Hi Lance,
Sorry for the late reply, I was out of office for the last two weeks. Looks like you indeed discovered a bug which I may have introduced during the last changes to the ylim code. Thanks for the report, and even more so for the patch! I will make the necessary code changes in both the release and the devel version of the packages in the next couple of days.
Cheers,
Florian

From: Lance Parsons <lparsons@princeton.edu<mailto:lparsons@princeton.edu>>
Date: Wednesday 30 April 2014 21:25
To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>>
Cc: "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: Gviz AnnotationTrack ylim patch

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.

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University


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