[BioC] Gviz AlignmentTrack - Consistent y-scales

[Hahne, Florian]

Hi Lance,
Indeed this is the only way to force consistent pixel-to-yrange
relationships. Somewhere on a long list of nice-to-haves there is a
constantAspect parameter that would help with exactly the case you are
describing. Let¹s see whether I can promote that for one of the future
releases.
Florian



On 05/05/14 16:46, "Lance Parsons" <lparsons at princeton.edu> wrote:

>Thanks Aliaksei.  This in fact does work, though it took a bit of
>tweaking.  There are some constant size portions of the coverage track,
>even when no reads are plotted.  This means that I had to add a constant
>to the sizes in addition to a variable value based on the ylim.  Took a
>bit of work, but I seem to have it fixed, at least for my single case.
>
>Lance
>
>Aliaksei Holik wrote:
>> Hi Lance,
>>
>> I wonder if the 'sizes' parameter in the plotTracks might be useful.
>> This would allow you to set the track height to be proportional to the
>> scale. E.g. if your first track's ylim=c(0, 3) and the second tracks's
>> ylim=c(0, 5), set the sizes=c(3, 5). I've only tried it plotting
>> DataTracks, but since it's passed to the plotTracks I can't see why it
>> shouldn't work with AlignmentTrack. Sorry if I'm stating the obvious
>> or missing the point again.
>>
>> Hope it helps,
>>
>> Aliaksei.
>>
>>
>> On 2/05/14 12:14 AM, Lance Parsons wrote:
>>> 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
>
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