[spec$LongName[i]]],spec$Mod[i]) - } - - return(Out) +getopt=function (spec=NULL,opt=commandArgs()) { + FindArgs=which(opt=="--args") + if(length(FindArgs)!=1) { + stop(length(FindArgs)," --args found where 1 expected.",call.=F) + } + ExecName=sub("--file=","",opt[FindArgs-1]) + + if(FindArgs<length(opt)) { + opt=opt[(FindArgs+1):length(opt)] + } + else { + opt="" + } + + min.columns=5 + colNames=c("LongName","ShortName","Flag","Mod","Default") + max.columns=6 + DimSpec=dim(spec) + if(DimSpec[2]>min.columns) { + colNames=c(colNames,"Description") + } + + if(is.null(spec) | !is.matrix(spec) | (DimSpec[2]<min.columns | DimSpec[2]>max.columns)) { + stop('argument "spec" is required and must be a matrix with 4|5 columns.',call.=F) + } + colnames(spec)=colNames + + spec=as.data.frame(spec,stringsAsFactors=F) + #spec validation + if(length(unique(c(spec$ShortName,"ARGUMENT","args")))!=DimSpec[1]+2 | length(unique(spec$LongName))!=DimSpec[1]) { + stop('Long|Short names for flags must be unique (Long name : "ARGUMENT" and "args" forbidden).', + "\n","List of duplicated :", + "\n","Short: ",paste(spec$ShortName[duplicated(c(spec$ShortName,"ARGUMENT","args"))],collapse=" "), + "\n","Long: ",paste(spec$ShortName[duplicated(spec$LongName)],collapse=" "),call.=F) + } + if(length(which(nchar(spec$ShortName)>1))!=0) { + stop('Short names flags can\'t be longer than 1 character.') + } + + #initialize + Out=list() + Short2Long=list() + NbFound=list() + isValue=list() + for(i in 1:DimSpec[1]) { + Short2Long[[spec$ShortName[i]]]=spec$LongName[i] + NbFound[[spec$LongName[i]]]=0 + isValue[[spec$LongName[i]]]=spec$Flag[i] + } + + #Map, retreive and suppress ARGUMENTs and arguments + #Value ARGUMENT --example=value + Out=RetreiveAndDestroy(opt,"^--","=.+$",".+=(.+)$",spec$LongName,Out,isValue,NbFound,spec$LongName) + opt=Out[["ARGUMENT"]][["opt"]] + NbFound=Out[["ARGUMENT"]][["NbFound"]] + Out[["ARGUMENT"]]=NULL + #boolean ARGUMENT --example + Out=RetreiveAndDestroy(opt,"^--","$","$",spec$LongName,Out,isValue,NbFound,spec$LongName) + opt=Out[["ARGUMENT"]][["opt"]] + NbFound=Out[["ARGUMENT"]][["NbFound"]] + Out[["ARGUMENT"]]=NULL + #short name ARGUMENT -t value OR boolean -t + Out=RetreiveAndDestroy(opt,"^-","$","next",spec$ShortName,Out,isValue,NbFound,spec$LongName) + opt=Out[["ARGUMENT"]][["opt"]] + NbFound=Out[["ARGUMENT"]][["NbFound"]] + Out[["ARGUMENT"]]=NULL + #Warn about non mapped ARGUMENTs + if(length(opt)>0) { + PosUnkArg=which(grepl("^-",opt)) + if(length(PosUnkArg)) { + message("Error, argument unreconized :","\n",paste(opt[PosUnkArg],collapse="\n"),"\n\n") + } + if(length(PosUnkArg)>0) { + opt=opt[PosUnkArg*-1] + } + } + #Arguments + Out[["ARGUMENT"]]=opt + + #Validation of ARGUMENTs + for(i in 1:DimSpec[1]) { + if(spec$Flag[i]=="0") {#verify boolean arguments + NbValue=length(Out[[spec$LongName[i]]]) + if(NbValue>1) { + message("Warning : ",spec$LongName[i]," found ",NbValue," times") + } + } + if(length(Out[[spec$LongName[i]]])==0) { + Out[[spec$LongName[i]]]=spec$Default[i] + } + library("methods") + Out[[spec$LongName[i]]]=as(Out[[spec$LongName[i]]],spec$Mod[i]) + } + + return(Out) } -### ========================================================================= -### Ving's methods -### ------------------------------------------------------------------------- -### - -##Converts the flag numbers into binary -integer.base.b = function(x, b=2){ - xi <- as.integer(x) +## Converts the flag numbers into binary +integer.base.b=function(x, b=2) { + xi=as.integer(x) if(any(is.na(xi) | ((x-xi)!=0))) print(list(ERROR="x not integer", x=x)) - N <- length(x) - xMax <- max(c(x,1)) - ndigits <- 11 - Base.b <- array(NA, dim=c(N, ndigits)) - for(i in 1:ndigits){#i <- 1 - Base.b[, ndigits-i+1] <- (x %% b) - x <- (x %/% b) + N=length(x) + xMax=max(c(x,1)) + ndigits=11 + Base.b=array(NA, dim=c(N, ndigits)) + for(i in 1:ndigits) {#i=1 + Base.b[, ndigits-i+1]=(x %% b) + x=(x %/% b) } Base.b } -##Checks if color used is an acceptable color -is.acceptable.color = function(character) { +## Checks if color used is an acceptable color +is.acceptable.color=function(character) { tmp=try(col2rgb(character),TRUE) return(class(tmp)!="try-error") } -##Combines two data frame -listOfDataFrame2DataFrame = function(x,vertical=TRUE) { - if(length(x)==1) { - x[[1]] - } - else { - if(vertical) { - ncol = dim(x[[1]])[2] - vect=unlist(lapply(x,t)) - retour = as.data.frame(t(array(vect,dim=c(ncol,length(vect)/ncol))),stringsAsFactors=FALSE) - names(retour)=names(x[[1]]) - } - else { - nline=dim(x[[1]])[1] - vect=unlist(x) - retour=as.data.frame(array(vect,dim=c(nline,length(vect)/nline))) - names(retour) = unlist(lapply(x,names)) - } - retour - } -} - -# utilise la fonction scanBam d'une façon plus partique pour moi -extractFromBam = function(file,which,what) { +extractFromBam=function(file,which,what) { return(scanBam(file, param=ScanBamParam(which=which,what=what))[[1]][[1]]) } -##Returns a list from cigar expression -interpreteCIGAR = function(cigar) { - cigar_un = strsplit(unique(cigar),split="") - n_cigar_un = length(cigar_un) - taille_cigar = list() - analise_cigar = function(cigar_) { - cigar_sortie = list() - acc = "" +## Returns a list from cigar expression +interpreteCIGAR=function(cigar) { + cigar_un=strsplit(unique(cigar),split="") + n_cigar_un=length(cigar_un) + taille_cigar=list() + analise_cigar=function(cigar_) { + cigar_sortie=list() + acc="" for(j in 1:length(cigar_)) { if(sum(cigar_[j]==as.character(0:9))==1) { acc=paste(acc,cigar_[j],sep="") @@ -218,15 +193,15 @@ } return(cigar_sortie) } - cigar_interprete = lapply(cigar_un,analise_cigar) - names(cigar_interprete) = unique(cigar) + cigar_interprete=lapply(cigar_un,analise_cigar) + names(cigar_interprete)=unique(cigar) return(cigar_interprete) } # prend un CIGAR splités et retourne la taille occupé par le read sur la séquence génomique (introns compris) -calcule_longueur_cigar = function(cigar_) { - lon = 0 +calcule_longueur_cigar=function(cigar_) { + lon=0 N=length(cigar_) for(j in seq(2,N,2)) { if(cigar_[[j]]!="I") { @@ -237,9 +212,9 @@ } # prend un CIGAR splités et retourne les positions -calcule_junction_cigar = function(cigar_) { +calcule_junction_cigar=function(cigar_) { retour=list() - lon = 0 + lon=0 N=length(cigar_) for(j in seq(2,N,2)) { if(cigar_[[j]]!="I") { @@ -252,8 +227,8 @@ return(retour) } -##Returns a list of numbers of single read with their coordinates -compresse_coordonnees = function(debut,fin) { +## Returns a list of numbers of single read with their coordinates +compresse_coordonnees=function(debut,fin) { if(length(debut)==0) { return(list(numeric(),numeric(),numeric())) } @@ -262,57 +237,57 @@ tmp_rle=rle(tmp) poids=tmp_rle$lengths values_split=strsplit(tmp_rle$values,split="_") - doit = function(j) { + doit=function(j) { return(as.integer(values_split[[j]][1])) } debut_uni=sapply(1:length(poids),doit) - doit = function(j) { + doit=function(j) { return(as.integer(values_split[[j]][2])) } fin_uni=sapply(1:length(poids),doit) - ordre_debut = order(debut_uni) + ordre_debut=order(debut_uni) return(list(debut_uni[ordre_debut],fin_uni[ordre_debut],poids[ordre_debut])) } } -RDataFileName = function(file) { +RDataFileName=function(file) { return(paste(file,".RData",sep="")) } -##Function converts and extracts the infos from bamfile -readBam_ <-function(file_,insert_max_=2000,stranded_=TRUE,ncore_=1,libraryType_=c("standard","inverse"),fileNameRData_=NA,normalized_=NULL,chrName_=NULL,from_=1,to_=NULL) { +## Function converts and extracts the infos from bamfile +readBam_=function(file_,insert_max_=2000,stranded_=TRUE,ncore_=1,libraryType_=c("standard","inverse"),fileNameRData_=NA,normalized_=NULL,chrName_=NULL,from_=1,to_=NULL) { suppressPackageStartupMessages(require("Rsamtools")) suppressPackageStartupMessages(require("GenomicRanges")) -##Declaration of variables - flagstat = numeric(11) +## Declaration of variables + flagstat=numeric(11) names(flagstat)=c("total","duplicates","mapped","paired","read1","read2","properly paired","itself and mate mapped","singletons","mate mapped on a different chr","QC-failed") genome_info=scanBamHeader(file_)[[1]]$targets - noms_chromosomes = names(genome_info) - longueur_chromosomes = as.integer(genome_info) - nombre_chromosomes = length(noms_chromosomes) - brin_F = list() - brin_R = list() - brin_F_junction = list() - brin_R_junction = list() - pas<-c(1,2,6,7) - i_zone = 0 + noms_chromosomes=names(genome_info) + longueur_chromosomes=as.integer(genome_info) + nombre_chromosomes=length(noms_chromosomes) + brin_F=list() + brin_R=list() + brin_F_junction=list() + brin_R_junction=list() + pas=c(1,2,6,7) + i_zone=0 if(is.null(chrName_)) { - chrName__ = noms_chromosomes + chrName__=noms_chromosomes } else { - chrName__ = chrName_ + chrName__=chrName_ } -##Fragments identification +## Fragments identification for(i in (1:nombre_chromosomes)) { - i_zone = i_zone +1 - nom_chromo = noms_chromosomes[i] - lon_chromo = longueur_chromosomes[i] + i_zone=i_zone +1 + nom_chromo=noms_chromosomes[i] + lon_chromo=longueur_chromosomes[i] if(!(nom_chromo %in% chrName__)) { - brin_F[[i]] = list(numeric(),numeric(),numeric()) - brin_R[[i]] = list(numeric(),numeric(),numeric()) - brin_F_junction[[i]] = list(numeric(),numeric(),numeric()) - brin_R_junction[[i]] = list(numeric(),numeric(),numeric()) + brin_F[[i]]=list(numeric(),numeric(),numeric()) + brin_R[[i]]=list(numeric(),numeric(),numeric()) + brin_F_junction[[i]]=list(numeric(),numeric(),numeric()) + brin_R_junction[[i]]=list(numeric(),numeric(),numeric()) } else { if(is.null(to_)) { @@ -323,19 +298,19 @@ } from_i=from_[min(i_zone,length(from_))] - commande = paste("RangesList(`",nom_chromo,"` = IRanges(",from_i,",",to_i,"))",sep="") + commande=paste("RangesList(`",nom_chromo,"`=IRanges(",from_i,",",to_i,"))",sep="") expr=try(parse(text=commande),TRUE) -##Function used from GenomicRanges package - which = eval(expr) - what<-c("flag","mpos","cigar","mrnm","isize") - param<- ScanBamParam(what=what, which=which) -##Case of no reads on the chromosome +## Function used from GenomicRanges package + which=eval(expr) + what=c("flag","mpos","cigar","mrnm","isize") + param=ScanBamParam(what=what, which=which) +## Case of no reads on the chromosome start=extractFromBam(file=file_,which=which,what="pos") - if(length(start) == 0 ){ - brin_F[[i]] = list(numeric(),numeric(),numeric()) - brin_R[[i]] = list(numeric(),numeric(),numeric()) - brin_F_junction[[i]] = list(numeric(),numeric(),numeric()) - brin_R_junction[[i]] = list(numeric(),numeric(),numeric()) + if(length(start)==0 ) { + brin_F[[i]]=list(numeric(),numeric(),numeric()) + brin_R[[i]]=list(numeric(),numeric(),numeric()) + brin_F_junction[[i]]=list(numeric(),numeric(),numeric()) + brin_R_junction[[i]]=list(numeric(),numeric(),numeric()) } else { strand=extractFromBam(file=file_,which=which,what="strand") @@ -344,235 +319,156 @@ cigar=extractFromBam(file=file_,which=which,what="cigar") mrnm=extractFromBam(file=file_,which=which,what="mrnm") isize=extractFromBam(file=file_,which=which,what="isize") - + first_read=integer.base.b(flag)[,5]==1 - strand[strand =="+" & !first_read ]="*" - strand[strand =="-" & !first_read ] ="+" - strand[strand =="*" & !first_read ] ="-" + strand[strand=="+" & !first_read ]="*" + strand[strand=="-" & !first_read ]="+" + strand[strand=="*" & !first_read ]="-" -##CIGAR's interpreter - cigar_interprete = interpreteCIGAR(cigar) - longueur_cigar = lapply(cigar_interprete,calcule_longueur_cigar) - junction_cigar = lapply(cigar_interprete,calcule_junction_cigar) - debut_junction = numeric() - fin_junction = numeric() - brin_junction = numeric() - i_junction = 0 +## CIGAR's interpreter + cigar_interprete=interpreteCIGAR(cigar) + longueur_cigar=lapply(cigar_interprete,calcule_longueur_cigar) + junction_cigar=lapply(cigar_interprete,calcule_junction_cigar) end=start+sapply(1:length(cigar),function(j) longueur_cigar[[cigar[j]]]) -##Case of pairend reads - is_on_same_chr = mrnm==nom_chromo - is_on_same_chr[is.na(is_on_same_chr)] = FALSE - is_paired = is_on_same_chr & abs(isize) <= insert_max_ - is_paired[first_read & strand=="+" & (isize<0 | isize>insert_max_)] = FALSE - is_paired[!first_read & strand=="+" & (isize>0 | isize < -insert_max_)] = FALSE - is_paired[first_read & strand=="-" & (isize>0 | isize < -insert_max_)] = FALSE - is_paired[!first_read & strand=="-" & (isize<0 | isize>insert_max_)] = FALSE - is_paired[is.na(is_paired)] = FALSE - - debut_fragment_paired_plus<-mpos[!first_read & strand =="+" & is_paired] - fin_fragment_paired_plus<-end[!first_read & strand=="+" & is_paired] - debut_fragment_paired_moins<-mpos[first_read & strand=="-" & is_paired] - fin_fragment_paired_moins<-end[first_read & strand =="-" & is_paired] +## Case of pairend reads + is_on_same_chr=mrnm==nom_chromo + is_on_same_chr[is.na(is_on_same_chr)]=FALSE + is_paired=is_on_same_chr & abs(isize) <=insert_max_ + is_paired[first_read & strand=="+" & (isize<0 | isize>insert_max_)]=FALSE + is_paired[!first_read & strand=="+" & (isize>0 | isize < -insert_max_)]=FALSE + is_paired[first_read & strand=="-" & (isize>0 | isize < -insert_max_)]=FALSE + is_paired[!first_read & strand=="-" & (isize<0 | isize>insert_max_)]=FALSE + is_paired[is.na(is_paired)]=FALSE + + debut_fragment_paired_plus=mpos[!first_read & strand=="+" & is_paired] + fin_fragment_paired_plus=end[!first_read & strand=="+" & is_paired] + debut_fragment_paired_moins=mpos[first_read & strand=="-" & is_paired] + fin_fragment_paired_moins=end[first_read & strand=="-" & is_paired] + +## Case of single reads + debut_fragment_singleton_plus=start[!is_paired & strand=="+"] + fin_fragment_singleton_plus=end[!is_paired & strand=="+"] + debut_fragment_singleton_moins=start[!is_paired & strand=="-"] + fin_fragment_singleton_moins=end[!is_paired & strand=="-"] -##Case of single reads - debut_fragment_singleton_plus = start[!is_paired & strand =="+"] - fin_fragment_singleton_plus = end[!is_paired & strand =="+"] - debut_fragment_singleton_moins=start[!is_paired & strand =="-"] - fin_fragment_singleton_moins= end[!is_paired & strand =="-"] - -##Fragments - debut_frag_plus = c(debut_fragment_paired_plus,debut_fragment_singleton_plus) - fin_frag_plus = c(fin_fragment_paired_plus,fin_fragment_singleton_plus) +## Fragments + debut_frag_plus=c(debut_fragment_paired_plus,debut_fragment_singleton_plus) + fin_frag_plus=c(fin_fragment_paired_plus,fin_fragment_singleton_plus) debut_frag_moins=c(debut_fragment_paired_moins,debut_fragment_singleton_moins) - fin_frag_moins = c(fin_fragment_paired_moins,fin_fragment_singleton_moins) - brin_F[[i]] = compresse_coordonnees(debut_frag_plus,fin_frag_plus) - brin_R[[i]] = compresse_coordonnees(debut_frag_moins,fin_frag_moins) + fin_frag_moins=c(fin_fragment_paired_moins,fin_fragment_singleton_moins) + brin_F[[i]]=compresse_coordonnees(debut_frag_plus,fin_frag_plus) + brin_R[[i]]=compresse_coordonnees(debut_frag_moins,fin_frag_moins) -##junction read +## Junction read + debut_junction=numeric() + fin_junction=numeric() + brin_junction=numeric() + i_junction=0 for(j in 1:length(cigar)) { - junctions_ = junction_cigar[[cigar[j]]] - if(length(junctions_)){ + junctions_=junction_cigar[[cigar[j]]] + if(length(junctions_)) { for(k in 1:length(junctions_)) { - i_junction = i_junction + 1 - debut_junction[i_junction] = start[j] + junctions_[[k]][1] - 1 - fin_junction[i_junction] = start[j] + junctions_[[k]][2] - 1 - brin_junction[i_junction] = as.character(strand[j]) + i_junction=i_junction + 1 + debut_junction[i_junction]=start[j] + junctions_[[k]][1] - 1 + fin_junction[i_junction]=start[j] + junctions_[[k]][2] - 1 + brin_junction[i_junction]=as.character(strand[j]) } } } if(i_junction==0) { - brin_F_junction[[i]] = list(numeric(),numeric(),numeric()) - brin_R_junction[[i]] = list(numeric(),numeric(),numeric()) + brin_F_junction[[i]]=list(numeric(),numeric(),numeric()) + brin_R_junction[[i]]=list(numeric(),numeric(),numeric()) } else { - brin_F_junction[[i]] = compresse_coordonnees(debut_junction[brin_junction=="+"],fin_junction[brin_junction=="+"]) - brin_R_junction[[i]] = compresse_coordonnees(debut_junction[brin_junction=="-"],fin_junction[brin_junction=="-"]) + brin_F_junction[[i]]=compresse_coordonnees(debut_junction[brin_junction=="+"],fin_junction[brin_junction=="+"]) + brin_R_junction[[i]]=compresse_coordonnees(debut_junction[brin_junction=="-"],fin_junction[brin_junction=="-"]) } -##Flagstat interpreter - flag_bits = integer.base.b(flag)#remplie les données stat pour un flag donné + +## Flagstat interpreter + flag_bits=integer.base.b(flag)#remplie les données stat pour un flag donné - ##flagstat - ##total - flagstat[1] = flagstat[1] + sum(flag_bits[,2]==0) - ##duplicates - flagstat[2] = flagstat[2] + sum((flag_bits[,1]==1)&(flag_bits[,2]==0)) - ##mapped - flagstat[3] = flagstat[3] + sum((flag_bits[,9]==0)&(flag_bits[,2]==0)) - ##paired - flagstat[4] = flagstat[4] + sum((flag_bits[,11]==1)&(flag_bits[,2]==0)) - ##read1 - flagstat[5] = flagstat[5] + sum((flag_bits[,5]==1)&(flag_bits[,2]==0)) - ##read2 - flagstat[6] = flagstat[6] + sum((flag_bits[,4]==1)&(flag_bits[,2]==0)) - ##iself and mate mapped - flagstat[8] = flagstat[8] + sum((flag_bits[,11]==1)&(flag_bits[,9]==0)&(flag_bits[,8]==0)&(flag_bits[,2]==0)) - ##singletons - flagstat[9] = flagstat[9] + sum((flag_bits[,8]==1)&(flag_bits[,2]==0)) - ##QC-failed - flagstat[11] = flagstat[11] + sum(flag_bits[,2]==1) - ##flagstat - ##mate on a different chr - flagstat[10] = flagstat[10] + sum((!is_on_same_chr)&(flag_bits[,11]==1)&(flag_bits[,9]==0)&(flag_bits[,8]==0)&(flag_bits[,2]==0)) - ##flagstat - ##properly paired - flagstat[7] = flagstat[7] + sum(is_paired) - + ## flagstat + ## total + flagstat[1]=flagstat[1] + sum(flag_bits[,2]==0) + ## duplicates + flagstat[2]=flagstat[2] + sum((flag_bits[,1]==1)&(flag_bits[,2]==0)) + ## mapped + flagstat[3]=flagstat[3] + sum((flag_bits[,9]==0)&(flag_bits[,2]==0)) + ## paired + flagstat[4]=flagstat[4] + sum((flag_bits[,11]==1)&(flag_bits[,2]==0)) + ## read1 + flagstat[5]=flagstat[5] + sum((flag_bits[,5]==1)&(flag_bits[,2]==0)) + ## read2 + flagstat[6]=flagstat[6] + sum((flag_bits[,4]==1)&(flag_bits[,2]==0)) + ## iself and mate mapped + flagstat[8]=flagstat[8] + sum((flag_bits[,11]==1)&(flag_bits[,9]==0)&(flag_bits[,8]==0)&(flag_bits[,2]==0)) + ## singletons + flagstat[9]=flagstat[9] + sum((flag_bits[,8]==1)&(flag_bits[,2]==0)) + ## QC-failed + flagstat[11]=flagstat[11] + sum(flag_bits[,2]==1) + ## flagstat + ## mate on a different chr + flagstat[10]=flagstat[10] + sum((!is_on_same_chr)&(flag_bits[,11]==1)&(flag_bits[,9]==0)&(flag_bits[,8]==0)&(flag_bits[,2]==0)) + ## flagstat + ## properly paired + flagstat[7]=flagstat[7] + sum(is_paired) } } } -##Data storing - names(brin_F) = noms_chromosomes - names(brin_R) = noms_chromosomes - names(brin_F_junction) = noms_chromosomes - names(brin_R_junction) = noms_chromosomes + +## Data storing + names(brin_F)=noms_chromosomes + names(brin_R)=noms_chromosomes + names(brin_F_junction)=noms_chromosomes + names(brin_R_junction)=noms_chromosomes - bamHandler = list() + bamHandler=list() if(libraryType_[1]=="inverse") { - bamHandler[[1]] = brin_R - bamHandler[[2]] = brin_F + bamHandler[[1]]=brin_R + bamHandler[[2]]=brin_F } else { - bamHandler[[1]] = brin_F - bamHandler[[2]] = brin_R + bamHandler[[1]]=brin_F + bamHandler[[2]]=brin_R } - bamHandler[[3]] = longueur_chromosomes - bamHandler[[4]] = flagstat - bamHandler[[5]] = stranded_ + bamHandler[[3]]=longueur_chromosomes + bamHandler[[4]]=flagstat + bamHandler[[5]]=stranded_ if(libraryType_[1]=="inverse") { - bamHandler[[6]] = brin_R_junction - bamHandler[[7]] = brin_F_junction + bamHandler[[6]]=brin_R_junction + bamHandler[[7]]=brin_F_junction } else { - bamHandler[[6]] = brin_F_junction - bamHandler[[7]] = brin_R_junction + bamHandler[[6]]=brin_F_junction + bamHandler[[7]]=brin_R_junction } - bamHandler[[8]] = FALSE -if(!is.null(normalized_)) { + bamHandler[[8]]=FALSE + if(!is.null(normalized_)) { for( i in pas) { - for(j in 1:nombre_chromosomes){ - bamHandler[[i]][[j]][[4]]=normalized_*bamHandler[[i]][[j]][[3]] - } + for(j in 1:nombre_chromosomes) { + bamHandler[[i]][[j]][[4]]=normalized_*bamHandler[[i]][[j]][[3]] + } } - bamHandler[[8]] = TRUE -} + bamHandler[[8]]=TRUE + } - names(bamHandler) = c("F","R","chrLength","flagstat","stranded","junctions_F","junctions_R","norm") + names(bamHandler)=c("F","R","chrLength","flagstat","stranded","junctions_F","junctions_R","norm") if((is.null(chrName_))&(from_==1)&(is.null(to_))) { if(is.null(fileNameRData_)|is.na(fileNameRData_)) { - save(bamHandler,file=RDataFileName(file_)) + save(bamHandler,file=RDataFileName(file_)) } else { - save(bamHandler,file=fileNameRData_) + save(bamHandler,file=fileNameRData_) } } return(bamHandler) } -chercheBamHandlerDansFichierRData = function(fichierRData) { - tmp=try(load(fichierRData),TRUE) - if(class(tmp)=="try-error") { - return(tmp) - } - else { - return(try(bamHandler,TRUE)) - } -} - -##Public Function -readBam = function(file,insert_max=2000,stranded=TRUE,reload=FALSE,ncore=1,libraryType=c("standard","inverse"),normalized=NULL,chrName=NULL,from=1,to=NULL) { - if(length(file)==1) { - nom_fichier_RData = RDataFileName(file) - if(!file.exists(nom_fichier_RData)|reload) { - return(try(readBam_(file_=file,insert_max_=insert_max,stranded_=stranded,ncore_=ncore,libraryType_=libraryType,normalized_=normalized,chrName_=chrName,from_=from,to_=to),TRUE)) - } - else { - load(nom_fichier_RData) - return(bamHandler) - } - } - else { - require("multicore") - chargeBamsDansFichiersRData = function(oneFile) { - nom_fichier_RData = RDataFileName(oneFile) - if(!file.exists(nom_fichier_RData)|reload) { - bamHandler=try(readBam_(oneFile,insert_max_=insert_max,stranded_=stranded,libraryType_=libraryType,normalized_=normalized,chrName_=chrName,from_=from,to_=to),TRUE) - } - return(nom_fichier_RData) - } - fichiersRData = mclapply(file,chargeBamsDansFichiersRData,mc.cores=ncore) - gc() - return(lapply(fichiersRData,chercheBamHandlerDansFichierRData)) - } -} - -## Returns an adjusted bamHandler object -ajustBam = function(bamHandler,coeff=1) { - if(class(bamHandler)=="try-error") { - return(bamHandler) - } - else { - bamHandler_ = bamHandler - L = length(bamHandler_$F) - for(i in 1:L) { - bamHandler_$F[[i]][[4]]=bamHandler_$F[[i]][[3]]*coeff - bamHandler_$R[[i]][[4]]=bamHandler_$R[[i]][[3]]*coeff - bamHandler_$junctions_F[[i]][[4]]=bamHandler_$junctions_F[[i]][[3]]*coeff - bamHandler_$junctions_R[[i]][[4]]=bamHandler_$junctions_R[[i]][[3]]*coeff - } - bamHandler_$norm=TRUE - return(bamHandler_) - } - } - -##Returns an ajusted bamHandler -normalizeBams = function(data,poids,which=1:length(poids),relative=TRUE) { - N=length(data) - j=0 - retour = list() - for(i in 1:N) { - - if(i %in% which) { - j = j + 1 - if(relative) { - coeff=min(poids)/poids[j] - } - else { - coeff=poids[j] - } - retour[[i]] = ajustBam(data[[i]],coeff) - } - else { - retour[[i]] = data[[i]] - } - } - return(retour) -} - -##Returns the sum of two bamHandler objects -addBam = function(bamHandler1,bamHandler2) { +## Returns the sum of two bamHandler objects +addBam=function(bamHandler1,bamHandler2) { if(class(bamHandler1)=="try-error"|class(bamHandler2)=="try-error") { if(class(bamHandler1)=="try-error") { return(bamHandler2) @@ -582,121 +478,99 @@ } } else { - brin_F = list() - junctions_brin_F = list() - brin_R = list() - junctions_brin_R = list() - L = length(bamHandler1$F) - bamHandler = list() - if(bamHandler1$norm != bamHandler2$norm ){ + brin_F=list() + junctions_brin_F=list() + brin_R=list() + junctions_brin_R=list() + L=length(bamHandler1$F) + bamHandler=list() + if(bamHandler1$norm !=bamHandler2$norm ) { warning(expr="Two different bam files(normalized and non normalized)!!",immediate.