Hi @cmartino!
After playing around with the --p-min-feature-frequency and --p-n-components, I found that increasing the rank to 6 or using auto-rpca actually helps a bit but setting the minimal frequency to 10 didn't help.
rpca-biplot-autorpca.qzv (1.2 MB) rpca-biplot-minFreq10.qzv (1.2 MB) rpca-biplot-ncomp6.qzv (1.2 MB)
Do you think the plots with an increased number of ranks look normal?