on NMDS graphics

Hi,

I have used Vegan to construct an NMDS ordination plot. I plotted sites of
three forest types with the site number in it. My reviewer has asked me to
use different symbols for each of the forest types.
Can anyone send me how I can do this in R in simple steps. I have used the
options like ordiplot, sel and pl syntaxes that are not working for the
question that I asked for.

Best,
Sinu

The commonly used procedure is to set up a vector of colours or symbols
you want to use, one per group. Then set up a variable that contains the
group identifier, as a factor. We then index the colours or symbols
vector with our grouping factor to produce the correct length and
specification of parameters col or pch for the plot.

Here is an example:

require(vegan)
data(varespec)

## Ordination
ord <- metaMDS(varespec)

## Dummy forest types, indicator
## stored as a factor
ftypes <- gl(3, nrow(varespec)/3)
## or via something like
ftypes <- factor(rep(paste("Type", 1:3), each = 8))

## plot the data
plot(ord, display = "sites", type = "n")

## add the points coloured by ftype
## 1) specify colours wanted for groups
vcols <- c("red","green","blue")
## or 1) specify symbols for groups
vpch <- c(16,17,18)
## 2) add points using ftypes to index vcols
points(ord, col = vcols[ftypes], pch = vpch[ftypes])

To see what is being done, try:

vcols[ftypes]

[1] "red"   "red"   "red"   "red"   "red"   "red"   "red"   "red"   "green"
[10] "green" "green" "green" "green" "green" "green" "green" "blue"  "blue" 
[19] "blue"  "blue"  "blue"  "blue"  "blue"  "blue"

HTH

G

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