add alpha and beta diversity values to sample metadata

qiime2 / cancer-microbiome-intervention-tutorial

JupyterBook for QIIME 2 FAES January 2022 workshop

Other

11 stars 15 forks source link

add alpha and beta diversity values to sample metadata #2

Closed gregcaporaso closed 2 years ago

gregcaporaso commented 2 years ago

Specific values to add are: Faith PD, umap axes for weighted and unweighted unifrac, Shannon diversity, evenness, observed features.

This should happen prior to generating the Emperor plots with custom axes, so we can color by these data in those plots.

gregcaporaso commented 2 years ago

Assigning this to myself as I'm adding this now as part of some other work I'm doing.

thermokarst commented 2 years ago

Keep in mind, Usage API can't be used to generate metadata programmatically (like you couldn't run metadata tabulate then extract the merged MD file from the viz) - if you want to include those values as metadata you might be better off just running use.view_as_metadata + use.merge_metadata.