[Bioc-devel] Gviz AlignmentTrack ylim patch

Lance Parsons lparsons at princeton.edu
Thu May 1 17:24:12 CEST 2014

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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