[BioC] Gviz AlignmentTrack - Consistent y-scales

[Lance Parsons]

Thanks for you help, you are correct that the ylim parameter works as 
expected with a DataTrack.  However, my issue is actually with the 
AlignmentTrack (my apologies for the confusion). With an AlignmentTrack 
(which looks much better when plotting coverage data, at least the way 
I'm using them), the scale is adjusted when setting a ylim, but the data 
is plotted according the automatically calculated ylim.

However, I still have an issue with plotting consistent scales, but 
different heights.  What I would like is for the scale on all of the 
graphs the same, in other words, the same number of pixels represents a 
consistent value (say 50 pixels equals a y-value of 50).  However, I 
would like some data tracks to be from 0-100 and others to be from 
0-200.  Is that possible?

Thanks for your help.

Aliaksei Holik wrote:
> 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.
>>

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