[R-sig-eco] Plot NMDS with size of the points related to abundance

[Roman Luštrik]

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 <bub14 at psu.edu>
wrote:

> 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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> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>



-- 
In God we trust, all others bring data.

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