plot.vf: Plots fitted vectors onto an ordination diagram

Description

Add vector fitting arrows to an existing ordination plot.

Usage

# S3 method for vf
plot(x, pval = NULL, r = NULL, cex = 0.8, ascale = 0.9, ...)

Value

Adds arrows to an existing ordination plot. Only arrows with a p-value less than pval are added. By default, all variables are shown.

Arguments

x: an object of S3 class vf, created by vf()
pval: optional, critical p-value for choosing variables to plot
r: optional, minimum Mantel r for choosing variables to plot
cex: text size
ascale: optional, proportion of plot area to use when calculating arrow length
...: optional, other graphics parameters

Author

Sarah Goslee

Examples

Run this code


# Example of multivariate analysis using built-in iris dataset
data(iris)
iris.d <- dist(iris[,1:4])

### nmds() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.nmds <- nmds(iris.d, nits=20, mindim=1, maxdim=4)
### save(iris.nmds, file="ecodist/data/iris.nmds.rda")
data(iris.nmds)

# examine fit by number of dimensions
plot(iris.nmds)

# choose the best two-dimensional solution to work with
iris.nmin <- min(iris.nmds, dims=2)

# fit the data to the ordination as vectors
### vf() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.vf <- vf(iris.nmin, iris[,1:4], nperm=1000)
### save(iris.vf, file="ecodist/data/iris.vf.rda")
data(iris.vf)
plot(iris.nmin, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="NMDS")
plot(iris.vf)