I am using Gviz to plot a region given by a gene name, for instance:

biomTrack <- BiomartGeneRegionTrack(genome ="sacCer3",name="ENSEMBL",gene="YBL087C")
plotTracks(list(btrack))

This works fine. I also want to add another annotation track:

btrack<-AnnotationTrack(start = c(100,200,300),width=100,chromosome = "chrII",name="test",showFeatureId=T)
plotTracks(list(biomTrack,btrack))

Now the region displayed appears to be all of chrII. I know I can use the from/to parameters in plotTracks but I want to select regions by gene name. Is this possible?

This is not possible. Unless explicitly provided via the from and to arguments, Gviz will derive the plotting region from the extremes of all provided tracks. So in your case it will plot everything from 100 to the rightmost exon of gene yBL08. You could of course use the ranges in biomTrack as limits:

plotTracks(list(biomTrack,btrack), from=min(biomTrack), to=max(biomTrack))

However I am not quite sure how that is supposed to make any sense, since the ranges you provide in btrack do not overlap with YBL08....

Florian