Plot Mixed Network — plot_mixed

Plots one network that combines the edges of a symmetric matrix, shown as straight undirected edges, with the edges of an asymmetric matrix, shown as curved directed edges.

Usage

plot_mixed_network(
  sym_matrix,
  asym_matrix,
  layout = "oval",
  sym_color = "ivory4",
  asym_color = COGRAPH_SCALE$tna_edge_color,
  curvature = 0.3,
  edge_width = NULL,
  node_size = 7,
  title = NULL,
  threshold = 0,
  edge_labels = TRUE,
  arrow_size = 0.61,
  edge_label_size = 0.6,
  edge_label_position = 0.7,
  initial = NULL,
  ...
)

Arguments

sym_matrix: A symmetric matrix of undirected relationships. Each non-zero pair is plotted once as a straight edge without arrows.
asym_matrix: An asymmetric matrix of directed relationships, with the same dimensions as sym_matrix. Its edges are plotted as curved arrows.
layout: Layout algorithm or coordinate matrix. Default "oval".
sym_color: Color for undirected edges. Default "ivory4".
asym_color: Color for directed edges. Either a single color, or two colors for reciprocal pairs: the first for the edge from the lower-indexed node and the second for the reverse edge. Non-reciprocal edges use the first color. Default "#003355" (dark blue, the TNA edge color).
curvature: Curvature magnitude for directed edges. Default 0.3.
edge_width: Edge width(s). If NULL (default), widths scale with edge weight as in TNA plots. A numeric value overrides the scaling.
node_size: Node size. Default 7.
title: Plot title. Default NULL.
threshold: Minimum absolute edge weight to display. Values with abs(value) < threshold are set to zero, and zero-weight edges are not plotted. Default 0.
edge_labels: Show edge weight labels. Default TRUE.
arrow_size: Arrow head size for directed edges. Default 0.61 (TNA style).
edge_label_size: Size of edge labels. Default 0.6.
edge_label_position: Position of edge labels along edge (0-1). Default 0.7.
initial: Optional numeric vector of initial state probabilities. A named vector is matched to the node names, with missing states set to 0; an unnamed vector is used in node order. Nodes are then plotted as donuts filled in proportion to the initial probability. A warning is issued when the values do not sum to 1 (tolerance 0.01). Default NULL.
...: Additional arguments passed to splot.

Value

Invisibly, a list with three elements: edges, a data frame with one row per plotted edge and columns from, to (node indices), weight, type ("undirected" or "directed") and color; and sym_matrix and asym_matrix, the input matrices after thresholding.

Examples

plot_mixed_network(symmetrize(regulation_net, keep_format = TRUE), regulation_net)