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

[Roman Luštrik]

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:
>
>> 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
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
>
>
> --
> In God we trust, all others bring data.
>



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

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