Dear Roman, Sara and Phil,
Thanks so much for your help!! After some playing around with your different
options, I got the graph I was looking for (attached).
I wasn't using the right words to look for help.
Thanks a lot!!
Barbara
----- Original Message -----
From: "Roman Luštrik" <roman.lust...@gmail.com>
To: "Barbara Baraibar Padro" <bu...@psu.edu>
Cc: r-sig-ecology@r-project.org
Sent: Tuesday, March 17, 2015 11:42:31 AM
Subject: Re: [R-sig-eco] Plot NMDS with size of the points related to abundance
After clicking send I remembered that you might want to scale circle sizes
according to their area, not radius (which is the default to draw). Then I went
to see the link Sarah posted and it deals with this, too (great minds think
alike? :) ).
Cheers,
Roman
On Tue, Mar 17, 2015 at 4:39 PM, Roman Luštrik < roman.lust...@gmail.com >
wrote:
Assuming you're working with metaMDS from vegan, it's trivial to extract NMDS
scores, add some variable and plot the data. The following code would be easy
to translate into a generic function.
library(vegan)
data(dune)
sol <- metaMDS(dune)
# add some variable that will correspond to size of points
spc <- as.data.frame(cbind(sol$species, mysize = runif(nrow(sol$species))))
pts <- as.data.frame(sol$points)
library(ggplot2)
ggplot(spc, aes(x = MDS1, y = MDS2)) +
theme_bw() +
geom_point(aes(size = mysize), pch = 1) +
geom_point(data = pts, color = "red")
Cheers,
Roman
On Tue, Mar 17, 2015 at 4:23 PM, Barbara Baraibar Padro < bu...@psu.edu >
wrote:
<blockquote>
Hello list,
I am analyzing species composition of weeds in 12 cover crop treatments and a
fallow plot. I have been using nmds and got good results and no problems with
it (although after some fighting!). My data is a matrix of biomass values
sorted by species. Now I'd like to know which of my species are contributing
with more biomass to the community in each treatment, that is, I'd like to
create a graph such as the one that you get from the option "plot (nmds_model,
type="t", display=c("species")) but instead of getting just the names of the
species, I'd like to see dots of different sizes that would refer to the
abundance of each of the species, is that possible at all? I know you can do it
with CANOCO but wanted to ask if there is a way to do it in R.
I have searched the internet and found something that looks like what I want to
do (enclosed to the mail) but haven't found the way to do it.
I have already done an Indicator Species Analysis with the multipatt function.
That gives me information about the species that are related to some treatments
but here I'm just looking for the species with more and less biomass in each
treatment.
Thank you very much!!
Barbara
--
Barbara Baraibar
Post-doctoral scholar - Weed and Applied Plant Ecology
Plant Sciences Department
Penn State University
University Park, Pennsylvania 16802
web-site: http://www.weedecologypsu.com
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--
In God we trust, all others bring data.
</blockquote>
--
In God we trust, all others bring data.
--
Barbara Baraibar
Post-doctoral scholar - Weed and Applied Plant Ecology
Plant Sciences Department
Penn State University
University Park, Pennsylvania 16802
web-site:http://www.weedecologypsu.com
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