[DAS] xyplot glyph in Ensembl genome browser

[Wouter Meuleman]

On 6/30/05, Harmen van der Spek <hvdspek at liacs.nl> wrote:
> I am currently working on CGH data visualisation (DAS annotation
> server). The idea is to draw a histogram or another kind of plot. I came
> across the xyplot glyph, which
> is being used in gbrowse. In the archives of May I found a post about
> the same problem, namely microarray data visualisation. Ensembl doesn't
> support the xyplot glyph yet.
> 
> I've been playing around a bit with the source code of Ensembl and found
> out that I could add glyphs myself in the Bio/Ensembl/Glyph/Symbol
> directory. I am able to use my own xyplot class to draw features, but
> I can't make it plot histograms or line plots.
> In das.pm, I modified get_featuredata in such a way that it returns the
> score feature (which I need to plot) entry too.
> 
> I still have some problems with rendering. Is someone else working on
> the same matter or can anyone give some help to get me on the right
> track. Is there still interest to include the xyplot glyph in the main
> Ensembl distribution?
> 

Dear Harmen,

  Questions to do with Ensembl are perhaps better asked on the
ensembl-dev list.
A few weeks ago this topic was addressed there by Andrew Nunberg
doing, I think,
something comparable. The question and subsequent responses by Ewan Birney 
and Steve Taylor follow. If this is what you mentioned, please ignore
(I wasn't sure
which archives you meant).

=============================
>> Is there a relatively simply way to display microarray data in ensembl?
>> I have a local copy running and I am exploring using DAS, except I do not
>> think that DAS supports the xyplot glyph.
>
> I don't think there is something out of the box, but being able to show
> "wiggle plots" via DAS is on our agenda - which I think it what you want.
>
> If you want to hack Ensembl, the GC glyph is the place to start whcih is
> a wiggle plot.
>
> James and/or Eugene might comment more about wiggle plots via DAS (we could
> use the Score slot, right?)
>

I know of several groups would be really interested in seeing this. It
would be useful if you could load 'wiggle' format data via URL as you
can in the UCSC Genome Browser (as well
as via DAS).
=============================

In addition, James Smith mentioned the following on the ensembl-dev list:

> By the September release we will also have "score-based"
> rendering on the sequence level displays, in the form of
> "wiggle-lines", "histograms" and colour based scoring.


Hope this helps.

-Wouter Meuleman.