This code:

Gviz::plotTracks(
  c(biomartBoth, axisTrack),
  from = biomartBoth@start,
  to = biomartBoth@end,
  chromosome = rep("chr15", 2),
  showId = TRUE,
  just.group = "below"
)

Produces this plot, as expected:

However, if I add the option reverseStrand=TRUE:

Gviz::plotTracks(
  c(biomartBoth, axisTrack),
  from = biomartBoth@start,
  to = biomartBoth@end,
  chromosome = rep("chr15", 2),
  showId = TRUE,
  just.group = "below",
  reverseStrand = TRUE
)

Then I get this:

I figured out that removing the ids, like this:

Gviz::plotTracks(
  c(biomartBoth, axisTrack),
  from = biomartBoth@start,
  to = biomartBoth@end,
  chromosome = rep("chr15", 2),
  showId = FALSE,
  just.group = "below",
  reverseStrand = TRUE
)

Plots the transcripts on the same line again:

But how can I plot the transcripts on the same line while showing the ids?

Complete code example.

Ok, also fixed this issue along with the other committed changes referenced here:

C: Gviz: HighlightTrack doesn't react to reverseStrand = TRUE ?

Thanks for reporting.

Could you please include the code that created the biomartBoth object in order to replicate the issue.

Also, out of curiosity, why are you explicitly passing in biomartBoth@start and biomartBoth@end as the from and to parameters? Gviz should pick those up automatically. Not forcing from and to will also allow Gviz to add some space before the beginning of each transcript in order to accommodate the labels if needed, which in most cases is beneficial.

Florian