plot_simplicial: Simplicial Complex Visualization

In cograph: Analysis and Visualization of Complex Networks

Simplicial Complex Visualization

Description

Visualize higher-order pathways as smooth blobs overlaid on a network layout. Source nodes are blue, target nodes are red.

Usage

plot_simplicial(
  x = NULL,
  pathways = NULL,
  method = "hon",
  max_pathways = 10L,
  pathway_index = NULL,
  anomaly = c("all", "over", "under"),
  layout = "circle",
  labels = NULL,
  node_color = "#4A7FB5",
  target_color = "#E8734A",
  ring_color = "#F5A623",
  node_size = 22,
  label_size = 5,
  label_color = "#e8e8e8",
  target_label_color = NULL,
  label_halo = TRUE,
  label_halo_color = NULL,
  label_halo_width = 0.035,
  label_halo_alpha = 0.6,
  blob_alpha = 0.25,
  blob_colors = NULL,
  blob_linetype = NULL,
  blob_linewidth = 0.7,
  blob_line_alpha = 0.8,
  shadow = TRUE,
  title = NULL,
  dismantled = FALSE,
  ncol = NULL,
  ...
)

Arguments

x	A network object: tna, netobject, matrix, igraph, cograph_network, net_hon, or net_hypa. When x is a tna or netobject with sequence data and pathways is NULL, higher-order pathways are built automatically using the method parameter.
pathways	Character vector of pathway strings, a list of character vectors, a net_hon / net_hypa object, or any data.frame with a path column (e.g., the output of Nestimate::mogen_transitions()). If a data.frame with a path column is passed as x and pathways is NULL, it is auto-promoted to pathways and the state set is derived from the path strings — plot_simplicial(mgt) works directly. String separators: "A B -> C", "A -> B -> C", "A, B, C", "A - B - C", "A B C". Last state is the target. When a data.frame is passed and a count column is present, rows are sorted by count descending before max_pathways is applied. When NULL and x is a model with sequence data, pathways are built automatically.
method	Pathway source when auto-building from a tna/netobject: "hon" (default, higher-order network), "hypa" (anomalous paths via hypergeometric null), or "rules" (association-rule itemsets via Nestimate::association_rules; rules are rendered as single-colored blobs because itemsets are undirected).
max_pathways	Maximum number of pathways to display. HON pathways are ranked by count, HYPA by anomaly ratio. NULL shows all. Default 10.
pathway_index	Optional positive integer vector selecting ranked pathways after extraction and ranking, before max_pathways is applied. For example, 2 plots the second-ranked pathway and 2:4 plots pathways ranked second through fourth.
anomaly	HYPA anomaly type to display when plotting a net_hypa object or auto-building HYPA pathways via method = "hypa". One of "all", "over", or "under". Default "all". Ignored (with a warning) for non-HYPA inputs such as net_hon, net_association_rules, net_link_prediction, character pathway vectors, or method = "hon" / "rules", which have no anomaly concept.
layout	"circle" (default) or a coordinate matrix.
labels	Display labels. NULL uses state names.
node_color	Source node fill color.
target_color	Target node fill color.
ring_color	Donut ring color.
node_size	Node point size.
label_size	Label text size.
label_color	Label text color (default "#e8e8e8", very light grey). Light grey reads on both white and dark fills when the auto-contrast halo is enabled (it is by default). Applied to both source and target labels unless target_label_color overrides for targets.
target_label_color	Target-node label color. NULL (default) reuses label_color.
label_halo	Logical. Draw a contrasting halo behind each label so it stays readable on any fill — node disc, blob, or the white canvas. Default TRUE. The halo is the only reliable way to keep, e.g., white labels legible when node_color is also light.
label_halo_color	Halo color. NULL (default) auto-picks black or white based on the luminance of label_color, so a white label gets a dark halo and vice versa.
label_halo_width	Halo thickness in plot units. Default 0.035; raise for chunkier outlines, lower for subtler ones, or set to 0 to disable without touching label_halo.
label_halo_alpha	Halo opacity (0–1). Default 0.6 reads as a soft glow rather than a hard outline; raise toward 1 for sharper contrast on very busy backgrounds.
blob_alpha	Blob fill transparency.
blob_colors	Blob fill colors (recycled).
blob_linetype	Blob border line styles (recycled).
blob_linewidth	Blob border line width.
blob_line_alpha	Blob border line transparency.
shadow	Draw soft drop shadows?
title	Plot title.
dismantled	If TRUE, one panel per pathway arranged in a grid layout.
ncol	Number of columns in the grid when dismantled = TRUE. Default NULL auto-selects based on the number of pathways.
...	Additional arguments passed to Nestimate::build_hon() or Nestimate::build_hypa() when auto-building.

Details

Supports direct use with tna and netobject models: when x has sequence data, HON or HYPA pathways are built automatically (requires the Nestimate package). Pathways can also be passed as net_hon or net_hypa objects, with labels auto-translated when x is a tna/netobject.

Value

A ggplot object (or combined grid if dismantled), invisibly.

Examples

set.seed(1)
mat <- matrix(runif(16), 4, 4,
              dimnames = list(LETTERS[1:4], LETTERS[1:4]))
diag(mat) <- 0
plot_simplicial(mat, c("A B -> C", "B C -> D"))

cograph documentation built on May 31, 2026, 5:06 p.m.