Re: [R-sig-eco] Fwd: metaMDS - avoid species overlap in plots
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
Re: [R-sig-eco] Fwd: metaMDS - avoid species overlap in plots
Hi, Thank you very much for your help! G. On 19 July 2012 18:13, Gavin Simpson gavin.simp...@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.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 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Fwd: metaMDS - avoid species overlap in plots
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.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
