ordi_plot.rda: ggplot-based plot for objects of class "rda"

In rasanderson/bio2020: Additional functions for vegan and ggvegan

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 class 'rda'
ordi_plot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  layers = c("species", "sites", "biplot", "centroids"),
  arrows = FALSE,
  legend.position = "none",
  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.

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

require(vegan)
data(dune)

pca <- ordi_rda(dune)
ordi_plot(pca)

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

rasanderson/bio2020 documentation built on Sept. 18, 2022, 11:40 a.m.