[R-sig-eco] Fwd: metaMDS - avoid species overlap in plots

[Gavin Simpson]

On Mon, 2012-06-25 at 16:46 +0200, Kay Cichini wrote:
> Hi!
> 
> library(vegan)
> data(dune)
> sol <- metaMDS(dune)
> 
> # use argument air! see ?orditorp:
> plot(sol, type = "n")
> orditorp(sol, displ = "sp", air = 1)
> 
> 
> # or use pointLabel() from maptools package. this should avoid overplotting
> of text -

To come to this late, but we have ordipointlabel() in vegan, which is
modelled on pointLabel() and aims to do the same thing without having to
rely upon the spatial stack. It also knows about ordination objects in
vegan.

G

> # here is an example where I added cex according to species frequencies.
> library(maptools)
> x = as.vector(sol$species[,1])
> y = as.vector(sol$species[,2])
> w = row.names(sol$species)
> cex.lab = colSums(dune > 0) / nrow(dune) + 1
> col.lab = rgb(0.2, 0.5, 0.4, alpha = 0.6)
> 
> plot(sol, type = "n")
> points(sol, displ = "species", cex = 1, pch = 4, col = 3)
> pointLabel(x, y, w, col = col.lab, cex = cex.lab)
> 
> 
> HTH,
> Kay
> 
> 
> 2012/6/25 Gian Maria Niccol Benucci <gian.benucci at gmail.com>
> 
> > Hi community,
> >
> > Very simple question. How to avoid overlap plot of species in a metaMDS()
> > diagram?
> >
> > I used this command...
> >
> > > text(metaMDS_new2, display=c("species"), cex=0.6)
> >
> > but some species are plotted one over the other and is not simple to read
> > the diagram.
> >
> > Thanks for helping,
> >
> > --
> > Gian
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> >
> 
> 	[[alternative HTML version deleted]]
> 
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