Gviz: control height of items within BiomartGeneRegionTrack (StackedTrack)
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Kort, Eric ▴ 220
@kort-eric-1483
Last seen 3.6 years ago
United States

I would like to keep the track heights in my Gviz plot the same between differing datasets, which I can do nicely with the sizes argument of plotTracks.

However, I would also like to control the height of items within a StackedTrack (actually, a BiomartGeneRegionTrack) so that the track can be fixed height, but the items do not become too tall (within the track of fixed height) if there are only a few items.

In other words, I would like the item in this plot (edited to remove extraneous "sizes" argument not germain to this example):

library(Gviz)
geneAll <- BiomartGeneRegionTrack(genome = "danRer10", symbol="Fzd7a", max.height=1)
plotTracks(geneAll)

To shrink so that it is similar to the height of the items in this plot:

geneAll <- BiomartGeneRegionTrack(genome = "danRer10", symbol="Fzd3a", max.height=1)
plotTracks(geneAll)

(but without shrinking the height of the entire track). I tried using the max.height parameter, but that does not work, and from the docs it seems that this parameter is only for AlignmentTrack.  As documented, min.height does control the height of feather/arrows within the introns in my BiomartGeneRegionTrack.

Is this possible?

If not, an alternative would be to create a spacer track that I adjust in height based on the number of rows in the BiomartGeneRegionTrack.  In that case, is their a way to tell how many rows of items will be in the track after it is squished so I can scale my spacer accordingly? If not, I can simply estimate based on the number of unique transcripts in the BiomartGeneRegionTrack.

Thank you!

-Eric

Gviz gviz-package • 773 views
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