Referring to a recent posting on r-sig-eco mailing list I’ll add this example to theBioBucket:

library(vegan)

library(vegan)

data(dune)

sol <- metaMDS(dune)

# use ordipointlabel -

# here is an example where I added cex according to species frequencies:

plot(sol, type = "n")

cex.lab = colSums(dune > 0) / nrow(dune) + 1

col.lab = rgb(0.2, 0.5, 0.4, alpha = 0.6)

ordipointlabel(sol, displ = "sp", col = col.lab, cex = cex.lab)

# you could also use pointLabel() from maptools package:

library(maptools)

x = as.vector(sol$species[,1])

y = as.vector(sol$species[,2])

w = row.names(sol$species)

plot(sol, type = "n")

points(sol, displ = "species", cex = 1, pch = 4, col = 3)

pointLabel(x, y, w, col = col.lab, cex = cex.lab)

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