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

[Barbara Baraibar Padro]

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.lustrik at gmail.com> 
To: "Barbara Baraibar Padro" <bub14 at psu.edu> 
Cc: r-sig-ecology at 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.lustrik at 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 < bub14 at 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