gneiss balance-taxonomy

Hello, I am using gneiss to determine taxonomy differentials between treatments with the balance-taxonomy command. It works well but I am receiving the following warning:
balance-taxonomy is deprecated and will be removed in a future version of this plugin.
Can you please tell me why this method is being discontinued, and what will replace it?
Thank you,
Nate

Hello Nate,

Welcome to the forums!

The gneiss and balance-taxonomy developer, @mortonjt, now recommends newer, better methods.

:balance_scale: -> :bird: :dango:
https://github.com/biocore/songbird
https://github.com/biocore/qurro

Colin

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Thank you very much for your reply, Colin,
I am working on implementing songbird and qurro now.
As a follow up although pretty unrelated:
Is there any way to label the taxa ratios visualized in the gneiss heatmap output?
Thanks again,
Nate

Hey Nate,

I think Jamie was recommending exporting the resulting data then graphing it using another program, say Python or R. You could label anything with those programs! :bar_chart:

Colin

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Exactly. It’s a bit outside our current capability to enable full customizability of the heatmap output from the command line.

But there is a python function in gneiss that you can call.

And we do have tutorials for this
https://biocore.github.io/gneiss/docs/v0.4.0/tutorials/python/cfs-python-tutorial.html

But also checkout ggtree and ape in R. They have quite a bit more functionality when it comes down to tree visualizations. Some cool examples can be found here: https://yulab-smu.github.io/treedata-book/chapter7.html

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