I'm using GVIZ with a custom built GFF3 file and am getting some curious artifacts in my output plot.
The main issue is the false incorporation of an exon into a multi-exon unit (right side of image). Here the red hatched box shows the exon which should stand alone at the position indicated by the blue box.
A second smaller issue (seen on the left) is that a thin horizontal line is drawn (not clear to me why) and the exon which should be placed at that location is vertically displaced (now at the bottom of the screen).
Both issues go away if I zoom in to specific loci but return when I zoom out (by changing the mapping co-ordinates) which suggests to me it is a stacking error rather than anything to do with the underlying GFF3 file (which looks normal in IGV).
I would appreciate any advice that can be offered on this
modelsfor<-makeTxDbFromGFF("annotation/virus_v8.1_forward.gff3") rtrackmodelsfor <- GeneRegionTrack(modelsfor, genome = "virus", chromosome = myChr, name = "Gene Model", col="black", fill="grey", stacking="squish", shape="smallArrow", background.title = "transparent", options(ucscChromosomeNames=FALSE)) plotTracks(list(rtrackmodelsfor,gtrack), from = myStart, to = myEnd, type="hist", col.histogram=NA, cex.title=1, cex.axis=1, title.width=1.2)