ggvegan (version 0.0-9)

autoplot.rda: ggplot-based plot for objects of class 'rda'

Description

Produces a multi-layer ggplot object representing the output of objects produced by rda.

Usage

# S3 method for rda
autoplot(object, axes = c(1, 2), geom = c("point", "text"),
  layers = c("species", "sites", "biplot", "centroids"), arrows = TRUE,
  legend.position = "right", title = NULL, subtitle = NULL,
  caption = NULL, ylab, xlab, const, ...)

Arguments

object

an object of class "rda", the result of a call to rda

axes

numeric; which axes to plot, given as a vector of length 2.

geom

character; which geoms to use for the layers. Can be a vector of length equal to length(display), in which case the ith element of type refers to the ith element of display.

layers

character; which scores to plot as layers

arrows

logical; represent species (variables) using vectors?

legend.position

character or two-element numeric vector; where to position the legend. See theme for details. Use "none" to not draw the legend.

title

character; subtitle for the plot

subtitle

character; subtitle for the plot

caption

character; caption for the plot

ylab

character; label for the y-axis

xlab

character; label for the x-axis

const

General scaling constant to rda scores. See plot.cca for details.

...

Additional arguments passed to fortify.cca.

Value

Returns a ggplot object.

Details

TODO

Examples

# NOT RUN {
data(dune)

pca <- rda(dune)
autoplot(pca, arrows = TRUE)

## Just the species scores
autoplot(pca, arrows = TRUE, display = "species")

# }