[R] Extracting arrows from CCA plots

kirchman kirchman at udel.edu
Mon Jun 29 23:04:27 CEST 2015


I would like to extract all of the results from a CCA analysis done in the
vegan package so that I have complete control of how the results are
plotted.  

How can I get the coordinates (the "bipplot scores") for the arrows? I mean
the arrows as they appear in  

     plot(results.cca, display=c("sites", "bp"))     

where "results.cca" is the file resulting from the cca function.

The following extracts the "Biplot scores of constraints", which seems close
to what I want:
     
     scores (results.cca, display="bp")

It gives the ends of the arrows in the right direction (it seems) but the
arrows are not as long. I'm guessing that they have not been scaled, at
least as done with plot(results.cca, display=c("sites", "bp")).

If the arrows in plot(results.cca, display=c("sites", "bp")) cannot be
extracted, how can the biplot scores be scaled to reproduce the arrows?          




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