Adding library sizes per group info in feature table interactive plots


On the topic of deciding whether to rarefy or use some other method of normalization, one recommendation recently stated in Knight et al. 2017:

Prior to analysis, researchers should assess the difference in average library size between groups. If large variability in library sizes across samples is observed, then rarefying is useful as a method of normalization.

I know there’s a lot more to this than just that but this would be a useful feature to add to the interactive plots of feature-table.qzv
Just being able to visually see the average library sizes would be a good starting point!

Hi @Mehrbod_Estaki,
Thanks for posting! This feature is already available in alpha-rarefaction. That visualizer performs alpha rarefaction at multiple depths for each samples, and supports grouping samples by metadata column values. Please give that method a try and let us know if you have additional needs that are not covered by that action, or any questions!

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Aha. This is perfect/exactly what I was referring to. Thanks @Nicholas_Bokulich ! Having used core-metrics before I totally didn’t realize this was available as a stand alone function. I wonder if it might be a useful addition to the core-metrics defaults since these figures are always submitted along with papers anyways, at least as supplementary material. Though on the other hand it would require a bunch of new inputs and parameters and take away from the simplicity of core-metrics…better just keep as is :stuck_out_tongue: