问题
I'm using the vegan package to plot a NMDS in R analyzing community similarities. This is based on a community matrix that includes different treatments:
NMDS=metaMDS(community_matrix,k=2,trymax=100)
plot(NMDS)
Could anybody tell me how to I can draw arrows to show how individual species respond to treatments?
回答1:
Arrows would be the wrong interpretation in such a plot; there is no reason whatsoever to assume that in a plot best preserving rank-order dissimilarity of samples the species respond linearly in that space.
We add species as they would be in a CA, as a weighted average of the sample scores, possibly expanded.
You can add species vectors by projecting them into the space using envfit(), by passing it the NMDS object and the species data, community_matrix in your case. If you have a lot of species, I would probably dispense with the permutations, unless you really need such an indication of significance.
来源：https://stackoverflow.com/questions/16732954/including-arrows-in-nmds-plot-in-r-vegan-package