How to represent the PCoA in 2 dimensions and how to add ellipses in the figure to differenciate between groups ?

[M_F (Meriem)]

Hello,

I created PCOA plot to investigate beta diversity metric using Emperor tool. I obtained 3D plot. I would like to generate 2D plot and to add ellipses in the figure to differenciate between groups for example affected versus controls. which command can i use to achieve this task ?

Thank you for your help

[Nicholas_Bokulich]

Hi @M_F ,
Emperor does not have an option to add ellipsoids, though it does have a 2D display option.

Other options for 2D + ellipsoids (using python or R) have been discussed here:

PCoA plots with confidence ellipsoids

I need to render 2D PCoA plots with confidence ellipsoids. After going through help forum posts here I found others looking to do the same and roadmap plans from 2017 to add this functionality--it seemed that this had been added. I generated a jackknifed Emperor plot using "qiime diversity beta-rarefaction", which I had hoped would have confidence ellipsoids, but it did not, so I exported the data from this visualization.qzv file using "qiime tools export" and then tried to render the 2D plot us…

[M_F (Meriem)]

@Nicholas_Bokulich Thanks