Plots fitted vectors onto an ordination diagram
Add vector fitting arrows to an existing ordination plot.
## S3 method for class 'vf' plot(x, pval = 1, cex = 0.8, ascale = 0.9, ...)
x |
an object of S3 class |
pval |
optional, critical p-value for choosing variables to plot |
cex |
text size |
ascale |
optional, proportion of plot area to use when calculating arrow length |
... |
optional, other graphics parameters |
Adds arrows to an existing ordination plot. Only arrows with a p-value less than pval are added. By default, all variables are shown.
Sarah Goslee
# 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)
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