Question: height boxes gene models GeneRegionTrack Gviz
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5 months ago by
wd10 wrote:


I created two GeneRegionTracks with Gviz, one for genes on the plus strand, and one for genes on the minus strand.

gffTrack_PLUS<- GeneRegionTrack(txdb_PLUS, chromosome=scaffold,from=st, to=en,showId=TRUE,utr3="#FFD58A",utr5="#FFD58A", background.title="transparent","#808080",,lwd=0.7,"above",shape="box",stackHeight=0.75,stacking="squish")
gffTrack_MINUS<- GeneRegionTrack(txdb_MINUS, chromosome=scaffold,from=st, to=en,showId=TRUE,utr3="#FFD58A",utr5="#FFD58A", background.title="transparent","#808080",,lwd=0.7,"above",shape="box",stackHeight=0.75,stacking="squish")

However when genes overlap, the height of the boxes (representing Gene Models) is lower compared to a Gene Region Track where genes do not overlap (see plus vs minus strand in this figure, 2780 (-) vs 2790, 2770 and 2760 (-): Playing with stackHeight does not help. One could say to change the stacking type, but when using "dense" the boxes do have the same height but then the gene IDs disappear ("teturs") and I would like to keep the gene IDs in the figure.

Any suggestions would be much appreciated!



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