plot.cograph_motif_analysis: Plot Motif Analysis Results

In cograph: Analysis and Visualization of Complex Networks

Plot Motif Analysis Results

Description

Create visualizations for motif analysis results including network diagrams of triads, bar plots of type distributions, and significance plots.

Usage

## S3 method for class 'cograph_motif_analysis'
plot(
  x,
  type = c("triads", "types", "significance", "patterns"),
  n = 20,
  colors = c("#2166AC", "#B2182B"),
  res = 72,
  node_size = 5,
  label_size = 7,
  title_size = 7,
  stats_size = 5,
  ncol = 5,
  legend = TRUE,
  color = "#800020",
  spacing = 1,
  ...
)

Arguments

x	A cograph_motif_analysis object from extract_motifs()
type	Plot type: "triads" (default network diagrams), "types" (bar plot), "significance" (z-score plot), or "patterns" (abstract MAN patterns)
n	Number of triads to show. Default 20.
colors	Colors for visualization. Default blue/red.
res	Resolution for scaling (not used with grid graphics). Default 72.
node_size	Size of nodes (1-10 scale, like splot). Default 5.
label_size	Font size for node labels (3-letter abbreviations). Default 7.
title_size	Font size for motif type title (e.g., "120C"). Default 7.
stats_size	Font size for statistics text (n, z, p). Default 5.
ncol	Number of columns in the plot grid. Default 5.
legend	Logical, show abbreviation legend at bottom? Default TRUE.
color	Color for nodes, edges, and labels. Default "#800020" (maroon).
spacing	Spacing multiplier between cells (0.5-2). Default 1.
...	Additional arguments (unused)

Value

Invisibly returns NULL for triad plots, or a ggplot2 object for other types.

See Also

extract_motifs() for the analysis that produces this object, motif_census() for statistical motif analysis

Other motifs: extract_motifs(), extract_triads(), get_edge_list(), motif_census(), motifs(), plot.cograph_motifs(), subgraphs(), triad_census()

Examples

## Not run: 
Mod <- tna::tna(tna::group_regulation)
m <- extract_motifs(Mod, significance = TRUE)

# Default network diagram
plot(m)

# Customize appearance
plot(m, node_size = 0.15, label_size = 6, title_size = 9)

# Change layout
plot(m, ncol = 4, n = 12)

# Other plot types
plot(m, type = "types")
plot(m, type = "significance")

## End(Not run)

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