# Generate BoxPlot for Alpha Diversity Analysis

**URL:** <https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364>\
**Category:** User Support\
**Tags:** boxplots\
**Created:** [April 6, 2020, 1:16am UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364 "2020-04-06T01:16:16Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![fhermanto96](https://forum.qiime2.org/user_avatar/forum.qiime2.org/fhermanto96/32/7333_2.png) [@fhermanto96](https://forum.qiime2.org/u/fhermanto96)\
**Post date:** [April 6, 2020, 1:16am UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364/1 "2020-04-06T01:16:16Z")

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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.

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**Author:** ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\
**Post date:** [April 6, 2020, 1:17pm UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364/2 "2020-04-06T13:17:22Z")

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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](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

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**Author:** ![fhermanto96](https://forum.qiime2.org/user_avatar/forum.qiime2.org/fhermanto96/32/7333_2.png) [@fhermanto96](https://forum.qiime2.org/u/fhermanto96)\
**Post date:** [April 6, 2020, 3:29pm UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364/3 "2020-04-06T15:29:32Z")

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

 ![Chao Boxplot](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/1/10ee3f4ae54dfdaf2c5745fc6f31ca904bdd2d79.jpeg)  
Because there are only 3 options in alpha rarefaction metric such as faith pd, shannon, and observed otus.  
Thank you for your help

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**Author:** ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\
**Post date:** [April 6, 2020, 8:40pm UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364/6 "2020-04-06T20:40:19Z")

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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/](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

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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\
**Post date:** [April 6, 2020, 9:25pm UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364/7 "2020-04-06T21:25:42Z")

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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.

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**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\
**Post date:** [May 8, 2020, 3:25am UTC](https://forum.qiime2.org/t/generate-boxplot-for-alpha-diversity-analysis/14364/8 "2020-05-08T03:25:45Z")

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