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point color in NMDS (vegan)

6 messages · Elaine Kuo, Baldwin, Jim -FS, Vít Syrovátka +1 more

Original
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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Vít Syrovátka
# 
Hi Elaine,

Maybe an easier way is to create a factor that will assign the islands 
into groups.
If you want to classify the islands manually, then it might be better 
to use Excel or another tabular processor.
Following your example:

groups<- factor(c('site2', 'site1', 'site1', 'site1', 'site2', 'site2', 
'site3', 'site3', 'site3'))
(supposing the islands are in alphabetical order)

And now one can use the factor as a subscript to pick the right colors:
points(island.NMDS, display = 'species', pch = '+', cex = 0.6, col= 
c('blue','green','red')[groups])

Note that this is a rather basic procedure, which you can learn from 
many documents related to R and easily accessible on the internet, e.g. 
see http://cran.r-project.org/other-docs.html

Cheers,
Vit


Dne 2013-08-19 03:59, Baldwin, Jim -FS napsal:
Gavin Simpson
# 
I have some posts on my blog that explain how to do this, ain the vein
of Vit's reply (indexing via a factor). This way is preferable to that
of Jim's brute-force way, but might seem somewhat magical if you
aren't familiar with indexing rules and how factors are handled.

Anyway, here is the link to the blog post with working examples:

http://www.fromthebottomoftheheap.net/2012/04/11/customising-vegans-ordination-plots/

Anjoy,

G
On 18 August 2013 17:02, Elaine Kuo <elaine.kuo.tw at gmail.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Gavin Simpson
    

    

      
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Yes, look at ?dune.env for what it contains.

G

        
On 19 August 2013 16:45, Elaine Kuo <elaine.kuo.tw at gmail.com> wrote: