Hello,
I am trying to understand the contents of the txt file exported from pcoa qza. I have noticed that the first three Eigvals do not have the same values as seen in the axes of the emperor plot neither fo the proportion explained columns. One example is: axis1 in the emperor plot is 12.12% whereas eigval 1 is 0.010833523394799403 and proportion explained 1st column is 0.20952564621022243. I cannot find in the file any 12,12 for pc1 (axis1) and i dont understand how to interpret it. I would like to create a concentration ellipse for the points in pcoa emperor plot for the points ploted by the first two principal coordinates (PC1-2).
Thank you very much