I have a phylogenetic tree.
Each branch ends have samples (s1, s2, ~ s16).
What I want to do is, I want to make PCA analysis plot for each sample.
First I thought each sample has each lineage (expressed in image as (1,1,1,1)~(2,2,2,2)).
So with that coordinates, I can do PCA analysis.
But on the second thought, the difference between (1,1,1,1) and (1,1,1,2) is much less than that of (1,1,1,1) and (2,1,1,1), but in the analysis, the difference between them will be same.
I am not sure if this kind of approach is suitable for making a PCA plot with a phylogenetic tree.
How can I make this work?