[R-sig-eco] point color in NMDS (vegan)

[Baldwin, Jim -FS]

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-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Elaine Kuo
Sent: Sunday, August 18, 2013 4:02 PM
To: <r-sig-ecology at 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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