=TRUE) } for(i in 1:L) { - brin_F[[i]] = list(c(bamHandler1$F[[i]][[1]],bamHandler2$F[[i]][[1]]),c(bamHandler1$F[[i]][[2]],bamHandler2$F[[i]][[2]]),c(bamHandler1$F[[i]][[3]],bamHandler2$F[[i]][[3]])) - junctions_brin_F[[i]] = list(c(bamHandler1$junctions_F[[i]][[1]],bamHandler2$junctions_F[[i]][[1]]),c(bamHandler1$junctions_F[[i]][[2]],bamHandler2$junctions_F[[i]][[2]]),c(bamHandler1$junctions_F[[i]][[3]],bamHandler2$junctions_F[[i]][[3]])) - brin_R[[i]] = list(c(bamHandler1$R[[i]][[1]],bamHandler2$R[[i]][[1]]),c(bamHandler1$R[[i]][[2]],bamHandler2$R[[i]][[2]]),c(bamHandler1$R[[i]][[3]],bamHandler2$R[[i]][[3]])) - junctions_brin_R[[i]] = list(c(bamHandler1$junctions_R[[i]][[1]],bamHandler2$junctions_R[[i]][[1]]),c(bamHandler1$junctions_R[[i]][[2]],bamHandler2$junctions_R[[i]][[2]]),c(bamHandler1$junctions_R[[i]][[3]],bamHandler2$junctions_R[[i]][[3]])) - if(bamHandler1$norm & bamHandler2$norm){ - brin_F[[i]][[4]] = c(bamHandler1$F[[i]][[4]],bamHandler2$F[[i]][[4]]) - junctions_brin_F[[i]][[4]] = c(bamHandler1$junctions_F[[i]][[4]],bamHandler2$junctions_F[[i]][[4]]) - brin_R[[i]][[4]] = c(bamHandler1$R[[i]][[4]],bamHandler2$R[[i]][[4]]) - junctions_brin_R[[i]][[4]] = c(bamHandler1$junctions_R[[i]][[4]],bamHandler2$junctions_R[[i]][[4]]) + brin_F[[i]]=list(c(bamHandler1$F[[i]][[1]],bamHandler2$F[[i]][[1]]),c(bamHandler1$F[[i]][[2]],bamHandler2$F[[i]][[2]]),c(bamHandler1$F[[i]][[3]],bamHandler2$F[[i]][[3]])) + junctions_brin_F[[i]]=list(c(bamHandler1$junctions_F[[i]][[1]],bamHandler2$junctions_F[[i]][[1]]),c(bamHandler1$junctions_F[[i]][[2]],bamHandler2$junctions_F[[i]][[2]]),c(bamHandler1$junctions_F[[i]][[3]],bamHandler2$junctions_F[[i]][[3]])) + brin_R[[i]]=list(c(bamHandler1$R[[i]][[1]],bamHandler2$R[[i]][[1]]),c(bamHandler1$R[[i]][[2]],bamHandler2$R[[i]][[2]]),c(bamHandler1$R[[i]][[3]],bamHandler2$R[[i]][[3]])) + junctions_brin_R[[i]]=list(c(bamHandler1$junctions_R[[i]][[1]],bamHandler2$junctions_R[[i]][[1]]),c(bamHandler1$junctions_R[[i]][[2]],bamHandler2$junctions_R[[i]][[2]]),c(bamHandler1$junctions_R[[i]][[3]],bamHandler2$junctions_R[[i]][[3]])) + if(bamHandler1$norm & bamHandler2$norm) { + brin_F[[i]][[4]]=c(bamHandler1$F[[i]][[4]],bamHandler2$F[[i]][[4]]) + junctions_brin_F[[i]][[4]]=c(bamHandler1$junctions_F[[i]][[4]],bamHandler2$junctions_F[[i]][[4]]) + brin_R[[i]][[4]]=c(bamHandler1$R[[i]][[4]],bamHandler2$R[[i]][[4]]) + junctions_brin_R[[i]][[4]]=c(bamHandler1$junctions_R[[i]][[4]],bamHandler2$junctions_R[[i]][[4]]) } } - - names(brin_F) = names(bamHandler1$F) - names(brin_R) = names(bamHandler2$R) - names(junctions_brin_F) = names(bamHandler1$junctions_F) - names(junctions_brin_R) = names(bamHandler2$junctions_R) - bamHandler[[1]] = brin_F - bamHandler[[2]] = brin_R - bamHandler[[3]] = bamHandler1[[3]] - bamHandler[[4]] = bamHandler1[[4]] + bamHandler2[[4]] - bamHandler[[5]] = bamHandler1[[5]] & bamHandler2[[5]] - bamHandler[[6]] = junctions_brin_F - bamHandler[[7]] = junctions_brin_R - bamHandler[[8]] = bamHandler1$norm & bamHandler2$norm - names(bamHandler) = c("F","R","chrLength","flagstat","stranded","junctions_F","junctions_R","norm") + names(brin_F)=names(bamHandler1$F) + names(brin_R)=names(bamHandler2$R) + names(junctions_brin_F)=names(bamHandler1$junctions_F) + names(junctions_brin_R)=names(bamHandler2$junctions_R) + bamHandler[[1]]=brin_F + bamHandler[[2]]=brin_R + bamHandler[[3]]=bamHandler1[[3]] + bamHandler[[4]]=bamHandler1[[4]] + bamHandler2[[4]] + bamHandler[[5]]=bamHandler1[[5]] & bamHandler2[[5]] + bamHandler[[6]]=junctions_brin_F + bamHandler[[7]]=junctions_brin_R + bamHandler[[8]]=bamHandler1$norm & bamHandler2$norm + names(bamHandler)=c("F","R","chrLength","flagstat","stranded","junctions_F","junctions_R","norm") return(bamHandler) } } -##Returns the sum of a list of bamHandler objects -sumBam = function(...) { - args = list(...) - retour = args[[1]] - if(length(args)>1) { - for(i in 2:length(args)) { - retour = addBam(retour,args[[i]]) - } - } - return(retour) -} - -##Returns the mean of bamHandler objects -meanBam = function(...) { - args = list(...) - bamsReduced=normalizeBams(args,rep(1,length(args))/length(args),relative=FALSE) - retour = bamsReduced[[1]] - if(length(bamsReduced)>1) { - for(i in 2:length(bamsReduced)) { - retour = addBam(retour,bamsReduced[[i]]) - } - } - return(retour) -} - -##Extracts the signal from bamHandler objects -extractSignal = function(bamHandlerList,chrName,from=1, to=NULL,normalized_=FALSE) { +## Extracts the signal from bamHandler objects +extractSignal=function(bamHandlerList,chrName,from=1, to=NULL,normalized_=FALSE) { forward=list() reverse=list() chr=which(names(bamHandlerList[[1]]$F)==chrName) - if(is.null(to)){ + if(is.null(to)) { to=bamHandlerList[[1]]$chrLength[chr] } - if(normalized_) { - end=4 - } - else { - end=3 - } - for(i in 1:length(bamHandlerList)){ + for(i in 1:length(bamHandlerList)) { + if(normalized_) { + if(bamHandlerList[[i]]$norm) { + end=4 + } + else { + end=3 + } + } + else { + end=3 + } forward_=numeric(to-from+1) - which_read = which((bamHandlerList[[i]]$F[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$F[[chrName]][[1]]<=to)) + which_read=which((bamHandlerList[[i]]$F[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$F[[chrName]][[1]]<=to)) n_reads=length(which_read) if(n_reads>0) { for(k in which_read) { - debut_read = max(1,bamHandlerList[[i]]$F[[chrName]][[1]][k]-from+1) - fin_read = min(bamHandlerList[[i]]$F[[chrName]][[2]][k]-from+1,to-from+1) + debut_read=max(1,bamHandlerList[[i]]$F[[chrName]][[1]][k]-from+1) + fin_read=min(bamHandlerList[[i]]$F[[chrName]][[2]][k]-from+1,to-from+1) forward_[debut_read:fin_read]=forward_[debut_read:fin_read]+bamHandlerList[[i]]$F[[chrName]][[end]][k] } } - which_junctions = which((bamHandlerList[[i]]$junctions_F[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$junctions_F[[chrName]][[1]]<=to)) + which_junctions=which((bamHandlerList[[i]]$junctions_F[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$junctions_F[[chrName]][[1]]<=to)) n_junctions=length(which_junctions) if(n_junctions>0) { for(k in which_junctions) { - debut_junction = max(1,bamHandlerList[[i]]$junctions_F[[chrName]][[1]][k]-from+1) - fin_junction = min(bamHandlerList[[i]]$junctions_F[[chrName]][[2]][k]-from+1,to-from+1) + debut_junction=max(1,bamHandlerList[[i]]$junctions_F[[chrName]][[1]][k]-from+1) + fin_junction=min(bamHandlerList[[i]]$junctions_F[[chrName]][[2]][k]-from+1,to-from+1) forward_[debut_junction:fin_junction]=forward_[debut_junction:fin_junction]-bamHandlerList[[i]]$junctions_F[[chrName]][[end]][k] } } - reverse_=numeric(to-from+1) - which_read = which((bamHandlerList[[i]]$R[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$R[[chrName]][[1]]<=to)) - n_reads= length(which_read) + which_read=which((bamHandlerList[[i]]$R[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$R[[chrName]][[1]]<=to)) + n_reads=length(which_read) if(n_reads>0) { for(k in which_read) { - debut_read = max(1,bamHandlerList[[i]]$R[[chrName]][[1]][k]-from+1) - fin_read = min(bamHandlerList[[i]]$R[[chrName]][[2]][k]-from+1,to-from+1) + debut_read=max(1,bamHandlerList[[i]]$R[[chrName]][[1]][k]-from+1) + fin_read=min(bamHandlerList[[i]]$R[[chrName]][[2]][k]-from+1,to-from+1) reverse_[debut_read:fin_read]=reverse_[debut_read:fin_read]+bamHandlerList[[i]]$R[[chrName]][[end]][k] } } - which_junctions = which((bamHandlerList[[i]]$junctions_R[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$junctions_R[[chrName]][[1]]<=to)) + which_junctions=which((bamHandlerList[[i]]$junctions_R[[chrName]][[2]]>=from)&(bamHandlerList[[i]]$junctions_R[[chrName]][[1]]<=to)) n_junctions=length(which_junctions) if(n_junctions>0) { for(k in which_junctions) { - debut_junction = max(1,bamHandlerList[[i]]$junctions_R[[chrName]][[1]][k]-from+1) - fin_junction = min(bamHandlerList[[i]]$junctions_R[[chrName]][[2]][k]-from+1,to-from+1) + debut_junction=max(1,bamHandlerList[[i]]$junctions_R[[chrName]][[1]][k]-from+1) + fin_junction=min(bamHandlerList[[i]]$junctions_R[[chrName]][[2]][k]-from+1,to-from+1) reverse_[debut_junction:fin_junction]=reverse_[debut_junction:fin_junction]-bamHandlerList[[i]]$junctions_R[[chrName]][[end]][k] } } @@ -711,27 +585,21 @@ reverse[[i]]=numeric(to-from+1) } } - chr_ = list() - chr_$F = forward - chr_$R = reverse + chr_=list() + chr_$F=forward + chr_$R=reverse return(chr_) } -##Intern function for -totalReads = function(bamHandler) { - return(bamHandler[[4]][1]+bamHandler[[4]][11]) -} - -##Intern function for readGff function +## Intern function for readGff function my.read.lines2=function(fname) { - - s = file.info( fname )$size - buf = readChar( fname, s, useBytes=T) + s=file.info( fname )$size + buf=readChar( fname, s, useBytes=T) strsplit( buf,"\n",fixed=T,useBytes=T)[[1]] } -##Extracts the annotation infos from Gff file -readGff = function(file_in, from=1, to=Inf, chr=NULL, infoName=c("ID","Name","Parent","gene","Alias","orf_classification","Ontology_term","Note","GO")) { +## Extracts the annotation infos from Gff file +readGff=function(file_in, from=1, to=Inf, chr=NULL, infoName=c("ID","Name","Parent","gene","Alias","orf_classification","Ontology_term","Note","GO")) { tmp=try(my.read.lines2(file_in)) if(!is.null(chr)) { tmp1=grep(chr, tmp, value=TRUE,useBytes=T) @@ -740,28 +608,28 @@ tmp1=tmp } N=length(tmp1) - Chr = array() - Start= array() - Stop= array() + Chr=array() + Start=array() + Stop=array() Strand=array() Type=array() info=list() - for(i in 1:length(infoName)) info[[i]] = array() + for(i in 1:length(infoName)) info[[i]]=array() names(info)=infoName - j<-1 + j=1 for (i in 1:N) { if(substr(tmp1[i],1,1)!="#") { line_split=unlist(strsplit(tmp1[i],"\t",fixed=T,useBytes=T)) if((as.integer(line_split[4])<=to) & (as.integer(line_split[5])>=from)) { - Chr[j] = line_split[1] - Start[j] = as.integer(line_split[4]) - Stop[j] = as.integer(line_split[5]) + Chr[j]=line_split[1] + Start[j]=as.integer(line_split[4]) + Stop[j]=as.integer(line_split[5]) Strand[j]=line_split[7] - Type[j] = line_split[3] + Type[j]=line_split[3] ninth=unlist(strsplit(line_split[9],";",fixed=T,useBytes=T)) element_ninth_empty=rep(TRUE,length(infoName)) for(element_ninth in ninth) { - element_ninth_split = unlist(strsplit(element_ninth,"=",fixed=T,useBytes=T)) + element_ninth_split=unlist(strsplit(element_ninth,"=",fixed=T,useBytes=T)) if(length(element_ninth_split)==2) { if(element_ninth_split[1] %in% infoName) { info[[element_ninth_split[1]]][j]=element_ninth_split[2] @@ -772,16 +640,16 @@ for(infoName_ in infoName[element_ninth_empty]) { info[[infoName_]][j]="." } - j<-j+1 + j=j+1 } } } - retour = data.frame(Chr,Type,Start,Stop,Strand,info,stringsAsFactors = FALSE) + retour=data.frame(Chr,Type,Start,Stop,Strand,info,stringsAsFactors=FALSE) return(retour) } -##Returns the classic visualisation -plotRNAseq = function(forward,reverse,debut_vue=1,fin_vue=length(forward),chr=NULL,annot=NULL,style=NULL,top=NULL,bottom=NULL,x="",y="",titre="",repeated=FALSE,name_flags="",decal=0,ataxises=NULL,classic_plus_color="navyblue",classic_minus_color="mediumvioletred",stranded=TRUE) { +## Returns the classic visualisation +plotRNAseq=function(forward,reverse,debut_vue=1,fin_vue=length(forward),chr=NULL,annot=NULL,style=NULL,top=NULL,bottom=NULL,x="",y="",titre="",repeated=FALSE,name_flags="",decal=0,ataxises=NULL,classic_plus_color="navyblue",classic_minus_color="mediumvioletred",stranded=TRUE) { if(repeated) { forward_=numeric(fin_vue) forward_[debut_vue:fin_vue]=forward @@ -805,6 +673,8 @@ plot(c(debut_vue,fin_vue)+decal,c(-bottom,top),ylim=c(-bottom,top),xlab=x,ylab=y,main=titre,col="white",xaxs="i",xaxt="n",cex.main=2,yaxt="n",cex.lab=1.8) ataxisesLabels=as.character(ataxises) ataxisesLabels[((1:length(ataxises))%%2)==0]="" + ataxisesLabels[1]="" + ataxisesLabels[length(ataxises)]="" lim=c(-bottom,top) ataxises_y=pretty(lim,n=4) ataxisesLabels_y=as.character(abs(ataxises_y)) @@ -814,7 +684,7 @@ axis(2, at=ataxises_y,labels=ataxisesLabels_y,cex.axis=2,line=-0.4,lwd=0) } polygon(c(debut_vue,debut_vue:fin_vue,fin_vue)+decal,c(0,forward_[debut_vue:fin_vue],0),col=classic_plus_color,border=NA) - if(stranded){ + if(stranded) { text(fin_vue+(fin_vue-debut_vue)*0.01,top/2,"+",xpd=NA,cex=3) text(fin_vue+(fin_vue-debut_vue)*0.01,-bottom/2,"-",xpd=NA,cex=3) text(fin_vue+(fin_vue-debut_vue)*0.025,(top-bottom)/2,"Strand",xpd=NA,cex=2,srt=-90) @@ -822,41 +692,24 @@ abline(h=0,lwd=2) abline(h=0,col="white") } - #if(!is.null(chr)&!is.null(annot)&!is.null(style)) { - # N=dim(annot)[1] - #if(N>0) { - # for(i in 1:N) { - #if(annot$Strand[i]=="+") { - # arrows(annot$Start[i],top,annot$Stop[i],top,col=style$col[style$Type==annot$Type[i]],length=0.10) - #} - #if(annot$Strand[i]=="-") { - # arrows(annot$Stop[i],-bottom,annot$Start[i],-bottom,col=style$col[style$Type==annot$Type[i]],length=0.10) - #} - #if(annot$Strand[i]==".") { - # segments(annot$Start[i],top,annot$Stop[i],top,col=style$col[style$Type==annot$Type[i]]) - #segments(annot$Stop[i],-bottom,annot$Start[i],-bottom,col=style$col[style$Type==annot$Type[i]]) - #} - #} - #} - #} if(name_flags!="") { - flags=try(get(name_flags),TRUE) - if(class(flags)!="try-error") { - f_=flags[(flags$Chr==chr)&(flags$Stop>=debut_vue)&(flags$Start<=fin_vue),] - N=dim(f_)[1] - points(f_$Start,rep(0,N),col=2,pch=19,cex=2) - } - } - if(decal<=0) { + flags=try(get(name_flags),TRUE) + if(class(flags)!