Question: Biomartgeneregiontrack/Generegiontrack Number Of Stacks
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gravatar for andreas.dander
6.5 years ago by
andreas.dander10 wrote:

Hello Community,

I'm using the Bioconductor GViz package for visualizing SNPs and INDELs automatically. As I would like to know the gene-models of the shown regions within tracks of the created image I try the GeneRegionTrack as well as the BiomartGeneRegionTrack.

For simplification reason I use the BiomartGeneRegionTrack in this example:

# create track
biomartTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr17", start=41277600, end=41280000)
# plot track
plotTracks(biomartTrack)

The generated track contains several transcripts of 2 genes (orange and red) nicely aligned. My problem is that I would like to adjust the size of the generated image dynamically therefore I need to now the height (number of stacks or lines) of the shown transcripts. In this case this number is 29 (manually counted). Is there a function which is able to determine this number before plotting?

Thanks, Andreas

This question is allready posted on seqanserwers under http://seqanswers.com/forums/showthread.php?t=30199

bioconductor • 1.9k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by andreas.dander10
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