cograph (version 2.0.0)

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,
  ...
)

Value

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

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)

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

if (FALSE) {
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")
}