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 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: AlignmentsTrack_ylim_fix.patch URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20140430/853beadc/attachment.pl>