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 -
# 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 Niccolò Benucci <gian.benucci@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
>
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