[R-sig-eco] modify plot of metaMDS (package vegan)

[Eduard Szöcs]

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
>
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>
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-- 
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