[Wavetiling-commits] r28 - in pkg: . R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 9 11:29:48 CET 2012
Author: ppipeler
Date: 2012-03-09 11:29:48 +0100 (Fri, 09 Mar 2012)
New Revision: 28
Modified:
pkg/NAMESPACE
pkg/R/allGenerics.R
pkg/R/methods-WfmInf.R
Log:
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2012-03-09 09:48:12 UTC (rev 27)
+++ pkg/NAMESPACE 2012-03-09 10:29:48 UTC (rev 28)
@@ -43,23 +43,19 @@
importFrom(methods, "@<-", callNextMethod, new)
-importFrom(waveslim, wave.filter, dwt, idwt)
+importFrom(oligo, read.celfiles)
importFrom(stats, contr.helmert, contr.treatment, lm, pnorm, qnorm,
rnorm)
-## importFrom(waveslim, wave.filter)
+importFrom(waveslim, wave.filter)
-## Plot
-importFrom(graphics, plot)
-
## Export Classes
exportClasses(WaveTilingFeatureSet, MapFilterProbe, GenomeInfo, WfmFit, WfmInf, WfmFitTime, WfmFitFactor, WfmFitCircadian, WfmFitCustom, WfmInfCompare, WfmInfEffects )
## Export Methods
exportMethods(show)
-exportMethods(plot)
## WaveTilingFeatureSet
exportMethods(addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap, selectProbesFromTilingFeatureSet,bgCorrQn,wfm.fit)
@@ -68,8 +64,8 @@
exportMethods(getFilteredIndices, getPosition, selectProbesFromFilterOverlap)
## WfmFit and WfmInf
-exportMethods(getProbePosition, getNoProbes, getBetaWav, getVarBetaWav, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getDesignMatrix, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj,getPrior, getAlpha, getDelta, getTwoSided, getSigProbes,getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff,getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions)
+exportMethods(getProbePosition, getNoProbes, getBetaWav, getVarBetaWav, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getDesignMatrix, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj,getPrior, getAlpha, getDelta, getTwoSided, getSigProbes,getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff,getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions, plotWfm)
## Other
-export(cel2TilingFeatureSet, makeContrasts, makeDesign, plotWfm)
+export(cel2TilingFeatureSet, makeContrasts, makeDesign)
Modified: pkg/R/allGenerics.R
===================================================================
--- pkg/R/allGenerics.R 2012-03-09 09:48:12 UTC (rev 27)
+++ pkg/R/allGenerics.R 2012-03-09 10:29:48 UTC (rev 28)
@@ -291,11 +291,11 @@
}
)
-# setGeneric("plotWfm",function(object, annoFile, minPos, maxPos, trackFeature="exon", overlayFeature=c("gene","transposable_element_gene"), two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
-# {
-# standardGeneric("plotWfm")
-# }
-# )
+setGeneric("plotWfm",function(object, annoFile, minPos, maxPos, trackFeature="exon", overlayFeature=c("gene","transposable_element_gene"), two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
+{
+ standardGeneric("plotWfm")
+}
+)
setGeneric("getSigGenes",function(fit, inf, annoFile)
{
@@ -309,10 +309,10 @@
}
)
-if (!isGeneric("plot")) {
- setGeneric("plot",function(fit,inf,...){
- standardGeneric("plot")
- }
-)
-}
+#if (!isGeneric("plot")) {
+# setGeneric("plot",function(fit,inf,...){
+# standardGeneric("plot")
+# }
+#)
+#}
Modified: pkg/R/methods-WfmInf.R
===================================================================
--- pkg/R/methods-WfmInf.R 2012-03-09 09:48:12 UTC (rev 27)
+++ pkg/R/methods-WfmInf.R 2012-03-09 10:29:48 UTC (rev 28)
@@ -153,6 +153,282 @@
return(out)
})
-setMethod("plot",signature=c(fit="WfmFit",inf="WfmInf"),plotWfm)
+setMethod("plotWfm",signature=c(fit="WfmFit",inf="WfmInf"),
+function(fit,inf,annoFile,minPos,maxPos,trackFeature="exon",overlayFeature=c("gene","transposable_element_gene"),two.strand=TRUE,plotData=TRUE,plotMean=TRUE,tracks=0)
+{
+ if (missing(annoFile)) {stop("Annotation File is missing!!")}
+ Gloc <- getProbePosition(fit)
