autoplot.barrel_ord: Autoplot method for barrel_ord objects
In barrel: Covariance-Based Ellipses and Annotation Tools for Ordination Plots

autoplot.barrel_ord

R Documentation

Autoplot method for barrel_ord objects

Description

Generates a ggplot of site scores from a vegan ordination object with optional group ellipses, centroids, and environmental arrows. This method is designed to work with ordination objects prepared using barrel_prepare.

Usage

## S3 method for class 'barrel_ord'
autoplot(object, ...)

Arguments

object

An object of class "barrel_ord" (a vegan ordination object with attached metadata).

...

Additional arguments:

group: Character. Grouping variable in the metadata. (Required)
data: Optional species or environmental data for envfit.
kind: Type of ellipse: "se" or "sd". Default is "se".
method: Covariance method: "classic" or "robust". Default is "classic".
conf: Confidence level for ellipses. Default is 0.95.
geom_type: "polygon" or "path" for ellipse. Default is "polygon".
show_arrows: Logical; whether to show envfit vectors. Default is TRUE.
show_centroids: Logical. Default is FALSE.
show_ellipses: Logical. Default is TRUE.
show_labels: Logical. Label envfit arrows. Default is TRUE.
p_thresh: Numeric. Significance threshold for arrows. Default 0.05.
alpha: Numeric. Transparency of ellipses. Default is 0.5.

Details

If geom_type = "polygon", group colors are mapped to fill for ellipses. If geom_type = "path", group colors are mapped to color. The grouping variable must be present in the metadata provided to barrel_prepare.

Value

A ggplot2 object with ordination scores and optional graphical layers.

Examples

library(vegan)
data(dune)
data(dune.env)
ord <- rda(dune, scale = TRUE)
ord <- barrel_prepare(ord, dune.env)
ggplot2::autoplot(ord,
  group = "Management", data = dune,
  method = "robust", kind = "sd", geom_type = "polygon", show_arrows = TRUE
)

barrel documentation built on Nov. 5, 2025, 7:40 p.m.