beta group significance: how to explain "n" 9under "group" in the group significance plots?

[lys (liu)]

Hi! I divided the samples into two groups, the first group is n=102, and the second group is n=75. After running the following code to calculate the core diversity, the beta diversity box plot is as follows. How does n explain?

qiime diversity core-metrics-phylogenetic
--i-phylogeny ./tree.qza
--i-table ./table.qza
--p-sampling-depth 12000
--m-metadata-file metadata.tsv
--output-dir core-metrics-results

Thanks！

[mverce (Marko Verce)]

Hi @lys,

The number is actually the number of distances between the group and itself or between the group and other groups.

Concretely, your left plot shows distances to LC.

Since the first group on the x-axis of this plot is LC, the first box plot represents the distances from LC to LC - all the distances within the group LC itself! This is calculated as 102*102/2 - 102/2 = 5151, or n(n-1)/2 in general. This is analogous to calculating the number of diagonals and sides in a polygon. Or how many handshakes occur in a room if everyone needs to shake hands with everyone else exactly once

The second group on the x-axis of this plot is NC, so this box plot represents distances between NC and LC, which is simply 75*102 = 7650. In other words, that is 102 distances for each of the 75 samples in NC.

And then the same for the other plot.

Cheers,
Marko