geometric_mean_barplot: Geometric Mean Barplot for Compositional Data

In coda.plot: Plots for Compositional Data

Geometric Mean Barplot for Compositional Data

Description

Generates a barplot based on the geometric mean of compositional parts. Optionally, it can compare groups, display the parts on the x-axis, overlay boxplots, or use centered log-ratio (clr) transformation.

Usage

geometric_mean_barplot(
  X,
  group,
  x_show_parts = TRUE,
  include_boxplot = FALSE,
  clr_scale = FALSE
)

Arguments

X	A numeric matrix or data frame representing compositional data. Each row is an observation and each column is a part (must be strictly positive).
group	A factor or character vector indicating group membership for each observation. Must have length nrow(X).
x_show_parts	Logical. If TRUE, the x-axis displays parts instead of group labels. Default is TRUE.
include_boxplot	Logical. If TRUE, a boxplot is overlaid on top of the barplot. Default is FALSE.
clr_scale	Logical. If TRUE, the data are transformed to clr coordinates before computing means. Default is FALSE.

Details

For each part, the function computes (within each group) the mean of either log(X) (default) or clr(X) (clr_scale = TRUE), and subtracts the overall mean across all observations. Therefore, bars represent deviations from the overall (global) mean on the chosen scale. Overlaying a boxplot can help visualize within-group variability.

Value

A ggplot2 object representing the geometric mean barplot.

Examples

set.seed(1)
X <- matrix(runif(30, 1, 10), ncol = 3)
colnames(X) <- c("A", "B", "C")
group <- rep(c("G1", "G2"), each = 5)
geometric_mean_barplot(X, group, include_boxplot = TRUE)
geometric_mean_barplot(X, group, clr_scale = TRUE)

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