[R-sig-eco] RDA with only dummy variable in environmental matrix

[amelie_can]

Hello all, 

I want to do a redundancy analysis (rda). My response matrix is filled with
species abundances (68 sites x 15 species). My environmental matrix (68
sitex x 3 classes) is only filled with a dummy variable with three classes
(NAT, NR, REST). Since dummy variables are linearly dependant, the variable
REST is automatically removed but this does not result in any information
loss as if a sites is not associated with NAT nor NR, it necessarily will be
associated to REST. But I have three problems :  

1)	For the moment, R only gives me a plot where NAT and NR are showed. I
need to be able to show REST as well. 
2)	My dummy variables are showed as arrows that are pointing to their
centroid but I would like to only have the centroid (showed as any kind of
shape). 
3)	How can I add the species names (currently they are only represented by
red cross). I tried the text function, but I could only add my sites names
and not my species names. 

Following is an R example of my problem that you can easily run : 

library(vegan)
mat.sp = matrix(c(40, 20, 37, 49, 52, 34, 35, 87, 90, 45, 49, 52, 34, 35,
87,5,39,99,8,45),nrow = 4, ncol=5, dimnames = list(c("sites1", "sites2",
"sites3","sites4"),c("sp1", "sp2", "sp3", "sp4", "sp5")))
mat.env = matrix(c(1,1,0,0,0,0,1,0,0,0,0,1),4,3, dimnames = list(c("sites1",
"sites2", "sites3","sites4"),c("NAT", "NR", "REST")))

rda = rda (mat.sp,mat.env)
summary(rda)
plot(rda, scaling=1, type="points")


Thank you for any kind of assistance! 

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