barrel_stats: 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,
  ...
)

Value

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

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.

Examples

Run this code

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()

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