How to plot PCA output?

-----Original Message-----
I avoid the biplot at all costs, because IMHO it violates one 
of the tenets of good graphic design:  It has two entirely 
different scales on axes.  These are maximally confusing to 
the end-user.  So I never use it.

I think you're being unnecessarily restrictive there. The confusion that arises when using multiple scales in the same graphical dimension arises from a tendency to read distances and locations on the wrong scale. In a biplot, the PC's have essentially no intuitive physical interpretation (by which I mean a 1:1 mapping onto an identifiable variable) so this doesn't matter much even if it happens (in fact you  cold probably lose the scales entirely in a biplot without compromising its interpretation much). And the alternative - sticking rigidly to the 'one axis per dimension' rule and to plot them with the _same_ scales - often leads to unreadable plots: invisibly tiny arrows or an invisibly tiny cloud of data points. 

But having indicated that I don't see a biplot's multiple scales as particularly likely to confuse or mislead, I'm always interested in alternatives. The interesting question is 'given the same objective - a qualitative indication of which variables have most influenced the location of particular data points (or vice versa) and in which general direction - what do you suggest instead?'

Steve Ellison

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