Hello Gavin,

Thanks for mentioning your blog.

I would like what dune.env is, since it is very important to generate
different colors.
Is dune.env different from dune?
What will the dune.env be in the case of metaMDS instead of rda?

Thank you again

Elaine


On Tue, Aug 20, 2013 at 12:08 AM, Gavin Simpson <ucfagls@gmail.com> wrote:

> 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@gmail.com> wrote:
> > 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')
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-ecology mailing list
> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
>
> --
> Gavin Simpson, PhD
>

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