cograph (version 2.7.2)

plot.cograph_motif_analysis: 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 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,
  combined = TRUE,
  ...
)

Value

Invisibly returns NULL for triad and pattern plots, or a ggplot2 object for types and significance plots.

Arguments

x

A cograph_motif_analysis object from extract_motifs()

type

Plot type:

"triads"

(default) Network diagrams of specific named triads, arranged in a grid. Each cell shows the three nodes and their edges.

"types"

Bar chart of MAN type frequencies.

"significance"

Z-score plot with one bar per node-triple and MAN type. Requires significance = TRUE in extract_motifs().

"patterns"

Abstract MAN pattern diagrams showing edge structure of each triad type without specific node labels.

n

Number of triads/patterns to show. Default 20.

colors

Two-element color vector mapped to a three-tone significance scale (used by type = "significance" and by type = "patterns" node fills): colors[1] fills items that are significantly under-represented (p < .05 and z < 0); colors[2] fills items that are significantly over-represented (p < .05 and z > 0); everything else is filled neutral grey ("#9E9E9E"). When significance was not run, patterns nodes use colors[1] as a single fill. Default c("#2166AC", "#B2182B") (blue for under, red for over).

res

Resolution for scaling (kept for backwards compatibility). Default 72.

node_size

Size of nodes in triad diagrams (1-10 scale). 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

Show abbreviation legend at bottom? Default TRUE.

color

Color for nodes, edges, and labels in triad diagrams. Default "#800020" (maroon).

spacing

Spacing multiplier between grid cells (0.5-2). Default 1.

combined

Logical: when TRUE (default) and type = "patterns", arrange the per-motif panels in an internal grid via graphics::par(mfrow=...). Set to FALSE to draw into a layout the caller has already configured (e.g. via panel_layout()).

...

Additional arguments (unused).

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

mat <- matrix(c(0,3,2,0, 0,0,5,1, 0,0,0,4, 2,0,0,0), 4, 4, byrow = TRUE)
rownames(mat) <- colnames(mat) <- c("Plan","Execute","Monitor","Adapt")
m <- extract_motifs(mat, significance = FALSE)
plot(m)
plot(m, type = "types")