i have problem interpreting PcoA. PcoA ordination plot using unifrac distances shows the variance on both the axis. what does variance means in these plots? why variance are taken on both axis?

Hello Khadija,

Welcome to the forums!

In a PCoA plot, the axes are made up to explain the maximum variance between samples.

The mathematical name for the 'vector of maximum variance' is Eigenvector.

Here's a less technical explanation with great examples:

https://occamstypewriter.org/boboh/2012/01/17/pca_and_pcoa_explained/

Does that help? You can post pictures of your own PCoA plots or ones from that post to answer follow-up questions.

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Thanks. link was very helpful to understand the general concept of PcoA.