Help with EIGENSOFT's SmartPCA

Question

[Junaid]

Hi everyone,

I’ve been experimenting with SmartPCA (EIGENSOFT), but I’m having trouble with some of the steps. I have a dataset with both ancient and modern samples, and I’m trying to figure out how to:

Plot the modern samples first, then project the ancients onto that (or vice versa).

I've tried messing around with the poplistname flag.

If anyone has experience with this and can guide me through the process (especially with parameter setup and projections), I’d really appreciate the help!