Alfa diversity indices for each sample

[SofiaDL (Sofia Diaz-Lundahl)]

Hello,

Concerning boxplots for alfa diversity and the command:
qiime diversity alpha-group-significance.

I am looking at my nice boxplots as I write this.
I am wondering if there is any way to generate boxplots which has two categorial variables (for example: healthy/infected on x-axis and sampletype1-sampletype2 indicated as boxes next to each other in diffrent color - This means 4 boxes in total) in qiime2.
If not, I am wondering how I can obtain the alfa indices from each sample (which is the foundation for the qiime2 boxplots that I am looking at) to take this further to for example R.

I have paired-end illumina Miseq-data of 162 (v3-v4) and use version 2021.8.
The question I am trying to look into is, if I can gain more/different information about disease x by sampletype 1 or 2.

Thank you very much.

[timanix (Timur Yergaliyev)]

Hello!
To get an image like this you will need to create it outside of qiime2 in R or Python.
You can find alpha diversity indices in the same files you used as input for alpha-group-significance command (alpha-metric_vector.qza). To export it as a .tsv table, please, check this tutorial.

[SofiaDL (Sofia Diaz-Lundahl)]

Thank you very much! I simply ran the following command on the shannon_vector.qza:

qiime tools export
--input-path feature-table.qza
--output-path exported-feature-table

The output file contained a tsv table with all samples and the Shannon index for each of them.

Happy happy