Hi, I'm having issues with Gviz plotting the highlights behind the data tracks:

The code used to produce the image:

library(Gviz)
library(GenomicRanges)

bigwig = "HCNE_density_hg19_mm10.bigWig"

region = GRanges("chr3", IRanges(180436331, 182390735))
gene = GRanges("chr3", IRanges(181661924, 181764436)) # 100kb around SOX2

itrack = IdeogramTrack(genome="hg19")
gtrack = GenomeAxisTrack(genome="hg19")
cnetrack = DataTrack(range = bigwig, genome = "hg19", type = "horiz", name = "Mouse HCNEs")
genetrack = UcscTrack(genome="hg19", chromosome=seqnames(region), track="refGene", from=start(region), to=end(region),
                      trackType="GeneRegionTrack", rstarts="exonStarts", rends="exonEnds",
                      gene="name2", symbol="name2", transcript="name", collapseTranscripts="longest")

hltrack = HighlightTrack(trackList=list(cnetrack, genetrack), gene, genome="hg19")

png("testplot.png", width=20, height=8, units="in", res=200)
plot = plotTracks(list(itrack, gtrack, hltrack), col=NULL, transcriptAnnotation = "symbol", from=start(region), to=end(region), chromosome=as.character(seqnames(region)), main="SOX2")
dev.off()

This was produced using R 3.1.1 with all dependencies fully up to date.

Hi Malcolm,

I finally found some minutes to take a look at this. My initial idea was to have the HighlightTrack region in the background with some filling color, but obviously that breaks when a lot of content gets drawn on the actual track elements. In version 1.10.3 which should be available in the next couple of days I have added the 'inBackground" display parameter to the HighlightTrack class. If set to FALSE, the box will be drawn in the foreground instead. 

In order for this to make sense you probably want to play with the transparency (display parameter 'alpha'), or not use filling for the highlight boxes (i.e., display parameter 'fill' = NA)

Hope that helps,

Florian

Hi Malcolm,

thanks for reporting this issue. I will take a closer look and get back with a fix soon.

Florian

So in your example, something like:

hltrack = HighlightTrack(trackList=list(cnetrack, genetrack), gene, genome="hg19", inBackground=FALSE, fill=NA) 
plot = plotTracks(list(itrack, gtrack, hltrack), col=NULL, transcriptAnnotation = "symbol", from=start(region), to=end(region), chromosome=as.character(seqnames(region)), main="SOX2")

Or on a device that supports transparency:

hltrack = HighlightTrack(trackList=list(cnetrack, genetrack), gene, genome="hg19", inBackground=FALSE, alpha=0.3) 
plot = plotTracks(list(itrack, gtrack, hltrack), col=NULL, transcriptAnnotation = "symbol", from=start(region), to=end(region), chromosome=as.character(seqnames(region)), main="SOX2")