clr_biplot: Compositional CLR Biplot

In coda.plot: Plots for Compositional Data

Compositional CLR Biplot

Description

Generates a centered log-ratio (CLR) biplot for compositional data.

Usage

clr_biplot(
  X,
  group = NULL,
  biplot_type = "covariance",
  alpha = NULL,
  shape_group = NULL,
  return_data = FALSE,
  repel = TRUE,
  repel_force = 1,
  repel_max_overlaps = Inf
)

Arguments

X	A matrix or data frame containing compositional data (strictly positive).
group	Optional factor/character used to color the observations.
biplot_type	Character string specifying the type of biplot. Either "covariance" (default) or "form".
alpha	Optional numeric in [0,1]. If provided, overrides biplot_type. alpha = 0: covariance biplot alpha = 1: form biplot
shape_group	Optional factor/character used to assign shapes to observations.
return_data	Logical. If TRUE, returns a list with data frames for observations, variables, and the ggplot object.
repel	Logical. If TRUE (default), use ggrepel for variable labels when available.
repel_force	Numeric. Repulsion force passed to ggrepel::geom_text_repel().
repel_max_overlaps	Numeric. Maximum overlaps allowed (ggrepel).

Value

A ggplot2 object. If return_data = TRUE, a list with elements obs, vars, and plot.

Examples

# Basic example (no groups)
set.seed(1)
X <- matrix(runif(120, 0.1, 10), ncol = 6)
colnames(X) <- paste0("p", 1:6)
clr_biplot(X)

# Grouped example (color)
grp <- factor(sample(c("A", "B"), nrow(X), replace = TRUE))
clr_biplot(X, group = grp)

# Color + shape
shp <- factor(sample(c("S1", "S2", "S3"), nrow(X), replace = TRUE))
clr_biplot(X, group = grp, shape_group = shp)

# Form biplot (alpha = 1) with repelled variable labels (requires ggrepel)
clr_biplot(X, group = grp, biplot_type = "form", repel = TRUE)

# Covariance biplot (alpha = 0) and custom repel settings
clr_biplot(X, group = grp, alpha = 0, repel = TRUE, repel_force = 1.5, repel_max_overlaps = 30)

coda.plot documentation built on April 12, 2026, 9:06 a.m.