plot_edge_diff_forest: Forest Plot for Bootstrap Edge Differences

In cograph: Analysis and Visualization of Complex Networks

Forest Plot for Bootstrap Edge Differences

Description

Visualises pairwise edge weight differences from a boot_glasso object. Each row (linear) or spoke (circular) is one edge pair; the CI bar spans the bootstrap CI of the difference; a dashed line/ring marks zero. Red = first edge larger; blue = second edge larger.

Usage

plot_edge_diff_forest(x, ...)

## S3 method for class 'boot_glasso'
plot_edge_diff_forest(
  x,
  alpha = NULL,
  layout = c("linear", "circular", "chord", "tile"),
  show_nonsig = FALSE,
  nonzero_only = FALSE,
  sort_by = c("estimate", "significance", "name"),
  n_top = NULL,
  pos_color = "#C0392B",
  neg_color = "#2C6E8A",
  nonsig_color = "#AAAAAA",
  ring_color = "#C8C8C8",
  label_size = 2.3,
  label_color = NULL,
  point_size = if (match.arg(layout) == "circular") 2 else 3,
  r_inner = 0.38,
  r_outer = 0.72,
  title = NULL,
  subtitle = NULL,
  ...
)

Arguments

x	A boot_glasso object with $boot_edges and $edge_diff_p.
...	Currently unused.
alpha	Significance threshold. Default: inherits from object.
layout	"linear" (default), "circular", or "chord". The chord layout places all edge names on a unit circle and connects significant pairs with bezier arcs; arc width and colour encode the mean bootstrap difference.
show_nonsig	Include non-significant pairs? Default FALSE.
nonzero_only	If TRUE, restrict to edges that are non-zero in the original network (identified via $original_pcor). Useful for EBICglasso results where many edges are regularised to exactly zero. Default FALSE.
sort_by	"estimate" (default), "significance", or "name" (linear only).
n_top	Restrict to top N pairs by absolute difference.
pos_color	Colour when edge1 > edge2. Default crimson.
neg_color	Colour when edge1 < edge2. Default teal.
nonsig_color	Colour for non-significant pairs.
ring_color	Ring colour (circular/chord). Default light grey.
label_size	Text size. Default 2.3.
label_color	Fixed label colour (NULL = inherit).
point_size	Size of estimate square (linear/circular).
r_inner	Inner ring radius (circular). Default 0.38.
r_outer	Outer ring radius (circular). Default 0.72.
title	Plot title.
subtitle	Plot subtitle.

Value

A ggplot object.

Examples

set.seed(1)
data1 <- as.data.frame(matrix(rnorm(60), 20, 3, dimnames = list(NULL, c("A","B","C"))))
bg <- Nestimate::boot_glasso(data1, iter = 50, centrality = c("strength", "expected_influence"))
plot_edge_diff_forest(bg)

cograph documentation built on April 1, 2026, 1:07 a.m.