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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]