ggplot-based plot for objects of class 'rda'

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

Usage

# S3 method for class 'rda'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  layers = c("species", "sites", "biplot", "centroids"),
  arrows = TRUE,
  legend.position = "none",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab = NULL,
  xlab = NULL,
  const = NULL,
  arrow.col = "navy",
  ...
)

Arguments

object: an object of class "rda", the result of a call to vegan::rda()
axes: numeric; which axes to plot, given as a vector of length 2.
geom: character; which geom to use for the species (variables) and sites (samples) layers. A vector of length 2; if a vector of length 1, geom is extended to the required length.
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 ggplot2::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 vegan::scores.rda() for details.
arrow.col: colour specification for biplot arrows and their labels.
...: Additional arguments passed to the fortify() method.

Value

Returns a ggplot object.

Details

TODO

Author

Gavin L. Simpson

Examples


library("vegan")

data(dune)

pca <- rda(dune)
autoplot(pca)


## Just the species scores
autoplot(pca, layers = "species")