="try-error") { + f_=flags[(flags$Chr==chr)&(flags$Stop>=debut_vue)&(flags$Start<=fin_vue),] + N=dim(f_)[1] + points(f_$Start,rep(0,N),col=2,pch=19,cex=2) + } + } + if(decal<=0) { lines(c(0,0),c(top,-bottom),col=1) - } + } } -##Intern function for heatmap visualisation -paletteFromColors = function(colMin="blue",colMax="red",n=300,method=c("hsv","rgb")) { - colMinRGB = col2rgb(colMin)[,1]/255 - colMaxRGB = col2rgb(colMax)[,1]/255 - seqList = list() +## Intern function for heatmap visualisation +paletteFromColors=function(colMin="blue",colMax="red",n=300,method=c("hsv","rgb")) { + colMinRGB=col2rgb(colMin)[,1]/255 + colMaxRGB=col2rgb(colMax)[,1]/255 + seqList=list() if(method[1]=="rgb") { for(i in 1:3) { seqList[[i]]=seq(colMinRGB[i],colMaxRGB[i],length.out=n) @@ -864,8 +717,8 @@ return(rgb(seqList[[1]],seqList[[2]],seqList[[3]])) } else { - colMinHSV = rgb2hsv(colMinRGB) - colMaxHSV = rgb2hsv(colMaxRGB) + colMinHSV=rgb2hsv(colMinRGB) + colMaxHSV=rgb2hsv(colMaxRGB) for(i in 1:3) { seqList[[i]]=seq(colMinHSV[i],colMaxHSV[i],length.out=n) } @@ -873,14 +726,14 @@ } } -##Retuns the heatmap visualisation -myHeatMap = function(data,debut_vue,fin_vue,ataxises=NULL,lim=NULL,heatmap_max_color="#000055",heatmap_min_color="#FFFFAA",heatmap_palette_method="hsv",textOnLeftSide="") { +## Retuns the heatmap visualisation +myHeatMap=function(data,debut_vue,fin_vue,ataxises=NULL,lim=NULL,heatmap_max_color="#000055",heatmap_min_color="#FFFFAA",heatmap_palette_method="hsv",textOnLeftSide="") { palette=paletteFromColors(heatmap_min_color,heatmap_max_color,method=heatmap_palette_method) if(is.null(lim)) { - image(debut_vue:fin_vue,1:dim(data)[1],t(data), col = palette,xlab="",ylab="",xaxt="n",yaxt="n") + image(debut_vue:fin_vue,1:dim(data)[1],t(data), col=palette,xlab="",ylab="",xaxt="n",yaxt="n") } else { - image(debut_vue:fin_vue,1:dim(data)[1],t(data), col = palette,xlab="",ylab="",xaxt="n",yaxt="n",zlim=lim) + image(debut_vue:fin_vue,1:dim(data)[1],t(data), col=palette,xlab="",ylab="",xaxt="n",yaxt="n",zlim=lim) } box() if(is.null(ataxises)) { @@ -898,49 +751,64 @@ text(fin_vue+(fin_vue-debut_vue)*0.015,(dim(data)[1]+1)/2,textOnLeftSide,xpd=NA,cex=1,srt=-90) } -##Returns the title of visualisation +## Returns the title of visualisation plotTitle=function(debut_vue=1,fin_vue=length(listForward[[1]]),chr=NULL,style=NULL) { - plot(c(0,1),c(0,1),col="white",ylab="",xlab="",fg="white",col.axis="white",xaxs="i",yaxs="i") - text(0,0.5,paste(chr,":",debut_vue,"-",fin_vue,sep=""),cex=2.2,adj=0) + plot(c(0,1),c(0,1),cex=0,ylab="",xlab="",fg="white",axes=FALSE,xaxs="i",yaxs="i") + text(0,0.5,paste(chr,":",debut_vue,"-",fin_vue,sep=""),cex=2.2,adj=0) +} + +openGraphicalDevice=function(file,widthPixels,heightPixels,fileType=c("png","jpeg","tiff","bmp","pdf"),resolutionDPI=72) { + widthInches=widthPixels/72 + heightInches=heightPixels/72 + doit=function(x) { + switch(x, + png(file,widthInches,heightInches,units="in",res=resolutionDPI), + jpeg=jpeg(file,widthInches,heightInches,units="in",res=resolutionDPI), + tiff=tiff(file,widthInches,heightInches,units="in",res=resolutionDPI), + bmp=bmp(file,widthInches,heightInches,units="in",res=resolutionDPI), + pdf=pdf(file,widthInches,heightInches)) + } + doit(fileType[1]) } -##The main function of visualisation -plotVisu = function(file,typeVisu="classic",listForward,listReverse,which=1:length(listForward),stranded=TRUE, +## The main function of visualisation +plotVisu=function(file,typeVisu="classic",listForward,listReverse,which=1:length(listForward),stranded=TRUE, debut_vue=1,fin_vue=length(listForward[[1]]),chr=NULL,annot=NULL,style=NULL,tops=NULL,bottoms=NULL,marks=NULL,strandMarks=NULL, titres="",repeated=FALSE,name_flags="",decal=0,log=TRUE,classic_plus_color="navyblue",classic_minus_color="deeppink3", -heatmap_max_color="#000055",heatmap_min_color="#FFFFAA",heatmap_palette_method="hsv", +heatmap_max_color="#000055",heatmap_min_color="#FFFFAA",heatmap_palette_method="hsv",heatmap_lane_height=round(10+40/(1+10^((length(which)-12)/9))), lines_samples_colors=c(1,3,4,2)[((0:length(listForward))%%4)+1],lines_samples_type_line=((0:length(listForward))%/%4)+1, -smoothLength=trunc((fin_vue-debut_vue)/1200),annotation_color_by_strand=FALSE,annotation_placed_by_strand=FALSE) { +smoothLength=trunc((fin_vue-debut_vue)/1200),annotation_color_by_strand=FALSE,annotation_placed_by_strand=FALSE,display_name=NULL,initialize_label_sizes=NULL, +fileType="png",resolutionDPI=72) { if(fin_vue-debut_vue+1>1000000) { - png(file,1200,400) + openGraphicalDevice(file,1200,400,fileType=fileType,resolutionDPI=resolutionDPI) plot(0:1,0:1,fg="white",col="white",axes=FALSE,frame=FALSE,xlab="",ylab="") text(0.5,0.5,"Window too long !",cex=5) } else { - n_element_vue = length(which) - i_data = which[1] + n_element_vue=length(which) + i_data=which[1] forward_matrice=NULL reverse_matrice=NULL - all_stranded = data[[i_data]]$stranded + all_stranded=data[[i_data]]$stranded if(!repeated) { for(i in 1:n_element_vue) { - i_data = which[i] - forward_matrice = rbind(forward_matrice,listForward[[i_data]][debut_vue:fin_vue]) - reverse_matrice = rbind(reverse_matrice,listReverse[[i_data]][debut_vue:fin_vue]) - all_stranded = all_stranded & data[[i_data]]$stranded + i_data=which[i] + forward_matrice=rbind(forward_matrice,listForward[[i_data]][debut_vue:fin_vue]) + reverse_matrice=rbind(reverse_matrice,listReverse[[i_data]][debut_vue:fin_vue]) + all_stranded=all_stranded & data[[i_data]]$stranded } } - else{ + else { for(i in 1:n_element_vue) { - i_data = which[i] - forward_matrice = rbind(forward_matrice,listForward[[i_data]]) - reverse_matrice = rbind(reverse_matrice,listReverse[[i_data]]) - all_stranded = all_stranded & data[[i_data]]$stranded + i_data=which[i] + forward_matrice=rbind(forward_matrice,listForward[[i_data]]) + reverse_matrice=rbind(reverse_matrice,listReverse[[i_data]]) + all_stranded=all_stranded & data[[i_data]]$stranded } } rownames(forward_matrice)=titres[which] rownames(reverse_matrice)=titres[which] - for( i in 1:n_element_vue){ + for( i in 1:n_element_vue) { if(smoothLength>1) { lo=smooth(forward_matrice[i,],L=smoothLength) forward_matrice[i,]=lo @@ -954,28 +822,29 @@ } else { annot_selec=annot[(annot$Chr==chr)&(annot$Stop>=debut_vue)&(annot$Start<=fin_vue),] - heights_ann=sizePlotAnnotation(annot=annot_selec,chr=chr,debut=debut_vue,fin=fin_vue,style=style,annotation_placed_by_strand=annotation_placed_by_strand)*50 + heights_ann=sizePlotAnnotation(annot=annot_selec,chr=chr,debut=debut_vue,fin=fin_vue,annotation_placed_by_strand=annotation_placed_by_strand,display_name=display_name,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes)*50 } ataxises=pretty((debut_vue:fin_vue)+decal,n=14) - if(log){ + if(log) { label_scal="log2 tag densities" - }else{ + } + else { label_scal="tag densities" } if(debut_vue==1&decal==0) { ataxises[1]=1 - }##Classic visualisation + }## Classic visualisation if(typeVisu=="classic") { - height_panels = c(40,rep(200,n_element_vue),heights_ann) - png(file,1200,sum(height_panels)) - prev=par(no.readonly = TRUE) + height_panels=c(40,rep(200,n_element_vue),heights_ann) + openGraphicalDevice(file,1200,sum(height_panels),fileType=fileType,resolutionDPI=resolutionDPI) + prev=par(no.readonly=TRUE) n_panels=length(height_panels) layout(matrix(1:n_panels,n_panels,1),heights=height_panels) par(mar=c(0, 5, 0, 4)+0.1) plotTitle(debut_vue=debut_vue,fin_vue=fin_vue,chr=chr) par(mar=c(2.5, 5, 2.5, 4)+0.1) for(element in 1:n_element_vue) { - i_data = which[element] + i_data=which[element] plotRNAseq(listForward[[i_data]],listReverse[[i_data]],debut_vue,fin_vue,chr,annot_selec,style,top=tops[min(element,length(tops))],bottom=bottoms[min(element,length(bottoms))],y=label_scal,titre=titres[min(i_data,length(titres))],name_flags=name_flags,repeated=repeated,decal=decal,ataxises=ataxises,classic_plus_color=classic_plus_color,classic_minus_color=classic_minus_color,stranded=stranded) if(!is.null(marks)) { if(is.null(tops)) { @@ -1007,27 +876,27 @@ } } } - } - par(mar=c(0,5,1,4)+0.1) - if(!is.null(annot_selec)) { - plot_annotation(annot_selec,chr,debut=debut_vue,fin=fin_vue,style=style,textSize=1.5,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand) - } + } + if(!is.null(annot_selec)) { + par(mar=c(0,5,1,4)+0.1) + plot_annotation(annot_selec,chr,debut=debut_vue,fin=fin_vue,style=style,textSize=1.5,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand,display_name=display_name,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) + } } - else {##Heatmap visualisation + else {## Heatmap visualisation if(typeVisu=="heatmap") { if(stranded) { - height_panels=c(40,50*n_element_vue+28,heights_ann,50*n_element_vue+10,100) + height_panels=c(40,heatmap_lane_height*n_element_vue+28,heights_ann,heatmap_lane_height*n_element_vue+10,100) } else { - height_panels=c(40,50*n_element_vue+28,heights_ann,100) + height_panels=c(40,heatmap_lane_height*n_element_vue+28,heights_ann,100) } - png(file,1200,sum(height_panels)) - prev=par(no.readonly = TRUE) + openGraphicalDevice(file,1200,sum(height_panels),fileType=fileType,resolutionDPI=resolutionDPI) + prev=par(no.readonly=TRUE) n_panels=length(height_panels) layout(matrix(1:n_panels,n_panels,1),heights=height_panels) par(mar=c(0, 8, 0, 2)+0.1) plotTitle(debut_vue=debut_vue,fin_vue=fin_vue,chr=chr) - limIntensity = c(0,max(forward_matrice,reverse_matrice,na.rm=TRUE)) + limIntensity=c(0,max(forward_matrice,reverse_matrice,na.rm=TRUE)) if(limIntensity[2]==0) { limIntensity[2]=0.01 } @@ -1043,8 +912,8 @@ tmp="Both strands" } myHeatMap(forward_matrice[(dim(forward_matrice)[1]):1,],debut_vue+decal,fin_vue+decal,ataxises,lim=limIntensity,heatmap_max_color=heatmap_max_color,heatmap_min_color=heatmap_min_color,heatmap_palette_method=heatmap_palette_method,textOnLeftSide=tmp) - axis(3,at=ataxises,labels=FALSE,cex.axis=1.4) - axis(3,at=ataxises,labels=ataxisesLabels,cex.axis=1.4,line=-0.4,lwd=0) + axis(3,at=ataxises,labels=FALSE,cex.axis=1.2) + axis(3,at=ataxises,labels=ataxisesLabels,cex.axis=1.2,line=-0.4,lwd=0) if(!is.null(marks)) { if(is.null(strandMarks)|!all_stranded) { segments(marks,-2,y1=dim(forward_matrice)[1]+2,col=2,lwd=2,xpd=TRUE) @@ -1065,7 +934,7 @@ } if(!is.null(annot_selec)) { par(mar=c(0,8,0,2)+0.1) - plot_annotation(annot_selec,chr,debut=debut_vue,fin=fin_vue,style=style,textSize=0.9,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand) + plot_annotation(annot_selec,chr,debut=debut_vue,fin=fin_vue,style=style,textSize=0.9,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand,display_name=display_name,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) } if(stranded) { par(mar=c(1, 8, 0, 2)+0.1) @@ -1080,7 +949,7 @@ } } } - axis(1,at=ataxises,labels=ataxisesLabels,cex.axis=1.4) + axis(1,at=ataxises,labels=ataxisesLabels,cex.axis=1.2) } palette=matrix(seq(limIntensity[1],limIntensity[2],length.out=2000),1,2000) rownames(palette)="0" @@ -1088,17 +957,16 @@ myHeatMap(palette,1,2000,ataxises=NA,heatmap_max_color=heatmap_max_color,heatmap_min_color=heatmap_min_color,heatmap_palette_method=heatmap_palette_method) labelAxisHeatmapLegend=pretty(c(limIntensity[1],limIntensity[2]),n=7) atAxisHeatmapLegend=1+((labelAxisHeatmapLegend-limIntensity[1])/(limIntensity[2]-limIntensity[1]))*1999 - axis(1,at=atAxisHeatmapLegend,labels=FALSE,cex.axis=1.4) - axis(1,at=atAxisHeatmapLegend,labels=labelAxisHeatmapLegend,cex.axis=1.4,line=-0.4,lwd=0) + axis(1,at=atAxisHeatmapLegend,labels=FALSE,cex.axis=1.2) + axis(1,at=atAxisHeatmapLegend,labels=labelAxisHeatmapLegend,cex.axis=1.2,line=-0.4,lwd=0) text(1000,2,label_scal,xpd=NA,font=2,cex=1.4) - - }##Lines visualisation - else if(typeVisu=="lines"){ - legendSize = (floor(n_element_vue/2)+n_element_vue%%2)*40 + }## Lines visualisation + else if(typeVisu=="lines") { + legendSize=(floor(n_element_vue/2)+n_element_vue%%2)*40 height_panels=c(40,legendSize,400,heights_ann) n_panels=length(height_panels) - png(file,1200,sum(height_panels)) - prev=par(no.readonly = TRUE) + openGraphicalDevice(file,1200,sum(height_panels),fileType=fileType,resolutionDPI=resolutionDPI) + prev=par(no.readonly=TRUE) par(mar=c(0, 5, 0,4)+0.1,cex=1.1) layout(matrix(c(1:n_panels),n_panels,4),heights=height_panels) par(mar=c(0, 5, 0,4)+0.1) @@ -1106,9 +974,9 @@ lines_legend(n_element_vue=n_element_vue,which,titres,lines_samples_colors=lines_samples_colors,lines_samples_type_line=lines_samples_type_line) par(mar=c(3, 5, 0,4)+0.1) plotlines(forward_matrice,reverse_matrice,which=which,debut_vue, fin_vue , chr, annot, style, tops, bottoms,marks,strandMarks,titres, repeated,name_flags,decal,ataxises=ataxises,n_element_vue=n_element_vue,y=label_scal,lines_samples_colors=lines_samples_colors,lines_samples_type_line=lines_samples_type_line,stranded=stranded) - par(mar=c(0,5,0,4)+0.1) if(!is.null(annot_selec)) { - plot_annotation(annot_selec,chr,debut=debut_vue,fin=fin_vue,style=style,textSize=1.5,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand) + par(mar=c(0,5,0,4)+0.1) + plot_annotation(annot_selec,chr,debut=debut_vue,fin=fin_vue,style=style,textSize=1.5,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand,display_name=display_name,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) } } @@ -1117,36 +985,36 @@ invisible(dev.off()) } -## -smooth = function(X,L=10) { +## +smooth=function(X,L=10) { x_smooth=filter(X,rep(1,L)/L) x_smooth[is.na(x_smooth)]=0 return(x_smooth) } -##Returns lines visualisation -plotlines = function(forward_matrice,reverse_matrice,which=1:length(forward), debut_vue = 1,fin_vue =length(forward), chr=NULL, annot=NULL, style=NULL, tops=NULL,bottoms=NULL,marks=NULL,strandMarks=NULL, titres="", repeated=FALSE,name_flags="",decal=0,ataxises=NULL,n_element_vue=length(which),y="",lines_samples_colors=c(1,3,4,2)[((0:length(forward))%%4)+1],lines_samples_type_line=((0:length(forward))%%4)+1,stranded=TRUE){ - limIntensity = c(-max(bottoms),max(tops)) -plot(c(debut_vue,fin_vue)+decal,limIntensity,col="white",ylab=y,main="",xaxs="i",xaxt="n",yaxt="n",cex.lab=1.2,xlab="",cex.lab=1.8) - lty=lines_samples_type_line - col=lines_samples_colors - ataxises_y= pretty(limIntensity,n=8) +## Returns lines visualisation +plotlines=function(forward_matrice,reverse_matrice,which=1:length(forward), debut_vue=1,fin_vue=length(forward), chr=NULL, annot=NULL, style=NULL, tops=NULL,bottoms=NULL,marks=NULL,strandMarks=NULL, titres="", repeated=FALSE,name_flags="",decal=0,ataxises=NULL,n_element_vue=length(which),y="",lines_samples_colors=c(1,3,4,2)[((0:length(forward))%%4)+1],lines_samples_type_line=((0:length(forward))%%4)+1,stranded=TRUE) { + limIntensity=c(-max(bottoms),max(tops)) + plot(c(debut_vue,fin_vue)+decal,limIntensity,col="white",ylab=y,main="",xaxs="i",xaxt="n",yaxt="n",cex.lab=1.2,xlab="",cex.lab=1.8) + lty=lines_samples_type_line + col=lines_samples_colors + ataxises_y=pretty(limIntensity,n=8) for(i in ataxises) abline(v=i,lty=2,col="#808080") for(i in ataxises_y) abline(h=i,lty=2,col="#808080") - for( i in 1:n_element_vue){ + for( i in 1:n_element_vue) { lo=forward_matrice[i,] - lines((debut_vue:fin_vue)+decal,lo,type="l",lty =lty[i],col=col[i],lwd=2,xaxt="n") + lines((debut_vue:fin_vue)+decal,lo,type="l",lty=lty[i],col=col[i],lwd=2,xaxt="n") if(stranded) { los=-reverse_matrice[i,] - lines((debut_vue:fin_vue)+decal,los,type="l",lty= lty[i],col=col[i],lwd=2,xaxt="n") + lines((debut_vue:fin_vue)+decal,los,type="l",lty=lty[i],col=col[i],lwd=2,xaxt="n") } } ataxisesLabels=as.character(ataxises) ataxisesLabels[((1:length(ataxises))%%2)==0]="" ataxisesLabels_y=as.character(abs(ataxises_y)) ataxisesLabels_y[((1:length(ataxises_y))%%2)==0]="" - axis(1,at=ataxises,labels=FALSE,cex.axis=2.6) - axis(1,at=ataxises,labels=ataxisesLabels,cex.axis=2.6,line=0.6,lwd=0) + axis(1,at=ataxises,labels=FALSE,cex.axis=2) + axis(1,at=ataxises,labels=ataxisesLabels,cex.axis=2,line=0.6,lwd=0) axis(2, at=ataxises_y,labels=FALSE,cex.axis=2) axis(2, at=ataxises_y,labels=ataxisesLabels_y,cex.axis=2,line=-0.4,lwd=0) if(stranded) { @@ -1188,11 +1056,11 @@ } } -##Returns lines legend -lines_legend=function(n_element_vue,which,titres,lines_samples_colors=c(1,3,4,2)[((0:n_element_vue)%%4)+1],lines_samples_type_line=((0:n_element_vue)%%4)+1){ +## Returns lines legend +lines_legend=function(n_element_vue,which,titres,lines_samples_colors=c(1,3,4,2)[((0:n_element_vue)%%4)+1],lines_samples_type_line=((0:n_element_vue)%%4)+1) { lty=lines_samples_type_line col=lines_samples_colors - n_y = floor(n_element_vue/2)+n_element_vue%%2 + n_y=floor(n_element_vue/2)+n_element_vue%%2 plot(c(0,4),c(0,-(n_y+1)),col="white", ylab="",xlab="",main="",fg="white",col.axis="white",yaxs="i") i_style=0 for(i in 1:n_y) { @@ -1209,43 +1077,62 @@ } } -##Returns the shape of plain arrow for the annotation -plain_arrow = function(left,right,y,thickness=1,pickSize=(right-left)*0.1,pickSide=c("right","left","both","none"),col="blue") { +## Returns the shape of plain arrow for the annotation +plain_arrow=function(left,right,y,thickness=1,pickSize=(right-left)*0.1,pickSide=c("right","left","both","none"),col="blue") { middle=(left+right)/2 if(pickSide[1]=="right") { - pick_point = max(right - pickSize,middle) + pick_point=max(right - pickSize,middle) polygon(c(left,pick_point,right,pick_point,left),c(y-thickness/2,y-thickness/2,y,y+thickness/2,y+thickness/2),col=col) } if(pickSide[1]=="left") { - pick_point = min(left + pickSize,middle) + pick_point=min(left + pickSize,middle) polygon(c(right,pick_point,left,pick_point,right),c(y-thickness/2,y-thickness/2,y,y+thickness/2,y+thickness/2),col=col) } if(pickSide[1]=="none") { polygon(c(right,left,left,right),c(y-thickness/2,y-thickness/2,y+thickness/2,y+thickness/2),col=col) } if(pickSide[1]=="both") { - pick_point_1 = min(left + pickSize,middle) - pick_point_2 = max(right - pickSize,middle) + pick_point_1=min(left + pickSize,middle) + pick_point_2=max(right - pickSize,middle) polygon(c(left,pick_point_1,pick_point_2,right,pick_point_2,pick_point_1),c(y,y-thickness/2,y-thickness/2,y,y+thickness/2,y+thickness/2),col=col) } } -##Returns the size of the panel of the annotation -sizePlotAnnotation=function(annot,chr,debut,fin,style=NULL,annotation_placed_by_strand=FALSE) { - left=c() - right=c() - annot_chr=annot[annot$Chr==chr,] - unique_ID=unique(annot_chr$ID) - for(j in 1:length(unique_ID)){ - left[j]=min(annot_chr$Start[annot_chr$ID==unique_ID[j]]) - right[j]=max(annot_chr$Stop[annot_chr$ID==unique_ID[j]]) - } - y_plot=parking(left,right) - return(max(y_plot)-min(y_plot)+1) +## Returns the size of the panel of the annotation +sizePlotAnnotation=function(annot,chr,debut,fin,annotation_placed_by_strand=FALSE,display_name=NULL,typeVisu="classic",initialize_label_sizes=NULL) { + left=c() + right=c() + labels=c() + annot_chr=annot[annot$Chr==chr,] + N=dim(annot_chr)[1] + all_names=annot_chr[,c(display_name,"ID")] + unique_ID=unique(annot_chr$ID) + for(j in 1:length(unique_ID)) { + left[j]=min(annot_chr$Start[annot_chr$ID==unique_ID[j]]) + right[j]=max(annot_chr$Stop[annot_chr$ID==unique_ID[j]]) + all_names=unlist(annot_chr[annot_chr$ID==unique_ID[j],c(display_name,"ID")]) + all_names=all_names[all_names!="."] + labels[j]=all_names[1] + } + if(annotation_placed_by_strand) { + y_plot=parking(left,right,debut,fin,annot_chr$Strand=="+",FALSE,labels=labels,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) + } + else { + y_plot=parking(left,right,debut,fin,biggestOnesInside=FALSE,labels=labels,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) + } + return(max(y_plot)-min(y_plot)+1) } -##Function to organise the annotation shapes to display -parking = function(left,right,plus=rep(TRUE,length(left)),biggestOnesInside=TRUE) { +## Function to organise the annotation shapes to display +parking=function(left,right,debut,fin,plus=rep(TRUE,length(left)),labels=c(),biggestOnesInside=TRUE,typeVisu="classic",initialize_label_sizes=NULL) { + if(length(labels)!=0) { + if(!is.null(initialize_label_sizes)) { + initialize_=initialize_label_sizes[[typeVisu]] + for(i in 1:length(left)) { + right[i]=max(right[i],left[i]+initialize_$size[initialize_$labels==labels[i]])+(fin-debut)/100 + } + } + } y=rep(0,length(left)) if(sum(plus)>0) { left_plus=left[plus] @@ -1302,30 +1189,33 @@ return(y) } -##Function to -plot_annotation = function(annot,chr,debut,fin,style=NULL,textSize=par("cex"),annotation_color_by_strand=FALSE,annotation_placed_by_strand=FALSE) { +## Function to +plot_annotation=function(annot,chr,debut,fin,style=NULL,textSize=par("cex"),annotation_color_by_strand=FALSE,annotation_placed_by_strand=FALSE,display_name=NULL,typeVisu="classic",initialize_label_sizes=NULL) { left=c() right=c() + labels=c() annot_chr=annot[annot$Chr==chr,] - N = dim(annot_chr)[1] - strand=c("-","+") + N=dim(annot_chr)[1] if(N>0) { + all_names=annot_chr[,c(display_name,"ID")] unique_ID=unique(annot_chr$ID) - par_prev=par(no.readonly=TRUE) - for(j in 1:length(unique_ID)){ + for(j in 1:length(unique_ID)) { left[j]=min(annot_chr$Start[annot_chr$ID==unique_ID[j]]) right[j]=max(annot_chr$Stop[annot_chr$ID==unique_ID[j]]) + all_names=unlist(annot_chr[annot_chr$ID==unique_ID[j],c(display_name,"ID")]) + all_names=all_names[all_names!="."] + labels[j]=all_names[1] } if(annotation_placed_by_strand) { - y_plot=parking(left,right,annot_chr$Strand=="+",FALSE) + y_plot=parking(left,right,debut,fin,annot_chr$Strand=="+",FALSE,labels=labels,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) } else { - y_plot=parking(left,right,biggestOnesInside=FALSE) + y_plot=parking(left,right,debut,fin,biggestOnesInside=FALSE,labels=labels,typeVisu=typeVisu,initialize_label_sizes=initialize_label_sizes) } plot(c(debut,fin),c(min(y_plot)-0.5,max(y_plot)+0.5),col="white",ylab="",xlab="",fg="white",col.axis="white",xaxs="i",yaxs="i") - for(j in 1:length(unique_ID)){ + for(j in 1:length(unique_ID)) { annot_ID=annot_chr[annot_chr$ID==unique_ID[j],] - x_text<-Inf + x_text=Inf for(i_annot_ID in 1:dim(annot_ID)[1]) { if(annot_ID$Strand[i_annot_ID]=="-") { orientation="left" @@ -1333,30 +1223,30 @@ else { orientation="right" } - iDraw = FALSE + iDraw=FALSE if(annot_ID$Strand[i_annot_ID]==".") { tmp="+" } else { tmp=annot_ID$Strand[i_annot_ID] } - style_demande = style[style$Type==annot_ID$Type[i_annot_ID]&style$Strand==tmp,] - x_text<-min(x_text,annot_ID$Start[i_annot_ID]) + style_demande=style[style$Type==annot_ID$Type[i_annot_ID]&style$Strand==tmp,] + x_text=min(x_text,annot_ID$Start[i_annot_ID]) if(style_demande$shape=="box") { plain_arrow(annot_ID$Start[i_annot_ID],annot_ID$Stop[i_annot_ID],y_plot[j],thickness=0.5, pickSide=orientation,col=style_demande$col,pickSize=(fin-debut)*0.02) iDraw=TRUE } - if(style_demande$shape =="line") { + if(style_demande$shape=="line") { segments(annot_ID$Start[i_annot_ID],y_plot[j],annot_ID$Stop[i_annot_ID],y_plot[j],col=style_demande$col) iDraw=TRUE } - if(style_demande$shape == "rectangle") { + if(style_demande$shape=="rectangle") { plain_arrow(annot_ID$Start[i_annot_ID],annot_ID$Stop[i_annot_ID],y_plot[j],thickness=0.5, pickSide="none",col=style_demande$col) iDraw=TRUE } - if(style_demande$shape == "arrow") { - arrowHeads = pretty(debut:fin,n=50) - x<-c(annot_ID$Start[i_annot_ID],arrowHeads[arrowHeads>annot_ID$Start[i_annot_ID]&arrowHeads<annot_ID$Stop[i_annot_ID]],annot_ID$Stop[i_annot_ID]) + if(style_demande$shape=="arrow") { + arrowHeads=pretty(debut:fin,n=50) + x=c(annot_ID$Start[i_annot_ID],arrowHeads[arrowHeads>annot_ID$Start[i_annot_ID]&arrowHeads<annot_ID$Stop[i_annot_ID]],annot_ID$Stop[i_annot_ID]) if(annot_ID$Strand[i_annot_ID]=="-") { arrows(x[2:length(x)],y_plot[j],x[1:length(x)-1],col=style_demande$col,length=0.08) } @@ -1365,11 +1255,11 @@ } iDraw=TRUE } - if(iDraw == FALSE) { + if(iDraw==FALSE) { segments(annot_ID$Start[i_annot_ID],y_plot[j],annot_ID$Stop[i_annot_ID],y_plot[j],col="black") } } - text(max(x_text,debut),y_plot[j]+0.4,adj=0,labels=unique_ID[j],cex=textSize) + text(max(x_text,debut),y_plot[j]+0.4,adj=0,labels=labels[j],cex=textSize) } if(annotation_placed_by_strand) { abline(h=0.125,lty=2,col="black") @@ -1377,16 +1267,16 @@ } } -html2rgb = function(codeHTML) { +html2rgb=function(codeHTML) { chiffres=c(0:9,"A","B","C","D","E","F") codeHTMLsplit=unlist(strsplit(codeHTML,split="")) - red = (((which(chiffres==codeHTMLsplit[2])-1)*16)+(which(chiffres==codeHTMLsplit[3])-1))/255 - green = (((which(chiffres==codeHTMLsplit[4])-1)*16)+(which(chiffres==codeHTMLsplit[5])-1))/255 - blue = (((which(chiffres==codeHTMLsplit[6])-1)*16)+(which(chiffres==codeHTMLsplit[7])-1))/255 + red=(((which(chiffres==codeHTMLsplit[2])-1)*16)+(which(chiffres==codeHTMLsplit[3])-1))/255 + green=(((which(chiffres==codeHTMLsplit[4])-1)*16)+(which(chiffres==codeHTMLsplit[5])-1))/255 + blue=(((which(chiffres==codeHTMLsplit[6])-1)*16)+(which(chiffres==codeHTMLsplit[7])-1))/255 return(c(red,green,blue)) } -rgb2hsv = function(vectRGB) { +rgb2hsv=function(vectRGB) { Cmax=max(vectRGB) Cmin=min(vectRGB) delta=Cmax-Cmin @@ -1410,24 +1300,23 @@ } ### ========================================================================= -### Ving's Main +### Ving's Main version beta 1.1 ### ------------------------------------------------------------------------- ### { -if(version$major != "3" & version$minor != "0.2") { +if(version$major !