ggplot-based plot for objects of class 'rda'

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

# 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 up to length 2, in which case, the first element of geom will be used for any site scores (both weighted sum or linear combination scores), and the second element will be used for species scores. The latter will be ignored if arrows = TRUE.
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 scores.rda for details.
...: Additional arguments passed to fortify.cca.

Value

Returns a ggplot object.

Details

TODO

Author

Gavin L. Simpson

Examples


data(dune)

pca <- rda(dune)
autoplot(pca)


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