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.benu...@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]] > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology