gneiss balance-taxonomy

User Support
1

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

2

Hello Nate,

Welcome to the forums!

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

:balance_scale: -> :bird: :dango:
GitHub - biocore/songbird: Vanilla regression methods for microbiome differential abundance analysis
GitHub - biocore/qurro: Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

Colin

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3

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

4

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

1 Like
5

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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