I have a question about PLS and its representation. According to mixOmics page (Chapter 5 Projection to Latent Structure (PLS) | mixOmics vignette) we can plot X scores, Y scores (two separated plots) or an average between both components rep.space = ‘XY-variate’.
My question is : Is there a particular interest to plot an average between X and Y scores? or it is just a way ti display data? Do average between X and Y scores have an implication in some further analysis? i.e. prediction? .
When I plot X scores and X-Y scores there are a huge difference. X-Y scores plot separates even more the groups (see exemple bellow).
Thanks very much.
X scores plot