R：在CCA图中添加双图箭头

Question

Starting with the following code:

library(vegan)
data(dune)
data(dune.env)
Ordination.model1 <- cca(dune ~ Management,dune.env)
plot1 <- plot(Ordination.model1, choices=c(1,2), scaling=1)

I get a plot with sites, species, centroids, and biplot arrows. I want to build up a plot with just the sites depicted by points, and the arrows with customized labels. So far, I have:

colvec <- c("red", "green", "blue")
plot(Ordination.model1, type="n", scaling=1)
with(dune.env, points(Ordination.model1, display ="sites", col=colvec[Use], scaling=1, pch =16, bg = colvec[Use]))

I am stuck as far as how to put the arrows in. Thanks in advance!

Answer 1

You can add arrows using text. I was not able to use your code as I kept getting errors, however here is a basic example that does what you want. I took it from R Help: CCA Plot Once you add text the arrows should show.

require(vegan) 
data(varespec) 
data(varechem)

vare.cca <- cca(varespec ~ ., data = varechem) 
plot(vare.cca, display = c("sites","species"), scaling = 3)
text(vare.cca, scaling = 3, display = "bp") 

Here is an example with the labels argument:

## S3 method for class 'cca':
text((x, display = "sites", labels, choices = c(1, 2),
scaling = "species", arrow.mul, head.arrow = 0.05, select, const,
axis.bp = TRUE, correlation = FALSE, hill = FALSE, ...))

labels: Optional text to be used instead of row names: Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis

Answer 2

I was able to rename the arrows: below is the full code.

library(vegan)
data(dune)
data(dune.env)
Ordination.model1 <- cca(dune ~ Management,dune.env)
summary(Ordination.model1)  # Lets you see the current biplot labels in the output.
colvec <- c("red", "green", "blue", "orange")   
plot(Ordination.model1, type="n", scaling=1)
with(dune.env, points(Ordination.model1, display ="sites", col=colvec[Management],scaling=1, pch =16, bg = colvec[Management]))
labl <- c("HF", "NM", "SF")   # new labels.  Need to be in the same order as the old biplot labels.
text(Ordination.model1, display="bp", scaling=1, labels=labl)