On orthogonality of components from PCA

Dear Jalview community,

I have used the PCA option on a moderately large alignment (approx. 150 sequences, many of which are very similar). The 3D viewer shows three axes which I assume indicate the directions of the currently selected principal components. Clusters are clearly visible, but what I find irritating is that the axes are not mutually orthogonal. They do appear orthogonal when using the tutorial sequences, and this is still the case when I use my sequences unaligned, but not after proper alignment.
Is this an expected effect for an alignment of (at least cluster-wise) highly conserved sequences? And if yes, which coordinate system do the “transformed points” refer to? Would it be appropriate to simply plot those coordinates in an orthogonal frame?

Thanks a lot for any pointer!

Best regards,

Hi there Oliver.

I think what you are seeing is a bug in the PCA viewer’s axis rendering code, which seems to be applying a scaling to the axes according to the extent of the projected sequence points in the first or second chosen component. The problem manifests most severely when there is low diversity:

Top: Jalview - showing different length Axes. Bottom: Patched axis rendering code.

I’ve raised this as a bug JAL-4045 and the patch will be available via Jalview Test and the patch release.