Core diversity analysis

Good afternoon, I was curious if there was some guidance on how to better pull out the specific taxa that describe the variance described in the PcoA plots within Beta-diversity and/or those that explain differences in alpha-diversity (Chao1 specifically). Perhaps this is obvious, but as someone who as usually just done a broad alpha and beta-diversity approach trying to dig deeper into these I would appreciate any guidance.

Thank you!

Hello Hannah,

Yes! You are looking for a biplot. Basically, this ordination plots both the samples, and the taxonomy common within those samples at the same time, so you can which taxa are strongest in which parts of your ordination. They look like this:

See this pull request, in which @yoshiki demos how to make a biplot in emperor.

The real question is, is there a tutorial for making biplots using emperor?



@hcunnin6 @colinbrislawn,
The pull request Colin linked to is for emperor — emperor can now generate biplots. However, this functionality has not yet made it over to QIIME 2 because some other lesser obstacles remain; but we have an open issue to track this so we hope to add it in an upcoming release! We will report back here when this happens. :radio:


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