The `plot.procrustes' function really should be more user-friendly and flexible. You should contact its author and ask for amendments.
I honestly though my problem was too trival to bother the author in person, and I thought that getting an answer would leave it in a public database, as future reference. I hope I did not cause undue inconvenience.
However, you have access to the internal results of the Procrustes analysis, and you can produce any kind of plots with them. The needed matrices are stored as items mod.pro$X and mod.pro$Yrot in your result object mod.pro. The following should do what you asked for: plot(mod.pro$X, asp=1, pch=1) points(mod.pro$Yrot, pch=2) segments(mod.pro$X[,1], mod.pro$X[,2], mod.pro$Yrot[,1], mod.pro$Yrot[,2])
The above solves my problem. Thanks for your help. Best regards, Federico Calboli
================================= Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 251 208 f.calboli at ucl.ac.uk