How can I colour boxes in Gviz AnnotationTrack in R?
Did you try the fill argument?

Something like this:

track &lt;- AnnotationTrack(start=c(1,5,7), end=c(2,6,10), strand=c('*','*','*'), stacking="dense", showFeatureId=TRUE, id=c('red','blue', 'red'), fill=c('red','blue', 'red'))