Forest Plot for Bootstrap Network Results — plot_bootstrap

Plots bootstrap results of net_bootstrap, net_bootstrap_group, tna_bootstrap and boot_glasso objects as a ggplot2 forest plot. Each row is one non-zero network edge. A square marks the point estimate, a horizontal bar spans the selected interval, and a dashed reference line marks zero. Significant edges are plotted in sig_color and non-significant edges in a faded nonsig_color.

Usage

plot_bootstrap_forest(x, ...)

# S3 method for class '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 class '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 class '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 class '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,
  ...
)

Arguments

x: A tna_bootstrap (from tna::bootstrap), net_bootstrap, net_bootstrap_group, or boot_glasso object.
...: Currently unused.
alpha: Significance threshold. Default NULL, which inherits from the object: $ci_level for net_bootstrap, $level for tna_bootstrap, $alpha for boot_glasso, each falling back to 0.05.
layout: "linear" (default) gives the standard forest plot; "circular" arranges each edge as a spoke around a circle, with the inner ring at the smallest lower bound and the outer ring just beyond the largest upper bound; "grouped" arranges edges in sectors by source node. The net_bootstrap_group method supports "linear" and "circular" only.
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. Default TRUE.
sort_by: Order of edges on the y-axis in the linear layout: "estimate" (default, ascending), "significance" (most significant at top), or "name" (alphabetical). When n_top is set, the retained edges are ordered by estimate. The circular layout orders edges alphabetically, clockwise from the top.
n_top: Integer. Keeps only the n_top edges with the largest absolute estimate. Applied after significance filtering. Default NULL.
node_colors: Optional named vector of node colors for the grouped layout. When NULL, node colors stored in the original network or tna model are used if present.
sig_color: Color for significant CI bars and points (linear and circular layouts). Default "#2C6E8A" (teal-blue).
cr_color: Color for the consistency range bar (interval = "cr" or "both"). Default "#D4829A".
nonsig_color: Color for non-significant edges (linear and circular layouts). Default "#CCCCCC".
ring_color: Color for the reference rings (circular and grouped layouts). Default "#C8C8C8".
median_color: Color for the dashed median ring (circular and grouped layouts). Default "#AAAAAA".
label_size: Text size for edge labels (circular and grouped layouts). Default NULL, which gives 2.9 in the circular layout and automatic sizing in the grouped layout. The net_bootstrap_group method defaults to 2.8.
label_color: Fixed color for edge labels (circular and grouped layouts). NULL (default) uses the edge color.
point_size: Size of the estimate square. Default NULL, which gives 3 (linear), 2 (circular), or automatic sizing (grouped).
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.
all_edges: For net_bootstrap_group, show the union of group edges instead of only edges common to all groups. Default FALSE.
pos_color: Currently unused by the net_bootstrap_group method.

Value

A ggplot object.

Details

Objects from stability inference (net_bootstrap and tna_bootstrap) carry both a bootstrap confidence interval and a consistency range, and interval = "both" overlays the two. When the consistency range is requested but absent, a message is issued and the confidence interval is shown. For boot_glasso, an edge is significant when its inclusion proportion is at least 1 - alpha.

The net_bootstrap_group method plots the groups side by side in the linear layout, with the edges ordered by their mean estimate across groups. Its interval = "both" shows the confidence interval only, and its circular layout shows the first group only.

Examples

boot <- tna::bootstrap(tna::tna(coding), iter = 50)
plot_bootstrap_forest(boot)