My apologies, my issue was with the AlignmentTrack, not the
AnnotationTrack as previously stated.
Lance Parsons wrote:
First, let me say thanks for such an excellent genome visualization
package. I simply couldn't find anything comparable when it came to
producing publication quality genome plots.
I've run what seems like a bug to me, and I've attempted to provide a
suitable patch. The bug is in the coverage portion of an
AnnotationTrack. It seems that if one supplies a `ylim` value, the
printed scale will be adjusted as requested, but the graph will still
be plotted in the automatically determined scale.
Example plotting graphs without setting ylim (not the scales for each
are different): http://i.imgur.com/68xObgx.png
Example of graphs with ylim set (but not properly honored):
http://i.imgur.com/MBvO2wA.png
Example of patched code with ylim set (now the ylim is used properly):
http://i.imgur.com/EXlrkqa.png
I hope this helps to resolve what I think is an unintended bug.
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Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
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