• What do the components called “variates” refer to?

The variates are the linear combinations of the initial variables, also called scores elsewhere. The function plotIndiv() uses these values to plot the individuals.

  • How should I refer to the various “association” measures handled in mixOmics?

The term canonical correlation is reserved for the correlation between the variates of each set of variables and not to refer to associations (correlations) between variables.
In fact, the associations showed in the networks are a kind of correlation calculated from the projections of variables on the “intermediate” space restricted to the first components of the Canonical Analysis