[BioC] Gviz AnnotationTrack - Consistent y-scales

[Aliaksei Holik]

Hi Lance,

I'm relatively new to Gviz myself, but I believe there might be a simple 
solution to your problem. I'm not sure, why the thread has 
AnnotationTrack - your problem doesn't seem to have anything to do with 
the annotation. If I understand correctly, you would like to ensure 
consistent y axis for your DataTracks between plots, while allowing 
DataTracks of different height within each plot. You can do so by 
passing ylim parameter to individual DataTrack commands, the same way I 
imagine you're passing the bam file, the col.histogram and 
fill.histogram parameters.

I've just checked and it seems to work ok in Gviz_1.7.10, and Gviz_1.8.0.

I hope it helps,

Aliaksei.

P.S. I'm not sure, why you needed a patch, if ylim is a standard 
parameter in Gviz. Apologies for possible confusion.

On 1/05/14 5:39 AM, Lance Parsons wrote:
> 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.
>