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

[Sarah Goslee]

Hi Barbara,

You don't provide a reproducible example or even tell us what
package/function you used to create your NMDS ordination, but you can
extract the coordinates, and use them plus your cover values to create
a bubble plot in several different ways, including symbols(), the pch
argument to base plotting functions, and ggplot().

There's a nice tutorial for one method here:
http://flowingdata.com/2010/11/23/how-to-make-bubble-charts/
but searching for "bubble plot in R" will get you many more options.

Sarah

On Tue, Mar 17, 2015 at 11:23 AM, 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
>
>


-- 
Sarah Goslee
http://www.functionaldiversity.org