="3" & version$minor !="0.2") { write("Ving has been developped on R 3.0.2, therefore it might misbehave here.",stderr()) } -tmp = unlist(strsplit(commandArgs()[4],split="="))[2] -path_split = unlist(strsplit(tmp,split="/")) -path = paste(path_split[1:(length(path_split)-1)],collapse="/") -arg<-commandArgs(TRUE) +arg=commandArgs(TRUE) if(length(arg)==0) { - write("Ving for visualisation of RNA seq data: + write("Ving for visualisation of RNA seq data: Usage: - ./visualiseur.R [options] <input> [<input2> <input3> ...] - options: + ./ving.R [options] <input> [<input2> <input3> ...] + Options: -o/--output <string> [default:./ouput.png] + -F/--fileType <integer> [default: same as -o] (png,jpeg,bmp,tiff,pdf) + -R/--resolution <integer> [default: 72 ] -v/--typeVisu <string> [default: classic ] (classic,lines,heatmap) -t/--description-data <string> [default: <filename>] -n/--normalization-coefficient <string> [default: none ] @@ -1453,8 +1342,9 @@ --annotation-placed-by-strand <logical> [default: FALSE ] -L/--smoothLength <integer> [default: NA ] ",stdout()) - q("no") -}else { + q("no") +} +else { tmp=suppressPackageStartupMessages(require("Rsamtools")) if(!tmp) { stop("Package Rsamtools required !!") @@ -1463,51 +1353,51 @@ if(!tmp) { stop("Package GenomicRanges required !!") } - optArgs=getopt( - rbind( + optArgs=getopt(rbind( + c('output','o', 1, 'character',"output.png"), + c('fileType','F',1,'character',NA), + c('resolution','R',1,'numeric',72), + c('typeVisu', 'v', 1, 'character', "classic"), + c('description-data','t',1,'character',NA), + c('chromosome-name', 'c', 1, 'character', NA), + c('start', 'S', 1, 'numeric',1), + c('end', 'E', 1, 'numeric',NA), + c('annotation','a',1,'character',NA), + c('typeTranscript','r',1,'character',NA), + c('annotation-colors','C',1,'character',NA), + c('annotation-shapes','s','1','character',NA), + c('normalization-coefficient','n','1','character',NA), + c('classic-plus-color',1,1,'character',"navyblue"), + c('classic-minus-color',2,1,'character',"deeppink3"), + c('heatmap-max-color',3,1,'character',"#000055"), + c('heatmap-min-color',4,1,'character',"#FFFFAA"), + c('heatmap-palette-method',7,1,'character',"hsv"), + c('lines-samples-colors',5,1,'character',NA), + c('lines-samples-type-line',6,1,'character',NA), + c('scale-log', 'l',0,'logical',FALSE), + c('inverseStrand','i',0,'logical', FALSE), + c('unstranded','u',0,'logical', FALSE), + c('symetric-scale','y',0,'logical', FALSE), + c('annotation-color-by-strand',8,0,'logical',FALSE), + c('annotation-placed-by-strand',9,0,'logical',FALSE), + c('smoothLength','L',1,'numeric',NA) + )) +} - c('output','o', 1, 'character',"output.png"), - c('typeVisu', 'v', 1, 'character', "classic"), - c('description-data','t',1,'character',NA), - c('chromosome-name', 'c', 1, 'character', NA), - c('start', 'S', 1, 'numeric',1), - c('end', 'E', 1, 'numeric',NA), - c('annotation','a',1,'character',NA), - c('typeTranscript','r',1,'character',NA), - c('annotation-colors','C',1,'character',NA), - c('annotation-shapes','s','1','character',NA), - c('normalization-coefficient','n','1','character',NA), - c('classic-plus-color',1,1,'character',"navyblue"), - c('classic-minus-color',2,1,'character',"deeppink3"), - c('heatmap-max-color',3,1,'character',"#000055"), - c('heatmap-min-color',4,1,'character',"#FFFFAA"), - c('heatmap-palette-method',7,1,'character',"hsv"), - c('lines-samples-colors',5,1,'character',NA), - c('lines-samples-type-line',6,1,'character',NA), - c('scale-log', 'l',0,'logical',FALSE), - c('inverseStrand','i',0,'logical', FALSE), - c('unstranded','u',0,'logical', FALSE), - c('symetric-scale','y',0,'logical', FALSE), - c('annotation-color-by-strand',8,0,'logical',FALSE), - c('annotation-placed-by-strand',9,0,'logical',FALSE), - c('smoothLength','L',1,'numeric',NA) - ) - ) -} ################### ## ARGUMENTS ################################################################################# files=optArgs$ARGUMENT -##Case file doesn't exist - for( i in 1:length(files)) { - if(!file.exists(files[i])) { - stop(paste(files[i],"do not exist!","\n")) - } +## Case file doesn't exist +for( i in 1:length(files)) { + if(!file.exists(files[i])) { + stop(paste(files[i],"do not exist!","\n")) } +} imagefile=optArgs$output typeVisu=optArgs$typeVisu description_data=optArgs$`description-data` -chrName = optArgs$`chromosome-name`[1] +chrName=optArgs$`chromosome-name`[1] start=optArgs$start[1] end=optArgs$end[1] annotation=optArgs$annotation @@ -1525,269 +1415,274 @@ log=optArgs$`scale-log` inverseStrand=optArgs$inverseStrand unstranded=optArgs$unstranded -symetric= optArgs$`symetric-scale` +symetric=optArgs$`symetric-scale` annotation_color_by_strand=optArgs$`annotation-color-by-strand` annotation_placed_by_strand=optArgs$`annotation-placed-by-strand` smoothLength=optArgs$`smoothLength` +resolution=optArgs$`resolution` +fileType=optArgs$`fileType` + ################### ## MAIN ################################################################################### - - genome_info=scanBamHeader(files[1])[[1]]$targets - noms_chromosomes = names(genome_info) - longueur_chromosomes = as.integer(genome_info) - nombre_chromosomes = length(noms_chromosomes) +genome_info=scanBamHeader(files[1])[[1]]$targets +noms_chromosomes=names(genome_info) +longueur_chromosomes=as.integer(genome_info) +nombre_chromosomes=length(noms_chromosomes) -##Case no chromosome specified - if(sum(is.na(chrName))) { - chrName = noms_chromosomes[1] - write(paste("No chromosome specified, processing chromosome :",chrName,"\n",sep=""),stderr()) - } - +## Case no chromosome specified +if(sum(is.na(chrName))) { + chrName=noms_chromosomes[1] + write(paste("No chromosome specified, processing chromosome :",chrName,"\n",sep=""),stderr()) +} + +## Case false chromosome name +if(!(chrName %in% noms_chromosomes)) { + stop(paste("\"",chrName,"\" is not a proper chromosome name")) +} -##Case false chromosome name - if(!(chrName %in% noms_chromosomes)) { - stop(paste("\"",chrName,"\" is not a proper chromosome name")) - } - - if(is.na(end)) { - end = longueur_chromosomes[chrName==noms_chromosomes] - } - - if(start > end) { - stop("The start is bigger than the end!") - } +if(is.na(end)) { + end=longueur_chromosomes[chrName==noms_chromosomes] +} + +if(start > end) { + stop("The start is bigger than the end!") +} -##Case asked coordinates outside the chromosome - if(start<0|end>longueur_chromosomes[chrName==noms_chromosomes]) { - stop("You are outside the chromosome") - } - - if(sum(is.na(weight))>0) { - normalized_data=NULL - isnormalized=FALSE - } - else { - isnormalized=TRUE - normalized_data=unlist(strsplit(weight,split=",")) - if(length(files)!=length(normalized_data)) { - stop("Different number of files and weights ") - } - else { - normalized_data=as.numeric(normalized_data) - } - } +## Case asked coordinates outside the chromosome +if(start<0|end>longueur_chromosomes[chrName==noms_chromosomes]) { + stop("You are outside the chromosome") +} - if(inverseStrand) { - libraryType="inverse" +if(sum(is.na(weight))>0) { + normalized_data=NULL + isnormalized=FALSE +} +else { + isnormalized=TRUE + normalized_data=unlist(strsplit(weight,split=",")) + if(length(files)!=length(normalized_data)) { + stop("Different number of files and weights ") } else { - libraryType="standard" - } -##Read the bam file and extract the infos - doit=function(i,libraryType) { - - try(readBam_(files[i], libraryType=libraryType, chrName_=chrName, from_=start, to_=end,normalized_=normalized_data[i])) - } - data=lapply(1:length(files),doit,libraryType=libraryType) - ctrl=unlist(lapply(data,class))=="try-error" - - if(sum(ctrl)>0) { - for(i in which(ctrl)) { - write(paste("Problem with file :",files[i],"\n",sep=""),stderr()) - } - stop("At least a file has problem") + normalized_data=as.numeric(normalized_data) } +} -##Read the GFF file and extract the infos - if(sum(is.na(annotation))==0) { - gff=try(readGff(annotation[1],from=start,to=end,chr=chrName),TRUE) - ctrl=class(gff)=="try-error" - if(sum(ctrl)>0) { - stop(paste("Problem with Gff file :",annotation,"\n")) - } - if(length(annotation)>1) { - for(i in 2:length(annotation)) { - gff1=try(readGff(annotation[i],from=start,to=end,chr=chrName),TRUE) - ctrl=class(gff1)=="try-error" - if(sum(ctrl)>0) { - stop(paste("Problem with Gff file :",gff1,"\n")) - } +if(inverseStrand) { + libraryType="inverse" +} +else { + libraryType="standard" +} +## Read the bam file and extract the infos +doit=function(i,libraryType) { + try(readBam_(files[i], libraryType=libraryType, chrName_=chrName, from_=start, to_=end,normalized_=normalized_data[i])) +} +data=lapply(1:length(files),doit,libraryType=libraryType) +ctrl=unlist(lapply(data,class))=="try-error" + +if(sum(ctrl)>0) { + for(i in which(ctrl)) { + write(paste("Problem with file :",files[i],"\n",sep=""),stderr()) + } + stop("At least a file has problem") +} + +## Read the GFF file and extract the infos +if(sum(is.na(annotation))==0) { + gff=try(readGff(annotation[1],from=start,to=end,chr=chrName),TRUE) + ctrl=class(gff)=="try-error" + if(sum(ctrl)>0) { + stop(paste("Problem with Gff file :",annotation,"\n")) + } + if(length(annotation)>1) { + for(i in 2:length(annotation)) { + gff1=try(readGff(annotation[i],from=start,to=end,chr=chrName),TRUE) + ctrl=class(gff1)=="try-error" + if(sum(ctrl)>0) { + stop(paste("Problem with Gff file :",gff1,"\n")) + } + if(sum(is.na(gff1))==0) { gff=rbind(gff,gff1) } } } - else { - gff=NA - } - - if(sum(is.na(description_data))>0) { - description_data = files - } +} +else { + gff=NA +} + +if(sum(is.na(description_data))>0) { + description_data=files +} - ##Case of different number of files and description - if(length(description_data)!=length(files)) { - stop("Different number of files and description") - } - -## pooling bam files (if necessary) - description_data_unique=unique(description_data) - data_pooled=list() - for(i_descri in description_data_unique) { - i_data_voulu=which(description_data==i_descri) - data_pooled_=data[[i_data_voulu[1]]] - if(length(i_data_voulu)>1) { - for(i_i_data_voulu in 2:length(i_data_voulu)) { - data_pooled_=addBam(data_pooled_,data[[i_data_voulu[i_i_data_voulu]]]) - } - } - data_pooled[[i_descri]]=data_pooled_ - } +## Case of different number of files and description +if(length(description_data)!