[Biopython] Cross-Links in circular GenomeDiagram?

[Leighton Pritchard]

Hi Ilya

On 19 Nov 2013, at Tuesday, November 19, 22:15, Ilya Flyamer <flyamer at gmail.com<mailto:flyamer at gmail.com>> wrote:

The documentation says, that 'Biopython 1.59 added the ability to draw
cross links between tracks - both simple linear diagrams as we will show
here, but also linear diagrams split into fragments and circular
diagrams.'  I hoped that it was possible to make crosslinks between
fragments of the same track (as Circos can draw), but, apparently, I was
wrong: if I try to do that, I get a NotImplementedError(). The source is
quite explicit on this matter:

       if trackobjA == trackobjB:                raise NotImplementedError()

So, it is really not implemented.

Yes - the docs say "cross-links *between* tracks", rather than 'between two points on the same track' because of that, I'm afraid.

But are there any plans on implementing Circos-style crosslinks
(intra-track in Circular Diagram)? That would be a really useful feature
(for me), and there are not many programmes, that can do such things.

It's something I've had kicking around in my head as an idea for the next iteration of the module, but I've not made a start. So, if anyone wants to dive in and implement it, they should feel free. Especially if they want to incorporate some cool edge bundling (e.g. http://blog.visualmotive.com/2009/graph-visualization-edge-bundling/).

Cheers,

L.

--
Dr Leighton Pritchard
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme
DG31, James Hutton Institute (Dundee)
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:leighton.pritchard at hutton.ac.uk<http://hutton.ac.uk>       w:http://www.hutton.ac.uk/staff/leighton-pritchard<http://www.hutton.ac.uk/staff/leighton-pritchard>
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