+ if (missing(minPos)) {minPos<-min(Gloc)}
+ if (missing(maxPos)) {maxPos<-max(Gloc)}
+ chromosome <- getChromosome(fit)
+ strand <- getStrand(fit)
+ selID <- (1:length(Gloc))[Gloc>minPos & Gloc<maxPos]
+ sta <- min(selID)
+ end <- max(selID)
+ minBase <- Gloc[sta]
+ maxBase <- Gloc[end]
+ trackCount <- 1
+ trackInfo <- list()
+ overlayInfo <- list()
+ if (plotData==TRUE)
+ {
+ Y <- getDataOrigSpace(fit)
+ replcs <- as.numeric(table(getPhenoInfo(fit)$group))
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(t(Y[,sta:end])),probeStart=Gloc[sta:end],dp=DisplayPars(color=rep(1:length(replcs),replcs),ylim=range(Y[,sta:end]),pointSize=.3,pch=sequence(replcs)))
+ names(trackInfo)[trackCount] <- "Data"
+ trackCount <- trackCount + 1
+ }
+ if (two.strand==TRUE)
+ {
+ trackInfo[[trackCount]] <- makeNewAnnotationTrack(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="forward",feature=trackFeature,dp=NULL)
+ names(trackInfo)[trackCount] <- "F"
+ overlayInfo[[trackCount]] <- makeNewAnnotationTextOverlay(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="forward",region=c(trackCount,trackCount),feature=overlayFeature,y=0.5)
+ trackCount <- trackCount + 1
+ trackInfo[[trackCount]] <- makeGenomeAxis(add53 = TRUE,add35 = TRUE)
+ trackCount <- trackCount + 1
+ trackInfo[[trackCount]] <- makeNewAnnotationTrack(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="reverse",feature=trackFeature)
+ names(trackInfo)[trackCount] <- "R"
+ overlayInfo[[trackCount]] <- makeNewAnnotationTextOverlay(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="reverse",region=c(trackCount,trackCount),feature=overlayFeature,y=0.5)
+ trackCount <- trackCount + 1
+ } else
+ {
+ trackInfo[[trackCount]] <- makeNewAnnotationTrack(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand=strand,feature=trackFeature)
+ if (strand=="forward")
+ {
+ names(trackInfo)[trackCount] <- "F"
+ }
+ if (strand=="reverse")
+ {
+ names(trackInfo)[trackCount] <- "R"
+ }
+ overlayInfo[[trackCount]] <- makeNewAnnotationTextOverlay(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand=strand,region=c(trackCount,trackCount),feature=overlayFeature,y=0.5)
+ trackCount <- trackCount + 1
+ gAxis <- makeGenomeAxis(add53 = TRUE,add35 = TRUE)
+ trackCount <- trackCount + 1
+ }
+ effects <- getEff(inf)
+ regions <- getRegions(inf)
+ noGroups <- length(table(getPhenoInfo(fit)$group))
+ if (inherits(inf,"WfmInfMeans")) {
+ plotMean <- FALSE
+ }
+ if (plotMean==TRUE)
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[1,sta:end])+c(-0.4,0.4),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- "Mean"
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[1]]),end(regions[[1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ trackCount <- trackCount + 1
+ }
+# if (getWfmFitMethod(object)=="twoGroup" | getWfmFitMethod(object)=="circadian")
+ if ((inherits(fit,"WfmFitFactor") & noGroups==2) | inherits(fit,"WfmFitCircadian"))
+ {
+ if (tracks==0)
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[2,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[2,sta:end])[1]),max(1.3,range(effects[2,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ #if (getWfmFitMethod(object)=="twoGroup")
+ if (inherits(inf,"WfmInfCompare"))
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[2,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[2,sta:end])[1]),max(1.3,range(effects[2,sta:end])[2])+c(-0.2,0.2)),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- "FC"
+ } else
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(sqrt(effects[2,sta:end]^2+effects[3,sta:end]^2)),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(sqrt(effects[2,sta:end]^2+effects[3,sta:end]^2))[1]),max(1.2,range(sqrt(effects[2,sta:end]^2+effects[3,sta:end]^2))))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- "Ampl"
+ }
