I want to plot something like this:
This was produced with Gviz. My problem with Gviz is the empty space added at the bottom of the plot (below the reads). I posted a question about that here.
Do you have any suggestions on how I can plot reads aligned to a reference sequence in R, and not use Gviz?
Edit: The observant might have noticed that the "empty space problem" with the Gviz plot was solved in the post I linked to. I'm still curious if there are other solutions, though.