modify plot of metaMDS (package vegan)
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/ 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]]
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Eduard Sz?cs 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