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[2]]),end(regions[[2]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ hlp <- which(!unlist(lapply(overlayInfo,is.null)))
+ if (two.strand==TRUE)
+ {
+ hlpAnno <- hlp[1:2]
+ } else
+ {
+ hlpAnno <- hlp[1]
+ }
+ hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
+ hlpEff <- hlp[!(hlp%in%hlpAnno)]
+ hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
+ hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
+ overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
+ gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
+ }
+ }
+# if (getWfmFitMethod(object)=="compareGroupsTime" | getWfmFitMethod(object)=="compareGroupsFactor")
+ else if (inherits(inf,"WfmInfCompare"))
+ {
+ if (length(tracks)==1 & tracks[1]==0)
+ {
+ effectsToPlot <- rep(0,noGroups)
+ effectId <- c(1,3,6,10,15)
+ effectNames <- c("2-1","3-2","4-3","5-4","6-5")
+ effectNo <- 1
+ while (effectNo<length(effectsToPlot))
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[effectId[effectNo]+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[effectId[effectNo]+1,sta:end])[1]),max(1.3,range(effects[effectId[effectNo]+1,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- effectNames[effectNo]
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[effectId[effectNo]+1]]),end(regions[[effectId[effectNo]+1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ effectNo <- effectNo + 1
+ trackCount <- trackCount + 1
+ }
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[effectId[length(effectsToPlot)-2]+2,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[effectId[length(effectsToPlot)-2]+2,sta:end])[1]),max(1.3,range(effects[effectId[length(effectsToPlot)-2]+2,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- "Last-First"
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[effectId[length(effectsToPlot)-2]+2]]),end(regions[[effectId[length(effectsToPlot)-2]+2]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ hlp <- which(!unlist(lapply(overlayInfo,is.null)))
+ if (two.strand==TRUE)
+ {
+ hlpAnno <- hlp[1:2]
+ } else
+ {
+ hlpAnno <- hlp[1]
+ }
+ hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
+ hlpEff <- hlp[!(hlp%in%hlpAnno)]
+ hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
+ hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
+ overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
+ gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
+ }
+ if (length(tracks)>1 | tracks[1]!=0)
+ {
+ if (length(tracks)>8)
+ {
+ stop("Too many tracks specified")
+ }
+ groupNames <- sapply(1:noGroups,function(x) paste("Gr",x,sep=""))
+ #groupNames <- sapply(8:13,function(x) paste("D",x,sep=""))
+ firstId <- rep(2:noGroups,1:(noGroups-1))
+ lastId <- sequence(1:(noGroups-1))
+ effectNames <- sapply(1:(noGroups*(noGroups-1)/2),function(x) paste(groupNames[firstId[x]],"-",groupNames[lastId[x]],sep=""))
+ for (i in tracks)
+ {
+ #trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[i+1,sta:end])[1]),max(1.3,range(effects[i+1,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[,sta:end])+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- effectNames[i]
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i+1]]),end(regions[[i+1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ trackCount <- trackCount + 1
+ }
+ hlp <- which(!unlist(lapply(overlayInfo,is.null)))
+ if (two.strand==TRUE)
+ {
+ hlpAnno <- hlp[1:2]
+ } else
+ {
+ hlpAnno <- hlp[1]
+ }
+ hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
+ hlpEff <- hlp[!(hlp%in%hlpAnno)]
+ hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
+ hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
+ overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
+ gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
+ }
+
+ }
