Thanks

I wanna to add the species labels in a cca biplot
based on species and environment conditions (maybe sites are of less
relevance here).

1.
Gavin's suggestion worked but the dots previously displayed
using plot(birdrich.cca, scaling  =  -1) were gone. Pls advise how to retain
the dots.

2. orditorp
orditorp in vegan seems to fit my demand.
However, the axis seems to be changed after running the code below.
Please kindly explain why or recommend any references.

Thanks again.

# Now with orditorp and abbreviated species names
cnam <- make.cepnames(names(birdrich))
plot(birdrich.cca, dis="sp", type="n")
stems <- colSums(birdrich)
orditorp(birdrich.cca, "sp", label = cnam, priority=stems, pch="+",
pcol="grey")


Elaine





original code

rm(list=ls())
plot.new()

library(vegan)
library(MASS)


# input richness
birdrich <-read.csv("c:/migration/CCA_Mig_richness_20100814.csv",header=T,
row.names=1)

# input environment
birdenvi <-read.csv("c:/migration/CCA_Mig_envi_20100815.csv",header=T,
row.names=1)

birdrich.cca  <-  cca(birdrich  ~  .,  birdenvi)
birdrich.cca
plot(birdrich.cca, scaling  =  3, dis="sp", type="t")


On Sat, Aug 14, 2010 at 8:30 PM, Gavin Simpson <gavin.simpson@ucl.ac.uk>wrote:

> If you only have seven species, why not draw the label for the species
> (the names() component of your data) at the species score, rather than a
> colour?
>
> plot(OBJ, display = c("sites","species"), scaling = 3, type = "n")
> points(OBJ, display = "sites", scaling = 3, type = "p")
> points(OBJ, display = "species", scaling = 3, type = "t")
>
> Not tested, am away at the moment but heading home. If you are still
> having trouble (and I see now why you wanted matplot) then email back and
> I'll given a longer example illustrating who to build up plots by hand.
>
> Gavin
>
>
>

	[[alternative HTML version deleted]]

