Beta and alpha diversity plot

Q1)How can I generate a beta diversity and alpha diversity plot at species level in qiime2.
The default bray curtis emperor plot I generated using qiime2 is as follow:

The next one i generated using a online software

Looking at both the emperor plot i generated shows clustering of two groups together and doesnt tell me p value. The other one tells me there is significant difference in two groups ( looking at the p value).

Q2) How can i generate b diversity plot with p value in qiiime2?

Thank you for your time and paitence.


Usually, with 16S amplicon data, it is recommended to work with ASVs rather than taxonomy-level tables. But if needed, you can collapse your feature table to the species level (7 with most databases) and use the collapsed table as core-metrics input to get beta diversity distances and PCoA plot (emperor qzv file). Then, the distance_matrix.qza file can be used to perform PERMANOVA test or Adonis.
I hope it helps.



thanks for the guidance. Just one last thing, I did the beta group significance test and got the following result.

So the p value is significant, right! Because below the plot there is another table :slight_smile:

the p value is not significant here.

I should be considering the p value of the top table??

Thank you.

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Your test is borderline - PERMANOVA will yield slightly different results every time you run it unless the random state is indicated. Your results are on the border, so when plugin run it for the first time (upper table), you get the significant result and in pairwise mode (lower table) insignificant. In theory, you don't need a lower table with only 2 groups, but be aware that p-value is on the very edge of significance.


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