Forest Plot for Bootstrap Edge Differences — plot_edge_diff

Plots pairwise edge weight differences from a boot_glasso object. Each row (linear) or spoke (circular) is one edge pair. The square marks the mean bootstrap difference, the bar spans its bootstrap percentile interval at level 1 - alpha, and a dashed line or ring marks zero. Significant pairs are plotted in pos_color when the first edge is larger and in neg_color when the second edge is 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 $edge_diff_p.
...: Currently unused.
alpha: Significance threshold. Default NULL, which inherits x$alpha, falling back to 0.05. The tile layout always uses x$alpha.
layout: "linear" (default), "circular", "chord", or "tile". The chord layout places all edge names on a unit circle and connects significant pairs with Bezier arcs whose width and color encode the mean bootstrap difference. The tile layout plots the full pairwise-difference matrix and ignores show_nonsig, nonzero_only, sort_by, n_top and the label and point arguments.
show_nonsig: Logical. Include non-significant pairs. Default FALSE.
nonzero_only: If TRUE, restrict to edges that are non-zero in the original network ($original_pcor). Without $original_pcor, edges whose absolute mean bootstrap weight is at least 10 percent of the largest are kept. Default FALSE.
sort_by: "estimate" (default), "significance", or "name" (linear layout only). When n_top is set, the retained pairs are ordered by estimate.
n_top: Restrict to top N pairs by absolute difference.
pos_color: Color when edge1 > edge2. Default "#C0392B" (crimson).
neg_color: Color when edge1 < edge2. Default "#2C6E8A" (teal-blue).
nonsig_color: Color for non-significant pairs. Default "#AAAAAA".
ring_color: Ring color (circular and chord layouts). Default "#C8C8C8".
label_size: Text size of edge labels (circular and chord layouts). Default 2.3.
label_color: Fixed label color (circular and chord layouts). NULL (default) uses the pair color in the circular layout and dark grey in the chord layout.
point_size: Size of estimate square (linear and circular layouts). Default 2 for layout = "circular" and 3 otherwise.
r_inner: Inner ring radius (circular). Default 0.38.
r_outer: Outer ring radius (circular). Default 0.72.
title: Plot title. Default NULL.
subtitle: Plot subtitle. Default NULL.

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, cs_iter = 25,
                             centrality = c("strength", "expected_influence"))
plot_edge_diff_forest(bg)