Plot a motif/subgraph result

Tab-completion-friendly wrapper around the plot.cograph_motif_result S3 method. Functionally identical to plot(x, ...) on a cograph_motif_result object, but exposes the type / n / ncol / colors arguments to editor autocompletion.

Usage

plot_motifs(
  x,
  type = c("triads", "types", "significance", "patterns"),
  n = 15,
  ncol = 5,
  colors = c("#2166AC", "#B2182B"),
  node_size = 5,
  label_size = 11,
  title_size = 12,
  stats_size = 13,
  legend_size = 13,
  legend = TRUE,
  motif_color = "#800020",
  spacing = 1,
  base_size = 12,
  ...
)

Arguments

x

A cograph_motif_result object from motifs() or subgraphs().

type

Plot type:

"triads": Network diagrams of specific node triples (instance mode) or falls back to patterns (census mode). Each panel title reads "<MAN code>: <description>" (e.g. "030T: Feed-forward") and, in census mode, appends the z-score and a significance star (* p<.05, ** p<.01, *** p<.001). Arranged in a grid.
"types": Bar chart of MAN type frequencies. In census mode bars are colored by significance direction (see colors); in instance mode bars use a single fill because per-type significance would need an aggregation rule across multiple node-triple rows of the same type.
"significance": Z-score bars per row of x$results. In census mode each bar is one MAN type; in instance mode each bar is one concrete node-triple, labeled "<triple> [<MAN code>: <description>]". Bars are colored with the same three-tone rule (see colors). Requires significance = TRUE in the motifs() call.
"patterns": Abstract MAN pattern diagrams showing the edge structure of each triad type. In census mode panel nodes are filled by significance direction (red sig over / blue sig under / grey ns); in instance mode panels use a single fill, same reason as "types".

n

Maximum number of items to plot. Default 15.

ncol

Number of columns in the triad/pattern grid. Default 5.

colors

Two-element color vector mapped to a three-tone significance scale (used by type = "significance", plus type = "types" and type = "patterns" in census mode): 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"). Default c("#2166AC", "#B2182B") (blue for under, red for over). When significance was not run, type = "types" falls back to a single colors[1] fill and patterns nodes use colors[1].

node_size

Triad node radius (relative). Default 5. (type = "triads" only.)

label_size

Triad node-label font size in points. Default 11.

title_size

Per-panel title font size in points. Default 12.

stats_size

Per-panel statistics caption font size in points (e.g., n=34 z=-55.3 p<.001). Default 13.

legend_size

Bottom legend font size in points. Default 13.

legend

Logical. Show the abbreviation legend strip below the triad grid. Default TRUE. (type = "triads" only.)

motif_color

Color of triad nodes/edges/labels. Default "#800020" (deep burgundy). (type = "triads" only.)

spacing

Triangle spread inside each panel; > 1 pulls nodes inward, < 1 pushes them apart. Default 1.

base_size

Base font size for the ggplot2 themes used by type = "types" and type = "significance". Default 12.

...

Additional arguments passed to internal plot helpers.

Value

Invisibly returns the input x (or the underlying ggplot for the "types" and "significance" types, matching the S3 method).

Examples

if (FALSE) { # \dontrun{
g <- igraph::sample_gnp(20, 0.2, directed = TRUE)
m <- motifs(g)
plot_motifs(m)
plot_motifs(m, type = "types")
} # }

Usage

Arguments

Value

See also

Examples