% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/render-grid.R
\name{soplot}
\alias{soplot}
\alias{sn_render}
\title{Plot Cograph Network}
\usage{
soplot(
  network,
  title = NULL,
  title_size = 14,
  margins = c(0.05, 0.05, 0.1, 0.05),
  layout_margin = 0.15,
  newpage = TRUE,
  background = "white",
  layout = NULL,
  theme = NULL,
  seed = 42,
  labels = NULL,
  threshold = NULL,
  maximum = NULL,
  node_size = NULL,
  node_shape = NULL,
  node_fill = NULL,
  node_border_color = NULL,
  node_border_width = NULL,
  node_alpha = NULL,
  label_size = NULL,
  label_color = NULL,
  label_position = NULL,
  show_labels = NULL,
  pie_values = NULL,
  pie_colors = NULL,
  pie_border_width = NULL,
  donut_values = NULL,
  donut_border_width = NULL,
  donut_inner_ratio = NULL,
  donut_bg_color = NULL,
  donut_show_value = NULL,
  donut_value_size = NULL,
  donut_value_color = NULL,
  donut_fill = NULL,
  donut_color = NULL,
  donut_colors = NULL,
  donut_shape = "circle",
  donut_value_fontface = "bold",
  donut_value_fontfamily = "sans",
  donut_value_digits = 2,
  donut_value_prefix = "",
  donut_value_suffix = "",
  donut2_values = NULL,
  donut2_colors = NULL,
  donut2_inner_ratio = 0.4,
  edge_width = NULL,
  edge_size = NULL,
  esize = NULL,
  edge_width_range = NULL,
  edge_scale_mode = "linear",
  edge_cutoff = NULL,
  cut = NULL,
  edge_width_scale = NULL,
  edge_color = NULL,
  edge_alpha = NULL,
  edge_style = NULL,
  curvature = NULL,
  arrow_size = NULL,
  show_arrows = NULL,
  edge_positive_color = NULL,
  positive_color = NULL,
  edge_negative_color = NULL,
  negative_color = NULL,
  edge_duplicates = NULL,
  edge_labels = NULL,
  edge_label_size = NULL,
  edge_label_color = NULL,
  edge_label_position = NULL,
  edge_label_offset = NULL,
  edge_label_bg = NULL,
  edge_label_fontface = NULL,
  edge_label_border = NULL,
  edge_label_border_color = NULL,
  edge_label_underline = NULL,
  bidirectional = NULL,
  loop_rotation = NULL,
  curve_shape = NULL,
  curve_pivot = NULL,
  curves = NULL,
  node_names = NULL,
  legend = FALSE,
  legend_position = "topright",
  scaling = "default",
  weight_digits = 2
)

sn_render(
  network,
  title = NULL,
  title_size = 14,
  margins = c(0.05, 0.05, 0.1, 0.05),
  layout_margin = 0.15,
  newpage = TRUE,
  background = "white",
  layout = NULL,
  theme = NULL,
  seed = 42,
  labels = NULL,
  threshold = NULL,
  maximum = NULL,
  node_size = NULL,
  node_shape = NULL,
  node_fill = NULL,
  node_border_color = NULL,
  node_border_width = NULL,
  node_alpha = NULL,
  label_size = NULL,
  label_color = NULL,
  label_position = NULL,
  show_labels = NULL,
  pie_values = NULL,
  pie_colors = NULL,
  pie_border_width = NULL,
  donut_values = NULL,
  donut_border_width = NULL,
  donut_inner_ratio = NULL,
  donut_bg_color = NULL,
  donut_show_value = NULL,
  donut_value_size = NULL,
  donut_value_color = NULL,
  donut_fill = NULL,
  donut_color = NULL,
  donut_colors = NULL,
  donut_shape = "circle",
  donut_value_fontface = "bold",
  donut_value_fontfamily = "sans",
  donut_value_digits = 2,
  donut_value_prefix = "",
  donut_value_suffix = "",
  donut2_values = NULL,
  donut2_colors = NULL,
  donut2_inner_ratio = 0.4,
  edge_width = NULL,
  edge_size = NULL,
  esize = NULL,
  edge_width_range = NULL,
  edge_scale_mode = "linear",
  edge_cutoff = NULL,
  cut = NULL,
  edge_width_scale = NULL,
  edge_color = NULL,
  edge_alpha = NULL,
  edge_style = NULL,
  curvature = NULL,
  arrow_size = NULL,
  show_arrows = NULL,
  edge_positive_color = NULL,
  positive_color = NULL,
  edge_negative_color = NULL,
  negative_color = NULL,
  edge_duplicates = NULL,
  edge_labels = NULL,
  edge_label_size = NULL,
  edge_label_color = NULL,
  edge_label_position = NULL,
  edge_label_offset = NULL,
  edge_label_bg = NULL,
  edge_label_fontface = NULL,
  edge_label_border = NULL,
  edge_label_border_color = NULL,
  edge_label_underline = NULL,
  bidirectional = NULL,
  loop_rotation = NULL,
  curve_shape = NULL,
  curve_pivot = NULL,
  curves = NULL,
  node_names = NULL,
  legend = FALSE,
  legend_position = "topright",
  scaling = "default",
  weight_digits = 2
)
}
\arguments{
\item{network}{A cograph_network object, matrix, data.frame, or igraph object.
Matrices and other inputs are auto-converted.}

