merge low abundant phyla in taxa barplots

[ja.morillo (Jose A. Morillo)]

Dear qiimers:

Is it possible -using Qiime2- to collapse all “low abundant taxa” (for example phyla <1%) into the same category? with the aim of a easier graphical visualization, leaving only 7-8 colours in the figs, accounting for the major taxa. Showing one category like “Minor phyla” to represent the sum of all “minor taxa” frequencies.

For example, in the Fig1. of qiime2-paper (https://peerj.com/preprints/27295/) all minor phyla are grouped in the category “Other low abundant taxa”.

thanks!

[Nicholas_Bokulich]

@ja.morillo

Is it possible -using Qiime2- to collapse all “low abundant taxa” (for example phyla <1%) into the same category?

Not currently, but this has been requested and discussed a few times on this forum and we agree it would be a useful feature (it is more challenging to implement, though, than it sounds!)

@ja.morillo

For example, in the Fig1. of qiime2-paper (QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science [PeerJ Preprints]) all minor phyla are grouped in the category “Other low abundant taxa”.

We did not actually cluster those taxa — because that option does not yet exist or we would certainly share that power with you! — we just removed them from the plot. You can click on individual taxa in the legend to display only those taxa. So we selected the top N most abundant so that the remaining low-abundance taxa were not visible and added the white color bar to the legend to indicate this (since the missing taxa are represented as white space in the barchart). Feel free to follow this crude but effective approach until we get a chance to add this feature to the barchart visualization.

Thanks for your suggestion!

[ja.morillo (Jose A. Morillo)]

Ha, good idea! For informative purposes it is what we need. But yes, it would be great to have that funcionality in future versions of q2. Then the figuers will be 100% optimized for publications etc.
Many thanks for the feedback!
Jose