barrel_stats: Comprehensive Ordination Visualization Layer

In barrel: Covariance-Based Ellipses and Annotation Tools for Ordination Plots

Comprehensive Ordination Visualization Layer

Description

Combines ordination ellipses, centroids, environmental arrows, and annotations into a ggplot2 layer.

Usage

stat_barrel(
  mapping = NULL,
  data = NULL,
  geom = "path",
  position = "identity",
  kind = "se",
  conf = 0.95,
  method = c("robust", "classic"),
  show.legend = NA,
  inherit.aes = TRUE,
  geom_type = c("path", "polygon"),
  ...
)

stat_barrel_centroid(
  mapping = NULL,
  data = NULL,
  geom = "point",
  position = "identity",
  method = c("classic", "robust"),
  show.legend = NA,
  inherit.aes = TRUE,
  shape = 3,
  ...
)

stat_barrel_arrows(
  mapping = NULL,
  data = NULL,
  ord,
  matrix,
  geom = "segment",
  position = "identity",
  labels = TRUE,
  labels.color = "black",
  labels.size = 3,
  labels.fontface = "plain",
  show.significant = FALSE,
  p_thresh = 0.05,
  arrow = grid::arrow(length = grid::unit(0.25, "cm")),
  arrow.color = "grey10",
  arrow.linetype = "solid",
  arrow.size = 0.3,
  labels.max.overlaps = Inf,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

compute_envfit_vectors(ord, matrix, p_thresh = 0.05, show.significant = FALSE)

stat_barrel_annotate(
  mapping = NULL,
  data = NULL,
  ord,
  position = "identity",
  show.legend = FALSE,
  inherit.aes = TRUE,
  xpad = 0.05,
  ypad = 0.05,
  hjust = 0,
  vjust = 1,
  ...
)

Arguments

mapping	Set of aesthetic mappings created by aes().
data	Data frame used for plotting.
geom	Character; geometric object to use for ellipses, either "path" or "polygon".
position	Position adjustment for ggplot2 layers (default "identity").
kind	Character; type of ellipse: "se" (standard error), "sd" (dispersion), or "ci" (confidence interval).
conf	Numeric; confidence level for ellipses (default 0.95).
method	Character; covariance estimation method: "classic" or "robust".
show.legend	Logical; whether to show legends (default NA).
inherit.aes	Logical; whether to inherit aesthetics (default TRUE).
geom_type	Character; geometric object to use for ellipses, either "path" or "polygon".
...	Additional parameters passed to underlying geoms or stats.
shape	Integer; shape code for centroid points (default 3).
ord	Ordination object from vegan, e.g. rda, cca, dbrda, or metaMDS.
matrix	Optional data frame of environmental variables for arrows.
labels	Logical; whether to show labels on environmental arrows (default TRUE).
labels.color	Color of arrow labels (default "black").
labels.size	Numeric size of arrow labels (default 3).
labels.fontface	Font face of arrow labels (default "plain").
show.significant	Logical; whether to show only significant arrows (default FALSE).
p_thresh	Numeric; p-value threshold for significance filtering (default 0.05).
arrow	A grid arrow object controlling arrow appearance (default created by grid::arrow()).
arrow.color	Color of arrows (default "grey10").
arrow.linetype	Line type of arrows (default "solid").
arrow.size	Numeric line width of arrows (default 0.3).
labels.max.overlaps	Maximum number of labels in the same space (default "Inf").
xpad	Numeric; horizontal padding for annotation text relative to x-axis range (default 0.05).
ypad	Numeric; vertical padding for annotation text relative to y-axis range (default 0.05).
hjust	Numeric; horizontal justification of annotation text (default 0).
vjust	Numeric; vertical justification of annotation text (default 1).

Details

Comprehensive Ordination Visualization Layer

This set of ggplot2 stats draws ellipses around groups, centroids, environmental arrows, and adds adjusted R^2 or stress annotation for ordination objects from vegan.

Value

A ggplot2 layer combining ellipses, centroids, arrows, and annotations.

Examples

library(ggplot2)
library(vegan)
library(robustbase)
data(dune)
data(dune.env)

pca <- vegan::rda(dune, scale = TRUE)
scores <- as.data.frame(vegan::scores(pca, display = "sites"))
scores$Management <- dune.env$Management

ggplot(scores, aes(PC1, PC2, group = Management, fill = Management)) +
  stat_barrel(
    method = "classic", kind = "se", conf = 0.95, geom_type = "polygon",
    alpha = 0.4, color = "black"
  ) +
  stat_barrel_centroid(method = "classic", shape = 3) +
  stat_barrel_arrows(
    ord = pca, matrix = dune,
    labels = TRUE, labels.color = "blue",
    arrow.color = "darkred", arrow.linetype = "solid",
    labels.fontface = "bold", show.significant = TRUE,
    labels.max.overlaps = Inf,
  ) +
  stat_barrel_annotate(ord = pca, xpad = 0.05, ypad = 0.05) +
  geom_point(aes(color = Management)) +
  theme_minimal()

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