[Biopython-dev] Enhancements to Bio.Graphics.BasicChromosome
Kevin Jacobs <firstname.lastname@example.org>
bioinformed at gmail.com
Wed Oct 5 13:16:56 UTC 2011
On Mon, Oct 3, 2011 at 6:24 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
> Notches in the chromosome which I assume are centromeres
> (I can see how that might be added to the Bio code as another
> segment type, similar to the telomeres).
Yes-- although the visual style for centromeres need not be precisely as
shown in my example.
> Coloured background regions in the chromosome (should be
> able to do this already), some of which are hatched (not possible
> right now... would have to look into ReportLab's capabilities here).
> This is what you meant by banding?
Yes-- being able to show cytobands and custom bands to designate regions
will be very useful for me. As before, I'm not wed to the cross-hatching,
in fact the standard displays use only grayscale.
Multiple coloured dots for labels. Doable, but a nice API might
> be tricky.
I don't much care about those -- I'd be happy with text labels.
> For layout did you mean the fact this isn't just a row of
> chromosomes left to right, but here there are two rows?
> I'm inclined to say the user should just move things in
> the PDF for a final version using Adobe of Inkscape ;)
Correct. I'd prefer to have some programmatic control of layout, since I'd
hate to have to manually edit every whole-genome plot. Since I'm working
exclusively with human data for now, it would be possible to pre-specify a
few standard layouts and avoid the trouble of supporting dynamic features.
Just let me know when the code is stable enough to start poking around.
I'll float a proposal for what I think could be done to obtain feedback
before I commit much time to coding.
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