baba analysis plotting in v0.9 is broken

dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets

http://ipyrad.readthedocs.io

GNU General Public License v3.0

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baba analysis plotting in v0.9 is broken #425

Closed isaacovercast closed 3 years ago

isaacovercast commented 3 years ago

That's it. It doesn't work. Sending people back to use the 0.7 version is becoming increasingly unfeasible.

eaton-lab commented 3 years ago

ugh, I have huge updates for tons of the tools, including a working baba -- just need to find time to finish the tutorials. Raising on my TODO list.

ksil91 commented 3 years ago

Just came here to open this issue! Finishing up a cool hybridization project using the API that I'd like to round out with the ABBA-BABA plot. Is there a way to get the plot now from an analysis done with v0.9.6 (Python3)?

eaton-lab commented 3 years ago

Hi @ksil91 and others,

There is an updated documentation notebook here https://github.com/dereneaton/ipyrad/blob/master/testdocs/analysis/cookbook-baba-ipcoal.ipynb which also includes simulations to confirm it is working accurately.

This uses ipyrad v0.9.57+ and toytree v2+. The notebook has conda installation instructions at the top.

This is part of the new documentation that is under development. Please let me know if you encounter any problems.

Deren

isaacovercast commented 3 years ago

Works as of these versions: