gg_ordiplot: Plot with Ellipses, Hulls, Spiders

In jfq3/ggordiplots: Make 'ggplot2' Versions of Vegan's Ordiplots

Plot with Ellipses, Hulls, Spiders

Description

gg_ordiplot uses ggplot2 to make an ordination plot with group ellipses by default, and optionally hulls and/or spiders. It is patterned after vegan's functions ordiellipse, ordihull, and ordispider and accepts similar parameters.

Usage

gg_ordiplot(
  ord,
  groups,
  scaling = 1,
  choices = c(1, 2),
  kind = c("sd", "se", "ehull"),
  conf = NULL,
  show.groups = "all",
  ellipse = TRUE,
  label = FALSE,
  hull = FALSE,
  spiders = FALSE,
  pt.size = 3,
  plot = TRUE
)

Arguments

ord	An ordination object.
groups	A vector of groups.
scaling	Scaling for ordination plot.
choices	Axes to be plotted.
kind	Type of ellipses to show ("se", sd", "ehull").
conf	Confidence value for ellipses if "se" or "sd."
show.groups	Subset of groups to plot.
ellipse	A logical for plotting ellipses; defaults to TRUE.
label	A logical for labeling group centroids.
hull	A logical for plotting group hulls.
spiders	A logical for plotting group spiders.
pt.size	Symbol size.
plot	A logical for plotting; defaults to TRUE.

Value

Silently returns the plot and data frames used for the plotting.

Examples

data("dune")
data("dune.env")
dune.hel <- decostand(dune, method = "hellinger")
ord <- rda(dune.hel)
gg_ordiplot(ord, groups = dune.env$Management)

jfq3/ggordiplots documentation built on Feb. 3, 2024, 11:50 p.m.