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lukejharmon / traitathon

for storing stuff associated with the trait group at the tree-for-all hackathon
MIT License
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tanglegram #2

Open lukejharmon opened 10 years ago

lukejharmon commented 10 years ago

Implement tanglegram plot in both R and Arbor.

curtislisle commented 10 years ago

@zackgalbreath, does Arbor have your VTK-based tanglegram in it now for reference and testing? Just asking, don't drop what you are doing.

zackgalbreath commented 10 years ago

On Wed, Sep 17, 2014 at 11:51 AM, Curtis Lisle notifications@github.com wrote:

@zackgalbreath https://github.com/zackgalbreath, does Arbor have your VTK-based tanglegram in it now for reference and testing? Just asking, don't drop what you are doing.

Yes it does, you should see it as an entry under the visualization tab.

lukejharmon commented 10 years ago

OK, we have this in arbor web but not R, we can add it later.

chodon commented 9 years ago

is tanglegram implemented in R yet? If not, how should the CSV be formatted in VTK-based version on the visualization tab? thanks!!

curtislisle commented 9 years ago

Hi Chodon! Missed talking with you. There are a few tangle grams implemented in R. Here is a URL with some information about one implementation:

http://stackoverflow.com/questions/12456768/duelling-dendrograms-in-r-placing-dendrograms-back-to-back-in-r

I have put a call into my Kitware colleagues. I think the VTK tangle gram our program developed is not currently online, but I’ll check.

Is your application heliconia vs. hummingbirds?

On Jul 5, 2015, at 11:00 AM, chodon sass notifications@github.com wrote:

is tanglegram implemented in R yet? If not, how should the CSV be formatted in VTK-based version on the visualization tab? thanks!!

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chodon commented 9 years ago

Thanks Curt! This isn't for Heliconia yet, but for a colleague. I'll pass this info along and let me know any updates! Thanks again, C

curtislisle commented 9 years ago

The VTK-based tanglegram in Arbor isn’t currently functional, but is planning to return to operation over the next few months. The pointer I sent matches up two trees with matching names in the taxa, the script would need to be extended a bit to have a look up table matching two different names at the edges.

On Jul 6, 2015, at 12:17 PM, chodon sass notifications@github.com wrote:

Thanks Curt! This isn't for Heliconia yet, but for a colleague. I'll pass this info along and let me know any updates! Thanks again, C

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lukejharmon commented 9 years ago

This is implemented in R now: http://blog.phytools.org/2015/07/more-on-new-method-for-co-phylogenetic.html. We can easily port this into Arbor.

curtislisle commented 9 years ago

I noticed something similar to this the other day. Agreed.

On Jul 13, 2015, at 11:26 PM, Luke Harmon notifications@github.com wrote:

This is implemented in R now: http://blog.phytools.org/2015/07/more-on-new-method-for-co-phylogenetic.html. We can easily port this into Arbor.

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