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Forest Plot for Bootstrap Network Results

Source: R/plot-forest.R
plot_bootstrap_forest.Rd

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 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, 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.

Value

A ggplot object.

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.