\item{title}{Optional plot title.}

\item{title_size}{Title font size.}

\item{margins}{Plot margins as c(bottom, left, top, right).}

\item{layout_margin}{Margin around the network layout (proportion of viewport). Default 0.15.}

\item{newpage}{Logical. Start a new graphics page? Default TRUE.}

\item{background}{Background color for the plot. Default "white".}

\item{layout}{Layout algorithm. Built-in: "circle", "spring", "groups", "grid",
"random", "star", "bipartite". igraph (2-letter): "kk" (Kamada-Kawai),
"fr" (Fruchterman-Reingold), "drl", "mds", "ni" (nicely), "tr" (tree), etc.
Can also pass a coordinate matrix or igraph layout function directly.}

\item{theme}{Theme name: "classic", "dark", "minimal", etc.}

\item{seed}{Random seed for deterministic layouts. Default 42. Set NULL for random.}

\item{labels}{Node labels. Can be a character vector to set custom labels.}

\item{threshold}{Minimum absolute edge weight to display. Edges with
abs(weight) < threshold are hidden. Similar to qgraph's threshold.}

\item{maximum}{Maximum edge weight for width scaling. Weights above this
are capped. Similar to qgraph's maximum parameter.}

\item{node_size}{Node size.}

\item{node_shape}{Node shape: "circle", "square", "triangle", "diamond",
"ellipse", "heart", "star", "pie", "donut", "cross".}

\item{node_fill}{Node fill color.}

\item{node_border_color}{Node border color.}

\item{node_border_width}{Node border width.}

\item{node_alpha}{Node transparency (0-1).}

\item{label_size}{Node label text size.}

\item{label_color}{Node label text color.}

\item{label_position}{Label position: "center", "above", "below", "left", "right".}

\item{show_labels}{Logical. Show node labels?}

\item{pie_values}{For pie/donut/donut_pie nodes: list or matrix of values for segments.
For donut with single value (0-1), shows that proportion filled.}

\item{pie_colors}{For pie/donut/donut_pie nodes: colors for pie segments.}

\item{pie_border_width}{Border width for pie chart segments.}

\item{donut_values}{For donut_pie nodes: vector of values (0-1) for outer ring proportion.}

\item{donut_border_width}{Border width for donut ring.}

\item{donut_inner_ratio}{For donut nodes: inner radius ratio (0-1). Default 0.5.}

\item{donut_bg_color}{For donut nodes: background color for unfilled portion.}

\item{donut_show_value}{For donut nodes: show value in center? Default FALSE.}

\item{donut_value_size}{For donut nodes: font size for center value.}

\item{donut_value_color}{For donut nodes: color for center value text.}

\item{donut_fill}{Numeric value (0-1) for donut fill proportion. This is the
simplified API for creating donut charts. Can be a single value or vector per node.}

\item{donut_color}{Fill color(s) for the donut ring. Simplified API:
single color for fill, or c(fill, background) for both.}

\item{donut_colors}{Deprecated. Use donut_color instead.}

\item{donut_shape}{Base shape for donut: "circle", "square", "hexagon", "triangle",
"diamond", "pentagon". Default inherits from node_shape.}

\item{donut_value_fontface}{Font face for donut center value: "plain", "bold",
"italic", "bold.italic". Default "bold".}

\item{donut_value_fontfamily}{Font family for donut center value. Default "sans".}

\item{donut_value_digits}{Decimal places for donut center value. Default 2.}

\item{donut_value_prefix}{Text before donut center value (e.g., "$"). Default "".}

\item{donut_value_suffix}{Text after donut center value (e.g., "\%"). Default "".}

\item{donut2_values}{List of values for inner donut ring (for double donut).}

\item{donut2_colors}{List of color vectors for inner donut ring segments.}

\item{donut2_inner_ratio}{Inner radius ratio for inner donut ring. Default 0.4.}

\item{edge_width}{Edge width. If NULL, scales by weight using edge_size and edge_width_range.}

\item{edge_size}{Base edge size for weight scaling. NULL (default) uses adaptive sizing
based on network size: \code{15 * exp(-n_nodes/90) + 1}. Larger values = thicker edges.}

