Generate BoxPlot for Alpha Diversity Analysis

[fhermanto96 (Feri Hermanto)]

Dear experts,

I work on 2019.10 version and I just want to get a box plot to visualize my alpha diversity analysis, but unfortunately as long as I try I can't found some post which explain how to generate box plot for alpha diversity visualization (for instance, I want to visualize Chao1 parameter result using box plot). Is it possible to get it? Do I missed some posts which explain about that?
Thank you for your help and kind attention.

[colinbrislawn (Colin J Brislawn)]

Good morning,

I think this a part of the Moving Pictures Tutorial. Check out this section:
https://docs.qiime2.org/2020.2/tutorials/moving-pictures/#alpha-rarefaction-plotting

The alpha-rarefaction.qzv output should include the Choa1 boxplots you are looking for.

Colin

[fhermanto96 (Feri Hermanto)]

Dear @colinbrislawn,
Is it possible to get something like this?

Because there are only 3 options in alpha rarefaction metric such as faith pd, shannon, and observed otus.
Thank you for your help

[colinbrislawn (Colin J Brislawn)]

Hello @fhermanto96,

Yes! I think that looks like the output of qiime diversity alpha-group-significance.

You can use qiime diversity alpha --p-metric 'chao1' to calculate Chao1 alpha diversity values, then use that as the input to the diversity plugin.

You can see all the settings for qiime diversity alpha in the docs:
https://docs.qiime2.org/2020.2/plugins/available/diversity/alpha/

Let me know what command you choose to run and if you are able to make the graph!

Colin

[thermokarst]

Hi @fhermanto96, I just wanted to clarify something @colinbrislawn wrote:

@colinbrislawn

then use that as the input to the diversity plugin.

Specifically, if you want to perform a group comparison of these results, alpha running qiime diversity alpha you can run qiime diversity alpha-group-significance, to generate interactive box plots of the group diversity distributions.