Re: [circos] Circos and phylogenetic trees

[Martin Krzywinski]

Circos doesn't draw trees ;(

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Tue, May 21, 2013 at 5:31 AM, Matteo Brilli <matteo.b...@gmail.com> wrote:

Dear all, I'm pretty new to circos but I would like to use it for visualizing some experimental data produced in our experimental lab. I would like to put a phylogenetic tree in circle layout with labels pointing inside the circle and then add edges between labels representing actual cross-regulations between genes in the tree. Is it possible with circos?

Thank you,

Matteo

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[Matteo Brilli]

This is bad.

I'm joking. Anyway, it should be doable to trick it making it drawing trees, isnt'it? I mean, a circular tree is a series of arcs connecting branches and the arcs are in concentric layers..surely it is a little bit complicated but knowing the coordinates and layer of each (internal) node in the tree it should be doable.

I don't think I'll try.

Thank for the answer,

Matteo

Il giorno martedì 21 maggio 2013 23:10:41 UTC+2, Martin ha scritto:

Circos doesn't draw trees ;(

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Tue, May 21, 2013 at 5:31 AM, Matteo Brilli <matteo.b...@gmail.com> wrote:

Dear all, I'm pretty new to circos but I would like to use it for visualizing some experimental data produced in our experimental lab. I would like to put a phylogenetic tree in circle layout with labels pointing inside the circle and then add edges between labels representing actual cross-regulations between genes in the tree. Is it possible with circos?

Thank you,

Matteo

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[Alex Putman]

Matteo:

You mind find the interactive tree of life tool useful: http://itol.embl.de/

Although I doubt you can use it to draw edges as you describe, perhaps adding tracks of highlights or something else would work and be visually clearer.

[rohan]

Hey Matteo,

Try looking Geneious (http://www.geneious.com) and Figtree (http://tree.bio.ed.ac.uk/software/figtree/)
They are both nice.I used them recently.

-Rohan

[Alex Putman]

Actually, I just found the tool GraPhlAn: https://bitbucket.org/nsegata/graphlan/wiki/Home

Scroll down and you will see circular trees annotated with highlights and histograms

[Martin Krzywinski]

That looks great.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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