Nice-looking PCoA with ellipsoid in Python

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1

Hi coomunity!

I have noticed there are soe topics in the forum regarding exporting PCoA results to R to generate publication-quality PCoA plots (with ellipsoids, which we often want).

I wonder - can someone help me with how to do it in matplotlib (/seaborn) as a python guy? Should I export the distance matrix or the PCoA artifact?
Would love to get some help from python users...

Happy new year!

2

Hello,

you export PCoA results and use this code to draw ellipses.

Good luck!
Valentyn

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Thanks!

The ax in that function is just the PCoA obtained from QIIME?

So let's say my workflow should be:

  • Creating PCoA in QIIME
  • exporting it to my python environmment
  • use it as ax in the function from that post
    ?

Thanks!

4

To clear up the confusion:

  • PCoA results are not a plot, they're numeric results of applying a method to a FeatureTable
  • You use 2 first dimensions of PCoA results to plot a regular scatterplot in matplotlib.
  • You operate on figure and ax objects from matplotlib.

Cheers
V

1 Like
5

Thanks for the clarification.
Is there a way to stratify ellipsoids between metadata column groups? (i.e different ellipsoids for different values in the metadata column)