Creating 2D PCoA plots

Hi QIIME community,

I am attempting to create 2D PCoA plots using QIIME2. I found instructions in a previous thread (below), but they seem to be outdated, as the below commands do not work in my version of QIIME. I am aware that it is possible to hide the axis 3 when viewing plots, but this does not change the appearance of the plot otherwise (including the proportion of the variance explained by each axis), which makes me think that a different technique is needed.

Thank you so much in advance!

Is it available to Make 2D PCoA Plots? - User Support - QIIME 2 Forum
qiime tools export --output-dir exported unweighted_unifrac_pcoa_results.qza -i exported/ordination.txt -m sample-metadata.tsv -o 2D-plots

Hello Daria,

In newer versions of Qiime2 (get the update here), you can make a standard Emperor plot, then toggle on 2D mode in the options:


Do you see this option inside your Emperor plots? What version of Qiime2 do you have installed?

Hi @dadaria ,
To add a few more solutions:

Exporting to R or Python:

You can also directly view PCoAs using Vega to make 2D and customize:

A separate python package, dokdo:

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