plot_bootstrap_forest: Forest Plot for Bootstrap Network Results

Description

A ggplot2-based forest plot for net_bootstrap and boot_glasso objects. Each row is one network edge; horizontal bars span the confidence interval and a filled square marks the point estimate. A dashed reference line runs through zero.

Produces a ggplot2 forest plot where each row is one network edge, the square marks the bootstrap mean estimate, and the horizontal bar spans the selected interval. A dashed reference line runs through zero. Significant edges are highlighted in colour; non-significant ones appear in grey (only shown when show_nonsig = TRUE).

Usage

plot_bootstrap_forest(x, ...)
# S3 method for net_bootstrap
plot_bootstrap_forest(
  x,
  alpha = NULL,
  layout = c("linear", "circular", "grouped"),
  interval = c("ci", "cr", "both"),
  show_nonsig = TRUE,
  sort_by = c("estimate", "significance", "name"),
  n_top = NULL,
  node_colors = NULL,
  sig_color = "#2C6E8A",
  cr_color = "#D4829A",
  nonsig_color = "#CCCCCC",
  ring_color = "#C8C8C8",
  median_color = "#AAAAAA",
  label_size = NULL,
  label_color = NULL,
  point_size = NULL,
  r_inner = NULL,
  r_outer = NULL,
  gap_rad = NULL,
  label_offset = NULL,
  src_label_size = NULL,
  margins = c(0.1, 0.1, 0.1, 0.1),
  scale = 1,
  title = NULL,
  subtitle = NULL,
  ...
)
# S3 method for tna_bootstrap
plot_bootstrap_forest(
  x,
  alpha = NULL,
  layout = c("linear", "circular", "grouped"),
  interval = c("ci", "cr", "both"),
  show_nonsig = TRUE,
  sort_by = c("estimate", "significance", "name"),
  n_top = NULL,
  node_colors = NULL,
  sig_color = "#2C6E8A",
  cr_color = "#D4829A",
  nonsig_color = "#CCCCCC",
  ring_color = "#C8C8C8",
  median_color = "#AAAAAA",
  label_size = NULL,
  label_color = NULL,
  point_size = NULL,
  r_inner = NULL,
  r_outer = NULL,
  gap_rad = NULL,
  label_offset = NULL,
  src_label_size = NULL,
  margins = c(0.1, 0.1, 0.1, 0.1),
  scale = 1,
  title = NULL,
  subtitle = NULL,
  ...
)
# S3 method for boot_glasso
plot_bootstrap_forest(
  x,
  alpha = NULL,
  layout = c("linear", "circular", "grouped"),
  interval = c("ci", "cr", "both"),
  show_nonsig = TRUE,
  sort_by = c("estimate", "significance", "name"),
  n_top = NULL,
  node_colors = NULL,
  sig_color = "#2C6E8A",
  cr_color = "#D4829A",
  nonsig_color = "#CCCCCC",
  ring_color = "#C8C8C8",
  median_color = "#AAAAAA",
  label_size = NULL,
  label_color = NULL,
  point_size = NULL,
  r_inner = NULL,
  r_outer = NULL,
  gap_rad = NULL,
  label_offset = NULL,
  src_label_size = NULL,
  margins = c(0.1, 0.1, 0.1, 0.1),
  scale = 1,
  title = NULL,
  subtitle = NULL,
  ...
)
# S3 method for net_bootstrap_group
plot_bootstrap_forest(
  x,
  layout = c("linear", "circular"),
  interval = c("ci", "cr", "both"),
  show_nonsig = TRUE,
  n_top = NULL,
  all_edges = FALSE,
  pos_color = NULL,
  title = NULL,
  subtitle = NULL,
  label_size = 2.8,
  ...
)

Value

A ggplot object.

Arguments

x: A tna_bootstrap (from tna::bootstrap), net_bootstrap, or boot_glasso object.
...: Currently unused.
alpha: Significance threshold. Default: inherits from the object ($ci_level or $alpha), falling back to 0.05.
layout: "linear" (default) draws the classic tall forest plot; "circular" arranges each edge as a spoke around a circle, with the inner ring at the data minimum and the outer ring at the data maximum.
interval: Which interval to display: "ci" (bootstrap confidence interval, default), "cr" (consistency range, stability inference only), or "both" (CI as outer bar, CR as inner bar).
show_nonsig: Logical: include non-significant edges (greyed out)? Default TRUE.
sort_by: How to order edges on the y-axis (linear layout) or clockwise from top (radial layout): "estimate" (default, ascending), "significance" (most significant at top), or "name" (alphabetical).
n_top: Integer: restrict to the n_top edges with the largest absolute estimate. Applied after significance filtering. Default NULL.
sig_color: Colour for significant CI bars and points. Default "#2C6E8A" (teal-blue).
cr_color: Colour for the consistency range bar (interval = "cr" or "both"). Default "#D4820A" (amber).
nonsig_color: Colour for non-significant edges. Default "#CCCCCC".
ring_color: Colour for the reference rings (radial layout only). Default "#C8C8C8".
median_color: Colour for the dashed median ring (radial layout only). Default "#AAAAAA".
label_size: Text size for edge labels (radial layout only). Default 2.3.
label_color: Fixed colour for edge labels (radial layout only). NULL (default) inherits the edge colour (teal for significant, grey for non-significant).
point_size: Size of the estimate square. Default 3 (linear) or 2 (radial).
r_inner: Inner ring radius (grouped layout). Default NULL (auto).
r_outer: Outer ring radius (grouped layout). Default NULL (auto).
gap_rad: Gap in radians between sectors (grouped layout). Default NULL (auto).
label_offset: Distance between outer ring and labels (grouped layout). Default NULL (auto).
src_label_size: Text size for source node labels in the center (grouped layout). Default NULL (auto, label_size * 0.80).
margins: Margins as c(bottom, left, top, right) fractions (grouped layout). Default c(0.1, 0.1, 0.1, 0.1).
scale: Scaling factor applied to all text and point sizes (grouped layout). Default 1. Use values > 1 for high-DPI output, < 1 for small devices.
title: Plot title. Default NULL.
subtitle: Plot subtitle. Default NULL.

Details

For net_bootstrap objects from stability inference, both a bootstrap confidence interval (ci_lower/ci_upper) and a consistency range (cr_lower/cr_upper) are available. Use interval = "both" to overlay both on the same plot.