+# if (getWfmFitMethod(object)=="meansByGroupTime" | getWfmFitMethod(object)=="meansByGroupFactor")
+ else if (inherits(inf,"WfmInfMeans"))
+ {
+ if (length(tracks)==1 & tracks[1]==0)
+ {
+ effectNames <- sapply(1:noGroups,function(x) paste("Gr",x,sep=""))
+ for (i in 1:noGroups)
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[i,sta:end])[1]),max(1.3,range(effects[i,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- effectNames[i]
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i]]),end(regions[[i]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ trackCount <- trackCount + 1
+ }
+ hlp <- which(!unlist(lapply(overlayInfo,is.null)))
+ if (two.strand==TRUE)
+ {
+ hlpAnno <- hlp[1:2]
+ } else
+ {
+ hlpAnno <- hlp[1]
+ }
+ hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
+ hlpEff <- hlp[!(hlp%in%hlpAnno)]
+ hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
+ hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
+ overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
+ gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
+ }
+ if (length(tracks)>1 | tracks[1]!=0)
+ {
+ if (length(tracks)>8)
+ {
+ stop("Too many tracks specified")
+ }
+ #effectNames <- sapply(1:noGroups,function(x) paste("Gr",x,sep=""))
+ effectNames <- paste("day",8:13,sep="")
+ for (i in tracks)
+ {
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[i,sta:end])[1]),max(1.3,range(effects[i,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ #trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[,sta:end])+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- effectNames[i]
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i]]),end(regions[[i]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ trackCount <- trackCount + 1
+ }
+ hlp <- which(!unlist(lapply(overlayInfo,is.null)))
+ if (two.strand==TRUE)
+ {
+ hlpAnno <- hlp[1:2]
+ } else
+ {
+ hlpAnno <- hlp[1]
+ }
+ hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
+ hlpEff <- hlp[!(hlp%in%hlpAnno)]
+ hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
+ hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
+ overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
+ gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
+ }
+ }
+# if (getWfmFitMethod(object)=="effectsTime")
+ else if (inherits(fit,"WfmFitTime") & inherits(inf,"WfmInfEffects"))
+ {
+ fct <- 0.2390457
+ if (tracks==0 | (length(tracks)==2 & tracks[1]==1 & tracks[2]==2) | tracks==1 | tracks==2)
+ {
+ if (tracks==0)
+ {
+ tracks <- c(1,2)
+ }
+ effectNames <- c("Linear","Quadratic")
+ for (i in tracks)
+ {
+ #trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[i+1,sta:end])+c(-0.5,0.5),pointSize=.3,pch=1,lwd=1,type="line"))
+ trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]*fct),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[i+1,sta:end]*fct)+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
+ names(trackInfo)[trackCount] <- effectNames[i]
+ overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i+1]]),end(regions[[i+1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
+ trackCount <- trackCount + 1
+ }
+ hlp <- which(!unlist(lapply(overlayInfo,is.null)))
+ if (two.strand==TRUE)
+ {
+ hlpAnno <- hlp[1:2]
+ } else
+ {
+ hlpAnno <- hlp[1]
+ }
+ hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
+ hlpEff <- hlp[!(hlp%in%hlpAnno)]
+ hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
+ hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
+ overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
+ gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
+ } else
+ {
+ stop("tracks argument has been misspecified")
+ }
+ }
+ else if (inherits(inf,"WfmInfCustom")) {
+ stop("Custom Inference plot not implemented!")
+ }
+ else {
+ stop("Unknown Design")
+ }
+}
+)
+
More information about the Wavetiling-commits
mailing list