An example that looks like expected:

Adding reverseStrand=TRUE to the line producing this gives this result:

The transcript and axis are reversed as expected, but not the highlight track.

It's easy enough to calculate a position for the highlight track that works even with this behaviour when I'm working with one transcript, but it's a nightmare when I'm working with multiple. Am I doing something wrong?

The code producing these images.

Thanks for reporting this issue. Indeed, the HighlightTrack did not pick up the strand reversal. Just committed a fix for this.

Florian

It takes about a day or so for new package versions to be built. If you cant wait that long, you can check out the code from the respective SVN repositories and build the package yourself. 

For the devel branch you want revision >= 113709 and for the 3.2 release branch you want revision >= 113710

the safest way however is to wait for the updates to become available through biocLite.

Florian