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.
I think this a part of the Moving Pictures Tutorial. Check out this section:
alpha-rarefaction.qzv output should include the Choa1 boxplots you are looking for.
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
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
You can see all the settings for
qiime diversity alpha in the docs:
Let me know what command you choose to run and if you are able to make the graph!
Hi @fhermanto96, I just wanted to clarify something @colinbrislawn wrote:
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.
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