=length(files)) { + stop("Different number of files and description") +} - if(sum(is.na(typeTranscript)>0)) { - if(sum(is.na(annotation))==0) { - typeTranscritSplit=unique(gff$Type) - }else { - typeTranscritSplit=NA - } - }else { - typeTranscritSplit=unlist(strsplit(typeTranscript,split=",")) - } - - if((sum(is.na(gff))>0)|(sum(is.na(typeTranscritSplit))>0)) { - annot=NULL - }else { - annot = gff[gff$Type %in% typeTranscritSplit,] - } - -##check the colors - - if(sum(is.na(colors)>0)) { - nTypeTranscrit = length(typeTranscritSplit) - if(annotation_color_by_strand) { - colorsSplit=c(classic_plus_color,classic_minus_color) - } - else { - colorsSplit=rainbow(nTypeTranscrit+1)[1:nTypeTranscrit] +## Pooling bam files (if necessary) +description_data_unique=unique(description_data) +data_pooled=list() +for(i_descri in description_data_unique) { + i_data_voulu=which(description_data==i_descri) + data_pooled_=data[[i_data_voulu[1]]] + if(length(i_data_voulu)>1) { + for(i_i_data_voulu in 2:length(i_data_voulu)) { + data_pooled_=addBam(data_pooled_,data[[i_data_voulu[i_i_data_voulu]]]) } } + data_pooled[[i_descri]]=data_pooled_ +} + +if(sum(is.na(typeTranscript)>0)) { + if(sum(is.na(annotation))==0) { + typeTranscritSplit=unique(gff$Type) + } else { - colorsSplit=unlist(strsplit(colors,split=",")) + typeTranscritSplit=NA } - for(i in 1:length(colorsSplit)) { - tmp=unlist(strsplit(colorsSplit[i],split="")) - if(length(tmp)==6|length(tmp)==8) { - if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { - colorsSplit[i] = paste("#",colorsSplit[i],sep="") - } - } +} +else { + typeTranscritSplit=unlist(strsplit(typeTranscript,split=",")) +} + +if((sum(is.na(gff))>0)|(sum(is.na(typeTranscritSplit))>0)) { + annot=NULL +} +else { + annot=gff[gff$Type %in% typeTranscritSplit,] +} + +## Check the colors +if(sum(is.na(colors)>0)) { + nTypeTranscrit=length(typeTranscritSplit) + if(annotation_color_by_strand) { + colorsSplit=c(classic_plus_color,classic_minus_color) } - - tmp=unlist(strsplit(classic_plus_color,split="")) + else { + colorsSplit=rainbow(nTypeTranscrit+1)[1:nTypeTranscrit] + } +} +else { + colorsSplit=unlist(strsplit(colors,split=",")) +} +for(i in 1:length(colorsSplit)) { + tmp=unlist(strsplit(colorsSplit[i],split="")) if(length(tmp)==6|length(tmp)==8) { if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { - classic_plus_color = paste("#",classic_plus_color,sep="") + colorsSplit[i]=paste("#",colorsSplit[i],sep="") } } - tmp=unlist(strsplit(classic_minus_color,split="")) - if(length(tmp)==6|length(tmp)==8) { - if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { - classic_minus_color = paste("#",classic_minus_color,sep="") - } +} + +tmp=unlist(strsplit(classic_plus_color,split="")) +if(length(tmp)==6|length(tmp)==8) { + if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { + classic_plus_color=paste("#",classic_plus_color,sep="") + } +} +tmp=unlist(strsplit(classic_minus_color,split="")) +if(length(tmp)==6|length(tmp)==8) { + if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { + classic_minus_color=paste("#",classic_minus_color,sep="") + } +} +tmp=unlist(strsplit(heatmap_max_color,split="")) +if(length(tmp)==6|length(tmp)==8) { + if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { + heatmap_max_color=paste("#",heatmap_max_color,sep="") + } +} +tmp=unlist(strsplit(heatmap_min_color,split="")) +if(length(tmp)==6|length(tmp)==8) { + if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { + heatmap_min_color=paste("#",heatmap_min_color,sep="") } - tmp=unlist(strsplit(heatmap_max_color,split="")) - if(length(tmp)==6|length(tmp)==8) { - if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { - heatmap_max_color = paste("#",heatmap_max_color,sep="") - } - } - tmp=unlist(strsplit(heatmap_min_color,split="")) - if(length(tmp)==6|length(tmp)==8) { - if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { - heatmap_min_color = paste("#",heatmap_min_color,sep="") +} +if(sum(is.na(lines_samples_colors))>0) { + lines_samples_colors_split=c(1,3,4,2)[((0:(length(files)-1))%%4)+1] +} +else { + lines_samples_colors_split=unlist(strsplit(lines_samples_colors,split=",")) + for(i in 1:length(lines_samples_colors_split)) { + tmp=unlist(strsplit(lines_samples_colors_split[i],split="")) + if(length(tmp)==6|length(tmp)==8) { + if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { + lines_samples_colors_split[i]=paste("#",lines_samples_colors_split[i],sep="") + } + } + } +} +colorToCheck=c(colorsSplit,classic_plus_color,classic_minus_color,heatmap_max_color,heatmap_min_color,lines_samples_colors_split) +ctrl=sapply(colorToCheck,is.acceptable.color) +if(sum(!ctrl)>0) { + for(i in which(!ctrl)) { + write(paste("\"",colorToCheck[i],"\" is not a proper color name.\n",sep=""),stderr()) + } + stop("At least one color has a problem") +} +if(annotation_color_by_strand) { + if(length(colorsSplit)>2) { + stop("You have to specify two and only two colors!") + } +} +else { + if(length(typeTranscritSplit)!=length(colorsSplit)) { + stop("Please specify the same number of transcript types and colors") + } +} +## Check the line types +if(sum(is.na(lines_samples_type_line))>0) { + lines_samples_type_line_split=((0:(length(files)-1))%/%4)+1 +} +else { + lines_samples_type_line_split=unlist(strsplit(lines_samples_type_line,split=",")) +} +if(typeVisu=="lines") { + ctrl=sapply(lines_samples_type_line_split,function(x) { + tmp=suppressWarnings(as.numeric(x)) + if(!is.na(tmp)) { + return((tmp==floor(tmp))&tmp>=1&tmp<=5) } - } - if(sum(is.na(lines_samples_colors))>0) { - lines_samples_colors_split=c(1,3,4,2)[((0:(length(files)-1))%%4)+1] - } - else{ - lines_samples_colors_split=unlist(strsplit(lines_samples_colors,split=",")) - for(i in 1:length(lines_samples_colors_split)) { - tmp=unlist(strsplit(lines_samples_colors_split[i],split="")) - if(length(tmp)==6|length(tmp)==8) { - if(sum(tmp %in% c(0:9,"A","B","C","D","E","F"))==length(tmp)) { - lines_samples_colors_split[i] = paste("#",lines_samples_colors_split[i],sep="") - } - } + else { + return(FALSE) } - } - colorToCheck=c(colorsSplit,classic_plus_color,classic_minus_color,heatmap_max_color,heatmap_min_color,lines_samples_colors_split) - ctrl=sapply(colorToCheck,is.acceptable.color) + }) if(sum(!ctrl)>0) { for(i in which(!ctrl)) { - write(paste("\"",colorToCheck[i],"\" is not a proper color name.\n",sep=""),stderr()) - } - stop("At least one color has problem") - } - if(annotation_color_by_strand){ - if(length(colorsSplit)>2) { - stop("You have to specify two and only two colors!") + write(paste("\"",lines_samples_type_line_split[i],"\" is not a proper line style.\n",sep=""),stderr()) } - }else { - if(length(typeTranscritSplit)!=length(colorsSplit)) { - stop("Please specify the same number of transcript types and colors") - } - } -##check the line types - if(sum(is.na(lines_samples_type_line))>0) { - lines_samples_type_line_split=((0:(length(files)-1))%/%4)+1 - } - else { - lines_samples_type_line_split=unlist(strsplit(lines_samples_type_line,split=",")) + stop("At least one line style has problem") } - if(typeVisu=="lines") { - ctrl=sapply(lines_samples_type_line_split,function(x) { - tmp=suppressWarnings(as.numeric(x)) - if(!is.na(tmp)) { - return((tmp==floor(tmp))&tmp>=1&tmp<=5) - } - else { - return(FALSE) - } - } - ) - if(sum(!ctrl)>0) { - for(i in which(!ctrl)) { - write(paste("\"",lines_samples_type_line_split[i],"\" is not a proper line style.\n",sep=""),stderr()) - } - stop("At least one line style has problem") - } - lines_samples_type_line_split=as.integer(lines_samples_type_line_split) - } -##check the shapes + lines_samples_type_line_split=as.integer(lines_samples_type_line_split) +} +## Check the shapes type_shape=rep(1,length(typeTranscritSplit)) if(sum(is.na(shape_data)>0)) { + for( i in 1:length(typeTranscritSplit)) { + type_shape[i]="box" + } +} +else { + shape=unlist(strsplit(shape_data,split=",")) + shape=as.array(shape) + if(length(typeTranscritSplit)!=length(shape)) { + stop("Please specify the same number of transcript types and shapes") + } + else { for( i in 1:length(typeTranscritSplit)) { - type_shape[i]="box" + type_shape[i]=shape[[i]] } -}else{ - shape=unlist(strsplit(shape_data,split=",")) - shape=as.array(shape) - if(length(typeTranscritSplit)!=length(shape)) { - stop("Please specify the same number of transcript types and shapes") - }else { - for( i in 1:length(typeTranscritSplit)){ - type_shape[i]= shape[[i]] - } } } - -##Style for the annotation +## Style for the annotation label=rep(1,length(typeTranscritSplit)) -style=data.frame(Type=c(typeTranscritSplit,typeTranscritSplit),Strand=c(rep("+",length(typeTranscritSplit)),rep("-",length(typeTranscritSplit))),col=NA,shape=NA,label,stringsAsFactors = FALSE) +style=data.frame(Type=c(typeTranscritSplit,typeTranscritSplit),Strand=c(rep("+",length(typeTranscritSplit)),rep("-",length(typeTranscritSplit))),col=NA,shape=NA,label,stringsAsFactors=FALSE) for(i in 1:length(typeTranscritSplit)) { style$shape[style$Type==typeTranscritSplit[i]]=type_shape[i] } @@ -1801,27 +1696,27 @@ } } -##Main for visualisation +## Main for visualisation databychr=extractSignal(data_pooled,chrName,from=start,to=end,normalized_=isnormalized) { reverse=list() forward=list() if(log) { - for(i in 1:length(databychr$F)){ - forward_ = numeric() - tmp=log2(1+databychr$F[[i]]) - forward_[1:length(tmp)]=tmp - forward[[i]]=forward_ - reverse_ = numeric() - tmp=log2(1+databychr$R[[i]]) - reverse_[1:length(tmp)]=tmp - reverse[[i]]=reverse_ - } + for(i in 1:length(databychr$F)) { + forward_=numeric() + tmp=log2(1+databychr$F[[i]]) + forward_[1:length(tmp)]=tmp + forward[[i]]=forward_ + reverse_=numeric() + tmp=log2(1+databychr$R[[i]]) + reverse_[1:length(tmp)]=tmp + reverse[[i]]=reverse_ + } } else { - forward=databychr$F - reverse=databychr$R + forward=databychr$F + reverse=databychr$R } } @@ -1832,25 +1727,40 @@ smoothLength=smoothLength[1] } if(unstranded) { - for(i in 1:length(databychr$F)){ - lo=smooth(forward[[i]]+reverse[[i]],L=smoothLength) + for(i in 1:length(databychr$F)) { + if(smoothLength>0) { + lo=smooth(forward[[i]]+reverse[[i]],L=smoothLength) + } + else { + lo=forward[[i]]+reverse[[i]] + } forward[[i]]=lo los=rep(0,length(lo)) reverse[[i]]=los } } else { - for(i in 1:length(databychr$F)){ - lo=smooth(forward[[i]],L=smoothLength) + for(i in 1:length(databychr$F)) { + if(smoothLength>0) { + lo=smooth(forward[[i]],L=smoothLength) + } + else { + lo=forward[[i]] + } forward[[i]]=lo - los=smooth(reverse[[i]],L=smoothLength) + if(smoothLength>0) { + los=smooth(reverse[[i]],L=smoothLength) + } + else { + los=reverse[[i]] + } reverse[[i]]=los } } -group_maximum = rep(1,length(databychr$F)) -max_forward = numeric(length(databychr$F)) -max_reverse = numeric(length(databychr$F)) +group_maximum=rep(1,length(databychr$F)) +max_forward=numeric(length(databychr$F)) +max_reverse=numeric(length(databychr$F)) for(i_data in 1:length(databychr$F)) { max_forward[i_data]=max(forward[[i_data]],na.rm=TRUE) max_reverse[i_data]=max(reverse[[i_data]],na.rm=TRUE) @@ -1860,13 +1770,23 @@ max_reverse[group_maximum==i_max]=max(max_reverse[group_maximum==i_max],na.rm=TRUE) } -if(symetric){ +if(symetric) { for(i_data in 1:length(databychr$F)) { max_forward[i_data]=max(max_forward[i_data],max_reverse[i_data],na.rm=TRUE) } max_reverse=max_forward } +if(is.na(fileType)) { + imageFileSplit=unlist(strsplit(imagefile,split=".",fixed=TRUE)) + if(length(imageFileSplit)>=2) { + fileType=imageFileSplit[length(imageFileSplit)] + } + else { + fileType="png" + } +} + plotVisu(imagefile,typeVisu=typeVisu,listForward=forward,listReverse=reverse, debut_vue=start,fin_vue=end,chr=chrName,annot=annot,repeated=TRUE, titres=description_data_unique,name_flags="",style=style,log=log,stranded=!unstranded, @@ -1874,6 +1794,7 @@ classic_plus_color=classic_plus_color,classic_minus_color=classic_minus_color, heatmap_max_color=heatmap_max_color,heatmap_min_color=heatmap_min_color,heatmap_palette_method=heatmap_palette_method, lines_samples_colors=lines_samples_colors_split,lines_samples_type_line=lines_samples_type_line_split, -smoothLength=1,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand) +smoothLength=1,annotation_color_by_strand=annotation_color_by_strand,annotation_placed_by_strand=annotation_placed_by_strand, +fileType=fileType,resolutionDPI=resolution) }
--- a/ving_wrapper.xml Tue Jul 29 09:47:47 2014 -0400 +++ b/ving_wrapper.xml Tue Jul 28 05:44:48 2015 -0400 @@ -1,6 +1,7 @@ -<tool id="ving" name="Ving" version="1.1.0"> +<tool id="ving" name="Ving" version="1.1.1"> <requirements> <requirement type='binary' version="3.0.2">R</requirement> + <requirement type='binary' >Samtools</requirement> <requirement type="package" version="2.14">Bioconductor</requirement> <requirement type="package" version="1.15.41">GenomicRanges</requirement> <requirement type="package" version="1.14.3">Rsamtools</requirement> @@ -8,14 +9,33 @@ <description>Visualization of NGS data</description> <parallelism method="basic"></parallelism> <command interpreter="Rscript"> +#silent sys.stderr.write("!!!! Cheetah Template Variables !!!!\n") +#silent sys.stderr.write(" searchList = '%s'\n" % (str($searchList)) ) +#silent sys.stderr.write("!!!! end-of-list !!!!\n") ./ving.R - #for $i in $series - #set $index = os.popen("samtools index " + str($i.bamfile) + " " + str($i.bamfile) + ".bai") - ${i.bamfile} --description-data=${i.description} - #end for - --output=$output - #if $normalizationCoefficient - --normalization-coefficient=$normalizationCoefficient + #set $norm='' + #set $coef=[] + #if $norm_coeff.condition: + #for $i, $input in enumerate ( $norm_coeff.series ): + #set $index = os.popen("samtools index " + str($input.bamfile) + " " + str($input.bamfile) + ".bai") + ${input.bamfile} + #if str($input.description) != '': + --description-data=${input.description} + #end if + #silent $coef.append( str($input.normalizationCoefficient)) + #end for + #set $norm=','.join($coef) + + --normalization-coefficient=$norm + #else: + #for $i, $input in enumerate ( $norm_coeff.series ): + #set $index = os.popen("samtools index " + str($input.bamfile) + " " + str($input.bamfile) + ".bai") + ${input.bamfile} + #if str($input.description) != '': + --description-data=${input.description} + #end if + #end for + #end if #if str($strand) == 'yes': --inverseStrand @@ -53,21 +73,75 @@ #if $smoothLength --smoothLength=$smoothLength #end if - + --fileType=$filetype + --resolution=$resolution + #if str($filetype) == 'png' : + --output=$output_png + #elif str($filetype) == 'bmp' : + --output=$output_bmp + #elif str($filetype) == 'jpeg' : + --output=$output_jpg + #elif str($filetype) == 'tiff' : + --output=$output_tiff + #elif str($filetype) == 'pdf' : + --output=$output_pdf + #end if + </command> <inputs> - <repeat name="series" title="Bam file"> - <param name="bamfile" format="bam" type="data" label="Bam file"/> - <param name="description" format="txt" type="text" label="Name for your data" help="Describes each data with a name."