[R] NMDS Ordination Graphics Problem

[Michael Denslow]

Hi Trey,

On Mon, Apr 5, 2010 at 1:58 PM, Trey <trey3_79 at hotmail.com> wrote:
>
> Dr. Stevens,
>
> Hi, my name is Trey Scott, and I'm a grad student of Brian McCarthy's.  He
> referred me to you because of your expertise in handling complex R problems.
> We were hoping you could help us solve a nagging problem that is prohibiting
> me from producing graphicl output.
>
> Here is a simple mock-up of the matrix I'm using
>
>        a     b     c     d     e     f
> 1i      1     4     7     9     2     5
> 2i      12   17    6     2     3     7
> 3i       2    5     8     1     3     2
> 1c      0    2     4     7     2     1
> 2c      0    1     4     6     9     10
> 3c      13   15   19   10    8     9
>
> Where:  1i-3i are "infested" sites, and 1c-3c are "control sites".  A-F are
> species found at each site.  I have several of these ordinations to perform
> on different variables (BA, density, RIV, cover, etc..., all in different
> matrices).  I'm running NMDS (metaMDS) ordinations on each matrices, and
> producing ordination graphs for each cloud of points.  The problem I have is
> that I cannot devise a way to split the cloud of points into infested and
> control so that I can deduce any significant groupings.  A simple difference
> in symbols/color (Ex. gray triangles for infested, black circles for
> control) would do.  Also, I understand the use of pch/col/cex, I just need
> to apply them to the "split".
>
> So:
>
> +   How would I split these out in R after I run the metaMDS in vegan?
> +   What code would be necessary to bring this about?
>
> McCarthy and I are at the end of our preoverbial rope on this; nothing has
> worked.
> --

Was the solution I sent you the other day not helpful?
http://n4.nabble.com/How-to-split-data-for-NMDS-plots-td1751101.html#a1751290

If not perhaps you can explain what went wrong. Also you can post a
small example of your data using dput().
The best way that I have found to make ordination plots in vegan is to
make them in pieces.

Michael

-- 
Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
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