[R-sig-eco] plotting CCA results in vegan

[Jari Oksanen]

On Wed, 2010-03-10 at 17:33 +0000, L Quinn wrote:
> 
> Hello, I have two related questions:
> 
> 1.) Is there a way to use ordipointlabel to jitter species names on a CCA plot AND get biplot arrows to be displayed as well? I tried
> 
> ordipointlabel(cca.inv,display=c("species","bp"))
> 
> But biplot arrows came out as points instead (see attached file). 
> 
> 2.) Can I combine the output of the above (assuming there's a way to do it) with ordihull, so that I have jittered species names, biplot arrows, and convex hulls around factor centroids all on the same figure??
> 
> 
> A subset of my data is attached, and the model I'm using is this (with spp<-inv[22:37] and env<-inv[13:21]):
> 
> cca.inv<-cca(spp~LU+cond+pH+po4+no3,env)
> 
> Thank you in advance.

Functions like 'ordipointlabel' and 'orditkplot' really cannot handle
biplot arrows -- contributions to improve the code are welcome, and they
will be credited to the authors when incorporated in vegan.

The only thing that you can do here is something like this:

ordipointlabel(cca.inv,display="species")
text(cca.inv, dis = "bp")

This adds biplot arrows to the jittered plot of species that
ordipointlabel() made. If you are lucky, the arrow labels won't
overwrite species names. You can adjust arrow scaling by setting
argument arrow.mul to a suitable value (the default is to find the value
of arrow.mul so that the arrows nicely fill the figure frame):

text(cca.inv, dis = "bp", arrow.mul = 0.9)

HTH,

Jari Oksanen