I've been using Gviz (1.8.0) to generate some figures using the 
AnnotationTrack feature.  Generally, things have worked quite well.  I'd 
like to plot a number of different coverage plots on the same figure and 
the coverage graphs have rather different heights.  I'd like to use a 
consistent sized Y-scale between each plot, which led to my writing a 
patch regarding an issue setting the ylim on those plots (submitted on 
bioc-devel list).  The patch I provided allows me to do that, but in 
order to ensure the scale are the same, I need to set the height of each 
graph the same.  This leads to a lot of wasted space in the figure for 
those plots with lower coverage.  Does anyone have any suggestions for 
how I might be able to ensure a consistent y-scale between the plots, 
but also allow some plots to be shorter than others, thus eliminating 
(or at least reducing) the wasted space?  Thanks in advance for any advice.

Example plotting graphs without setting ylim (not the scales for each 
are different): http://i.imgur.com/68xObgx.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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