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rplotvegan

Decluttering NMDS ordination plot

I have breeding bird assemblages data from quarry and calcareous grassland sites and want to display them in a nmds ordination plot, together with environmental parameters as vectors. How can I unclutter the species tags? I'm using the vegan package for ordination.

I have already reduced the number of species displayed using the ordiselect function from goeveg package. Tags are still overlapping but I don't want to further reduce species.

With the orditkplot function I can't seem to get a result that looks as good as I want it to in terms of aesthetics. I also failed to display only a subset of species when using that function.

ord.nmds <- metaMDS(species, trace=FALSE)
sel <- ordiselect(species, ord.nmds, ablim = 0.5, method = "axes", freq = TRUE)

ef <- envfit(ord.nmds ~ cgr + L_wdl + str + Hab_Div, env_var, permu=999)

grp <- factor(rep(c("GRASS", "QUARRY"), each = 14))
cols <- c("gray70","gray30")

plot(ord.nmds, type="n", xlim = c(-1.1, 1.1), ylim = c(-0.9,0.9))
points(ord.nmds, display = "sites", pch = 15, col = rep(cols, each = 14), cex=1)
text(ord.nmds, display = "species", col="black", cex=0.55, select = sel)
plot(ef, p.max = 0.05, col ="black", cex = 0.8)
legend(x = 0.6, y = 1.05, legend = tools::toTitleCase(levels(grp)), fill = cols, bty = "n", cex = 0.8)

So far, my plot looks like this: ordination graph

Solution

  • Have you tried using ordipointlabel() from vegan? I usually get quite good results with that. For this kind of plots it is also very helpful and recommendable to predefine the final size of the plot graphic by directly exporting it (e.g. with png() or svg() function). Just put the plottting functions inside a code like this and run the whole chunk:

    svg("ordinationdiagram.svg", width = 8, height = 6)

plot(ord.nmds, type = "n", ...)
points(ord.nmds, ...)
ordipointlabel(ord.nmds, add = T, ...)
legend(...)

dev.off()

    Until you run dev.off() all graphics operations will be put inside the svg-graphic.

    If you export in a vector format (like svg) you can load the graphic afterwards in any vector graphics editor (e.g. Inkscape) for manual re-arrangement of overlapping names (if it still occurs).