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Plot Motif Analysis Results

Source: R/motifs-extract.R
plot.cograph_motif_analysis.Rd

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 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 showing over- and under-represented types. 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 for the types/significance plots: first color for over-represented, second for under-represented. Default c("#2166AC", "#B2182B") (blue/red).

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.

...

Additional arguments (unused).

Value

Invisibly returns NULL for triad plots, or a ggplot2 object for types/significance/patterns plots.

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) { # \dontrun{
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")
} # }