Thanks Florian. This does seem to work, albeit with some trial and 
error. I do have a related question. Is there a way to pull out the 
automatically determined ylim from an AlignmentTrack (or DataTrack)? The 
automatically selected value is often a good one, and if I could use 
that when setting the track size it would be very nice. Thanks.

Lance

Hahne, Florian wrote:
>
> 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@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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