/> - </repeat> - <param name="strand" type="select" label="Inversed strand" help="Use this if the library type is fr-first-strand. All your bam files will treated the same way."> + <conditional name="norm_coeff"> + <param name="condition" type="boolean" checked="false" truevalue="yes" falsevalue="NULL" label="Normalization coefficient" help="Coverage will be multiplied by coefficient. If not provided, no normalization will occur (default no)."/> + <when value="NULL"> + <repeat name="series" title="Bam file" min="1"> + <param name="bamfile" format="bam" type="data" label="Bam file"/> + <param name="description" format="txt" type="text" label="Sample label" help="Assigns label or name to each sample."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + </repeat> + </when> + <when value="yes"> + <repeat name="series" title="Bam file" min="1"> + <param name="bamfile" format="bam" type="data" label="Bam file"/> + <param name="description" format="txt" type="text" label="Sample label" help="Assigns label or name to each sample."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + <param name="normalizationCoefficient" format="txt" type="text" value="1.0" label="Normalization coefficient"/> + </repeat> + </when> + </conditional> + <param name="strand" type="select" label="Inversed strand" help="Use this if the library type is fr-first-strand. All bam files will treated the same way."> <option value="yes" >yes</option> <option value="no" selected="True">no</option> </param> - <param name="normalizationCoefficient" format="txt" type="text" value="" label="Normalization coefficient" help="If it is not precised no normalization will be done. Each bam file will be multiplied by a coefficient."/> <param name="chrom" format="txt" type="text" value="chr01" label="Chromosome name" /> - <param name="start" format="txt" type="text" value="100" label="Begin of the region" /> - <param name="end" format="txt" type="text" value="10000" label="End of the region" /> + <param name="start" format="txt" type="text" value="100" label="Start of region" > + <sanitizer> + <valid initial="string.digits" invalid_char=""> + <add value="_" /> + </valid> + </sanitizer> + </param> + <param name="end" format="txt" type="text" value="10000" label="End of the region" > + <sanitizer> + <valid initial="string.digits" invalid_char=""> + <add value="_" /> + </valid> + </sanitizer> + </param> <conditional name="annotation"> <param name="gff" type="select" label="Will you select a reference annotation file from your history?" help=""> <option value="no">No</option> @@ -77,19 +151,19 @@ </when> <when value="yes"> <repeat name="serie" title="GFF file"> - <param name="ownFile" type="data" format="gff" metadata_name="dbkey" label="Select the annotation file (gff)" /> + <param name="ownFile" type="data" format="gff" metadata_name="dbkey" label="Select annotation file (gff)" /> </repeat> - <param name="typeTranscript" format="txt" type="text" value="all" label="Type of transcripts to visualize" help="Use this option if you want to choose the transcripts to visualize. Many transcripts are seperated by a comma-separated list." /> - <param name="annotColor" format="txt" type="text" value="red" label="Different colors for the transcripts" help="Any color name accepted by R. Hexadecimal color code is possible, but without the #. You have to set the same number of colors and transcripts. Comma-separated list."/> - <param name="shapes" format="txt" type="text" value="box" label="Shape used for the annotation" help="You have four choices: box, rectangle, arrow, line. The default is box. You have to set the same number of shapes and transcripts. For yeast data, we use 'box' for every type of transcripts. For human data, we use 'rectangle' for exons and 'arrow' for introns. Comma-separated list."/> - <param name="annotationColorByStrand" type="boolean" truevalue="--annotation-color-by-strand" falsevalue="" checked="True" label="Annotation color by strand" help="Use this if you want the transcripts are colored by the strand." /> + <param name="typeTranscript" format="txt" type="text" value="gene" label="Type of transcripts to visualize" help="Use this option if you want to select the transcripts to visualize. Multiple transcripts are provided as a comma-separated list." /> + <param name="annotColor" format="txt" type="text" value="red" label="Colors for transcripts" help="Use any color name accepted by R, or Hexadecimal color codes without the # sign. Numbers of colors and transcripts should be equal. Comma-separated list."/> + <param name="shapes" format="txt" type="text" value="box" label="Shape used for annotation" help="Four choices: box, rectangle, arrow, line. Default is box. Numbers of shapes and transcripts should be the same. Suggestions: for yeast data, we use 'box' for every type of transcripts; for human data, we use 'rectangle' for exons and 'arrow' for introns. Comma-separated list."/> + <param name="annotationColorByStrand" type="boolean" truevalue="--annotation-color-by-strand" falsevalue="" checked="True" label="Annotation color by strand" help="Use this for coloring transcripts by strand." /> </when> </conditional> - <param name="scaleLog" type="boolean" truevalue="--scale-log" falsevalue="" checked="False" label="Scale log" help="Use this if you want a logarithmic scale." /> - <param name="symetricScale" type="boolean" truevalue="--symetric-scale" falsevalue="" checked="False" label="Symetric scale" help="This option is for a symetric scale with the same maximum and minimum for both strand in the 'classic' and 'lines' visualization." /> - <param name="annotationPlacedByStrand" type="boolean" truevalue="--annotation-placed-by-strand" falsevalue="" checked="False" label="Annotation placed by strand" help="Use this if you want the transcripts placed according to their strand. It takes more place, but it can be more clear." /> - <param name="unstrand" type="boolean" truevalue="--unstranded" falsevalue="" checked="False" label="Unstranded" help="Use this for an non-strand-specific visualization." /> - <param name="smoothLength" format="txt" type="text" value="" label="Sets the length of the sliding window smoothing. The default is NA and allows ving to compute an optimal length, according to the length of the asked genomic region. If you don't want any smoothing, set this to zero" /> + <param name="scaleLog" type="boolean" truevalue="--scale-log" falsevalue="" checked="False" label="Scale log" help="Use this for logarithmic coverage scale." /> + <param name="symetricScale" type="boolean" truevalue="--symetric-scale" falsevalue="" checked="False" label="Symmetric scale" help="This option is for a symmetric coverage scale with the same maximum and minimum for both strands ('classic' and 'lines' visualization)." /> + <param name="annotationPlacedByStrand" type="boolean" truevalue="--annotation-placed-by-strand" falsevalue="" checked="False" label="Annotation placed by strand" help="Use this to position transcripts according to their strand. Takes more space but may be neater" /> + <param name="unstrand" type="boolean" truevalue="--unstranded" falsevalue="" checked="False" label="Unstranded" help="Use this for a non-strand-specific visualization." /> + <param name="smoothLength" format="txt" type="text" value="" label="Sets the length of sliding window for smoothing. Default is NA and allows ving to compute an optimal length, according to the length of the displayed genomic region. To avoid any smoothing, set this to zero" /> <conditional name="visuType"> <param name="visu" type="select" label="Type of visualization" > <option value="classic" selected="True">classic</option> @@ -97,13 +171,13 @@ <option value="heatmap">heatmap</option> </param> <when value="classic"> - <param name="plusColor" format="txt" type="text" value="purple" label="Classic plus strand color" help="Sets the color of plus strand for the classic visualization." /> - <param name="minusColor" format="txt" type="text" value="pink" label="Classic minus strand color" help="Sets the color of minus strand for the classic visualization." /> + <param name="plusColor" format="txt" type="text" value="purple" label="Classic plus strand color" help="Sets the color of plus strand for classic visualization." /> + <param name="minusColor" format="txt" type="text" value="pink" label="Classic minus strand color" help="Sets the color of minus strand for classic visualization." /> </when> <when value="heatmap"> - <param name="heatmapMax" format="txt" type="text" value="yellow" label="Heatmap maximum color" help="Sets the maximum color of the palette for the heatmap visualization." /> - <param name="heatmapMin" format="txt" type="text" value="green" label="Heatmap minimum color" help="Sets the minimum color of the palette for the heatmap visualization." /> + <param name="heatmapMax" format="txt" type="text" value="yellow" label="Heatmap maximum color" help="Sets the maximum color of the palette for heatmap visualization." /> + <param name="heatmapMin" format="txt" type="text" value="green" label="Heatmap minimum color" help="Sets the minimum color of the palette for heatmap visualization." /> <param name="method" type="select" label="Method of the palette for the heatmap visualization" help="Two settings : - hsv : varies the hues - rgb : varies the shades"> <option value="hsv" selected="True">hsv</option> <option value="rgb" >rgb</option> @@ -111,16 +185,46 @@ </when> <when value="lines"> - <param name="linesColors" format="txt" type="text" value="" label="Sample colors" help="Sets the colors for the lines visualization. Comma-separated list. You must specify as many colors as bam files." /> - <param name="linesType" format="txt" type="text" value="" label="Sample type lines" help="Sets the kind of lines for the lines visualization. Comma-separated list. You must specify as many line types as bam files."/> + <param name="linesColors" format="txt" type="text" value="" label="Sample colors" help="Sets colors for lines visualization. Specify as many colors as there are bam files. Comma-separated list." /> + <param name="linesType" format="txt" type="text" value="" label="Sample type lines" help="Sets line types for lines visualization. Specify as many line types as there are bam files. Comma-separated list."/> </when> </conditional> - + <param name="filetype" type="select" label="Output format" > + <option value='png' selected="True">png</option> + <option value='jpeg' >jpeg</option> + <option value='bmp'>bmp</option> + <option value='tiff'>tiff</option> + <option value='pdf'>pdf</option> + </param> + <param name="resolution" format="txt" type="text" value="72" label="Sets the resolution of the output, in dot per inch" > + <sanitizer> + <valid initial="string.digits" invalid_char=""> + <add value="_" /> + </valid> + </sanitizer> + </param> + </inputs> <outputs> - <data name="output" format="png" label="ving result on ${on_string}" /> + + <data name="output_png" format="png" label="ving result on ${on_string}" > + <filter> filetype == 'png' </filter> + </data> + <data name="output_jpg" format="jpg" label="ving result on ${on_string}" > + <filter> filetype == 'jpeg' </filter> + </data> + <data name="output_bmp" format="bmp" label="ving result on ${on_string}" > + <filter> filetype == 'bmp' </filter> + </data> + <data name="output_tiff" format="tiff" label="ving result on ${on_string}" > + <filter> filetype == 'tiff' </filter> + </data> + <data name="output_pdf" format="pdf" label="ving result on ${on_string}" > + <filter> filetype == 'pdf' </filter> + </data> + </outputs> <tests>