[Biopython-dev] Enhancements to Bio.Graphics.BasicChromosome

[Peter Cock]

On Monday, October 3, 2011, Kevin Jacobs &lt;jacobs at bioinformed.com&gt; <
bioinformed at gmail.com> wrote:
> On Mon, Oct 3, 2011 at 7:20 AM, Peter Cock <p.j.a.cock at googlemail.com
>wrote:
>
>> You might have seen on Twitter at the end of last week I mentioned
>> some work to extend Brad's Bio.Graphics.BasicChromosome to allow
>> features within a chromosome segment, optionally with labels.
>>
>>
>
> This looks to be extremely useful.  Is there any support for layouts to
> stack or pack chromosomes?  I'm thinking of diagrams for humans, where we
> don't fit as well in linear displays.  I also think supporting chromosome
> bands would be extremely useful.  These could include full cytobands,
> centromeres, euchromatic vs hetrochromatic regions, user configurable
bands
> (e.g. linkage regions, IBD blocks, etc.)
>
> The figure shows off what I'm thinking about the banding and layout, even
> though it uses colored circles instead of text labels:
> http://www.genome.gov/multimedia/illustrations/GWAS_2011_1.pdf
>
> If there is interest, I may have some time to work on these features once
> the basic infrastructure is stable.
>
> Best regards,
> -Kevin

Hi Kevin,

I'm glad to hear there is some interest in this :)

That example you linked to is interesting - there are several
things of specific interest - and helps as I'm not yet
familiar with all the technical terms you used.

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).

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?

Multiple coloured dots for labels. Doable, but a nice API might
be tricky.

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 ;)

Regards,

Peter