This code:

alTrack <- Gviz::AlignmentsTrack(
  system.file(package = "Gviz", "extdata", "gapped.bam"),
  isPaired = TRUE)

Gviz::plotTracks(
  alTrack,
  from = 3048500,
  to = 3049000,
  chromosome = "chr12")

Produces this plot:

How can I avoid the not-used whitespace at the bottom of the plot, below the reads? Regardless of the device height I set, there's always empty whitespace below the reads.

The specific region I don't want to appear:

Edit with answer:

Florian to the rescue again! The max.height parameter did it. Updated code with result:

alTrack <- Gviz::AlignmentsTrack(
  system.file(package = "Gviz", "extdata", "gapped.bam"),
  isPaired = TRUE)

Gviz::displayPars(alTrack) <- list(
  min.height = 25
)

Gviz::plotTracks(
  alTrack,
  from = 3048500,
  to = 3049000,
  chromosome = "chr12")

My bad. But it is the max.height parameter that will do the trick for you. Set this to a large value, and the white space will be filled with expanded reads. Doesn't look very nice. 

Changing the device height not having any effect is not true btw. Just limit the height of your plotting device and you will see less white space. 

Could you try and play around with the min.height and max.height and coverageHeight parameters to see if that fixes the issue? Without having the data to reproduce it is hard to give any more advise.