[R] Vegan plotting- color help

[Gavin Simpson]

On Thu, 2008-04-10 at 23:34 -0400, stephen sefick wrote:
> I have looked all over the internet for being able to color sites
> differently in a plot of an MDS (metaMDS)-  I would like to color the
> different sites in the ordination plot (plot or ordiplot).  I have set
> the matrix up so that my site code is 1 .... 296 (first column).   is
> there a way to make 1-23 blue, 24-40 red etc.
> thanks
> 
> Stephen
> 

This requires a bit of manipulation. Using the example from ?metaMDS

data(dune)
require(MASS)
sol <- metaMDS(dune)

shrink <- FALSE ## see argument shrink in ?metaMDS

## these are the plotting colours, must be a vector of the same
## length (nrow) as the input data, here 20
cols <- rep(c("red","blue","green","black"), each = 5)

## get species and site scores
spp.sc <- scores(sol, display = "species", shrink = shrink)
site.sc <- scores(sol, display = "sites")

## work out the ranges
ylim <- range(spp.sc[,2], site.sc[,2])
xlim <- range(spp.sc[,1], site.sc[,1])

## set-up the plotting region
plot(site.sc, xlim = xlim, ylim = ylim, type = "n", asp = 1,
     xlab = "NMDS1", ylab = "NMDS2")

## add the row
text(site.sc, col = cols, labels = rownames(dune), cex = 0.8)
text(spp.sc, labels = colnames(dune), cex = 0.8)

is one way to do this,

HTH

G

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