% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot-mixed-network.R
\name{plot_mixed_network}
\alias{plot_mixed_network}
\title{Plot Mixed Network}
\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{
\item{sym_matrix}{A symmetric matrix representing undirected relationships.
These edges will be drawn straight without arrows.}

\item{asym_matrix}{An asymmetric matrix representing directed relationships.
These edges will be drawn curved with arrows. Reciprocal edges curve in
opposite directions.}

\item{layout}{Layout algorithm or coordinate matrix. Default "oval".}

\item{sym_color}{Color for symmetric/undirected edges. Default "#457B9D" (steel blue).}

\item{asym_color}{Color for asymmetric/directed edges. Can be a single color
or a vector of two colors for positive/negative directions. Default
"#003355" (dark blue, matching TNA style).}

\item{curvature}{Curvature magnitude for directed edges. Default 0.3.}

\item{edge_width}{Edge width(s). If NULL (default), scales automatically by
edge weight like TNA plots. Pass a numeric value to override.}

\item{node_size}{Node size. Default 7.}

\item{title}{Plot title. Default NULL.}

\item{threshold}{Minimum absolute edge weight to display. Values with
\code{abs(value) < threshold} are set to zero (edge removed). Default 0.
Zero-weight edges are always removed regardless of this setting.}

\item{edge_labels}{Show edge weight labels. Default TRUE.}

\item{arrow_size}{Arrow head size for directed edges. Default 0.61 (TNA style).}

\item{edge_label_size}{Size of edge labels. Default 0.6.}

\item{edge_label_position}{Position of edge labels along edge (0-1). Default 0.7.}

\item{initial}{Optional named numeric vector of initial state probabilities
(length = number of nodes). When provided, nodes are drawn as donuts with
the fill proportion equal to the initial probability. Default NULL.}

\item{...}{Additional arguments passed to splot().}
}
\value{
Invisibly returns the combined cograph_network object.
}
\description{
Plot a network combining symmetric (undirected) and asymmetric
(directed) matrices with appropriate edge styling.

Creates a network visualization combining edges from a symmetric matrix
(rendered as straight undirected edges) and an asymmetric matrix
(rendered as curved directed edges).
}
\examples{
# Create symmetric matrix (undirected)
sym <- matrix(0, 4, 4, dimnames = list(LETTERS[1:4], LETTERS[1:4]))
sym[1,2] <- sym[2,1] <- 0.5
sym[3,4] <- sym[4,3] <- 0.6

# Create asymmetric matrix (directed)
asym <- matrix(0, 4, 4, dimnames = list(LETTERS[1:4], LETTERS[1:4]))
asym[1,3] <- 0.7
asym[3,1] <- 0.3
asym[2,4] <- 0.8
asym[4,2] <- 0.4

# Plot combined network
plot_mixed_network(sym, asym, title = "Mixed Network")

}
