I assume that the dataset "island" is yours so I've made that equivalent to an
example dataset in vegan named "dune". Below is a rather brute force way to
assign colors.
library(MASS)
library(vegan)
data(dune)
island = dune
island.NMDS <- metaMDS(island,k=2, distfun = betadiver,
distance = "sim", trymax=100, zerodist="add")
plot(island.NMDS, type = "n")
# species as symbols
col = rep("black",dim(island)[2])
c = colnames(island)
col[c=="Belper" | c=="Elepal" | c=="Viclat" | c=="Brarut"] = "blue"
col[c=="Airpra" | c=="Rumace" | c=="Potpal" | c=="Tripra"] = "red"
col[c=="Sagpro" | c=="Agrsto" | c=="Hyprad" | c=="Poapra"] = "green"
points(island.NMDS, display = 'species', pch = '+', cex = 0.6, col=col)
# sites as text
col = rep("black",dim(island)[1])
r = rownames(island)
col[r=="2" | r=="17" | r=="18"] = "blue"
col[r=="3" | r=="10" | r=="20"] = "red"
text(island.NMDS, display = 'sites',col=col)
Jim Baldwin
USDA Forest Service
-----Original Message-----
From: r-sig-ecology-boun...@r-project.org
[mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Elaine Kuo
Sent: Sunday, August 18, 2013 4:02 PM
To: <r-sig-ecology@r-project.org>
Subject: [R-sig-eco] point color in NMDS (vegan)
Dear List,
This is Elaine.
I am using metaMDS in package vegan to plot NMDS.
However, I want to draw the points using different colors according to island
sites.
For example:
island site 1: island B, C, D => blue
island site 2: island A, E, F => green
island site 3: island G, H, J => red
Please kindly advise how to modify the following code to classify the sites by
colors.
Thank you
Elaine
library(MASS)
library(vegan)
island.NMDS <- metaMDS(island,k=2, distfun = betadiver, distance =
"sim",trymax=100,zerodist="add")
plot(island.NMDS, type = "n")
# species as symbols
points(island.NMDS, display = 'species', pch = '+', cex = 0.6)
# sites as text
text(island.NMDS, display = 'sites')
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