Thanks Ed. I checked the website but found a small problem.
I ran the code below but an error jumped up. Please kindly advise what 'priSite' is here. Thank you. Elaine Error in orditorp(island.NMDS, display = "sites", priority = priSite, : object 'priSite' not found priSite <- diversity(dune, index = "invsimpson", MARGIN = 1) plot(ord, type = "n", scaling = 3) orditorp(ord, display = "sites", priority = priSite, scaling = scl, + col = "blue", cex = 1, pch = 19) On Fri, Aug 2, 2013 at 3:04 PM, Eduard Szöcs <szoe8...@uni-landau.de> wrote: > Hai Elaine, > > You can add the sites and species separately to your plot. > > > So first create an empty plot: > > require(vegan) > data(dune) > mds <- metaMDS(dune) > plot(mds, type = 'n') > > > > And then add the information you want (points, text, etc...): > > # species as symbols > points(mds, display = 'species', pch = '+', cex = 0.6) > > # sites as text > text(mds, display = 'sites') > > > See also Gavin Simpsons series on ordination plots: > http://www.**fromthebottomoftheheap.net/**2013/01/12/decluttering-** > ordination-plots-in-vegan-**part-1-ordilabel/<http://www.fromthebottomoftheheap.net/2013/01/12/decluttering-ordination-plots-in-vegan-part-1-ordilabel/> > > > Cheers, > > Eduard > > > > On 08/02/2013 08:46 AM, Elaine Kuo wrote: > >> Hello, >> >> I am running NMDS using metaMDS, based on a matrix. >> The matrix has rows as islands and columns as species ID. >> >> I generated a plot of the result of metaMDS using type="t". >> However, the island names are mostly covered by species ID and thus become >> unclear. >> >> Please kindly advise any method to show island names (row names) only >> for the plot of metaMDS. >> >> Thank you >> >> Elaine >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/r-sig-ecology<https://stat.ethz.ch/mailman/listinfo/r-sig-ecology> >> >> > > -- > Eduard Szöcs > Quantitative Landscape Ecology > Institute for Environmental Sciences > University Koblenz-Landau > Fortstrasse 7 > 76829 Landau > Germany > http://www.uni-koblenz-landau.**de/landau/fb7/**umweltwissenschaften/** > landscape-ecology/Staff/**eduardszoecs<http://www.uni-koblenz-landau.de/landau/fb7/umweltwissenschaften/landscape-ecology/Staff/eduardszoecs> > > ______________________________**_________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/**listinfo/r-sig-ecology<https://stat.ethz.ch/mailman/listinfo/r-sig-ecology> > [[alternative HTML version deleted]]
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