From here , I see the annotation track can be added above by this:

plotTracks(list(detesTrack, dmrTrack),  legend = TRUE, groupAnnotation="id", just.group = "above")

My question is that how could I just add annotation to one track when there are multiple.

If I used the codes above, it will add annotation to all track as below. But, I only want to keep the annotation for DETEs not the "unknown" ones for DMRs.

Thanks a lot!

You have to specify the arguments groupAnnotation="id", just.group = "above" while you create the track object itself and not later when you call the plotTracks function. If you specify it in plotTracks function, it is applied to all the tracks.

In your case set it once you create the "DETEs" object and then call plotTracks function without those parameters. Something along these lines:

dmrTrack <- AnnotationTrack(...)
detesTrack <- AnnotationTrack(..., groupAnnotation="id", just.group = "above")

plotTracks(list(detesTrack, dmrTrack),  legend =TRUE)