Hi,

Thank you very much for your help!

G.



On 19 July 2012 18:13, Gavin Simpson <gavin.simpson@ucl.ac.uk> wrote:

> 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@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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> > >
> >
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>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
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