How to use pcoa-biplot

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Hi @suzukik!

Great question, there’s a few steps to this:

  1. Use qiime feature-table relative-frequency to generate the table for pcoa-biplot. You need this to be based on the rarefied table you are using for your beta and pcoa steps. You can use provenance to prove that you’re using the same rarefied table in both relative-frequency and pcoa :slight_smile:

  2. Run pcoa-biplot with that table and an existing PCoAResults (generated by your previous pcoa).

  3. Use qiime emperor biplot with --m-feature-metadata-file set to your FeatureData[Taxonomy] artifact. This will let you color the biplot vectors by taxonomy (it’s at the bottom of the normal color dropdown in the Emperor UI).

Abstractly the pipeline looks like this:

`rarefy` ---> `beta` -> `pcoa` -> `pcoa-biplot` -> `emperor biplot`
       \-> `relative-frequency`--/                /
                                   taxonomy.qza -/
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