\item{esize}{Deprecated. Use \code{edge_size} instead.}

\item{edge_width_range}{Output width range as c(min, max) for weight-based scaling.
Default c(0.5, 4). Edges are scaled to fit within this range.}

\item{edge_scale_mode}{Scaling mode for edge weights: "linear" (default),
"log" (for wide weight ranges), "sqrt" (moderate compression),
or "rank" (equal visual spacing).}

\item{edge_cutoff}{Two-tier cutoff for edge width scaling. NULL (default) = auto 75th percentile.
0 = disabled. Positive number = manual threshold.}

\item{cut}{Deprecated. Use \code{edge_cutoff} instead.}

\item{edge_width_scale}{Scale factor for edge widths. Values > 1 make edges thicker.}

\item{edge_color}{Edge color.}

\item{edge_alpha}{Edge transparency (0-1).}

\item{edge_style}{Line style: "solid", "dashed", "dotted".}

\item{curvature}{Edge curvature amount.}

\item{arrow_size}{Size of arrow heads.}

\item{show_arrows}{Logical. Show arrows?}

\item{edge_positive_color}{Color for positive edge weights.}

\item{positive_color}{Deprecated. Use \code{edge_positive_color} instead.}

\item{edge_negative_color}{Color for negative edge weights.}

\item{negative_color}{Deprecated. Use \code{edge_negative_color} instead.}

\item{edge_duplicates}{How to handle duplicate edges in undirected networks.
NULL (default) = stop with error listing duplicates. Options: "sum", "mean",
"first", "max", "min", or a custom aggregation function.}

\item{edge_labels}{Edge labels. Can be TRUE to show weights, or a vector.}

\item{edge_label_size}{Edge label text size.}

\item{edge_label_color}{Edge label text color.}

\item{edge_label_position}{Position along edge (0 = source, 0.5 = middle, 1 = target).}

\item{edge_label_offset}{Perpendicular offset from edge line.}

\item{edge_label_bg}{Background color for edge labels (default "white"). Set to NA for transparent.}

\item{edge_label_fontface}{Font face: "plain", "bold", "italic", "bold.italic".}

\item{edge_label_border}{Border style: NULL, "rect", "rounded", "circle".}

\item{edge_label_border_color}{Border color for label border.}

\item{edge_label_underline}{Logical. Underline the label text?}

\item{bidirectional}{Logical. Show arrows at both ends of edges?}

\item{loop_rotation}{Angle in radians for self-loop direction (default: pi/2 = top).}

\item{curve_shape}{Spline tension for curved edges (-1 to 1, default: 0).}

\item{curve_pivot}{Pivot position along edge for curve control point (0-1, default: 0.5).}

\item{curves}{Curve mode: TRUE (default) = single edges straight, reciprocal edges
curve as ellipse (two opposing curves); FALSE = all straight; "force" = all curved.}

\item{node_names}{Alternative names for legend (separate from display labels).}

\item{legend}{Logical. Show legend?}

\item{legend_position}{Legend position: "topright", "topleft", "bottomright", "bottomleft".}

\item{scaling}{Scaling mode: "default" for qgraph-matched scaling where node_size=6
looks similar to qgraph vsize=6, or "legacy" to preserve pre-v2.0 behavior.}

\item{weight_digits}{Number of decimal places to round edge weights to before
plotting. Edges that round to zero are automatically removed. Default 2.
Set NULL to disable rounding.}
}
\value{
The updated \code{cograph_network} object, invisibly. Called
primarily for the side effect of drawing.

The updated \code{cograph_network} object, invisibly. Called
primarily for the side effect of drawing.
}
\description{
Main plotting function for Cograph networks. Renders the network visualization
using grid graphics. Accepts all node and edge aesthetic parameters.
}
\details{
\subsection{soplot vs splot}{

\code{soplot()} uses grid graphics while \code{splot()} uses base R graphics.
Both accept the same parameters and produce visually similar output. Choose based on:
\itemize{
\item \strong{soplot}: Better for integration with ggplot2, combining plots,
and publication-quality vector graphics.
\item \strong{splot}: Better for large networks (faster rendering), interactive
exploration, and traditional R workflows.
}
}

\subsection{Edge Curve Behavior}{

Edge curving is controlled by the \code{curves} and \code{curvature} parameters:
\describe{
\item{\strong{curves = FALSE}}{All edges are straight lines.}
\item{\strong{curves = TRUE}}{(Default) Reciprocal edge pairs (A\code{->}B and
B\code{->}A) curve in opposite directions to form a visual ellipse. Single
edges remain straight.}
\item{\strong{curves = "force"}}{All edges curve inward toward the network center.}
}
}

\subsection{Weight Scaling Modes (edge_scale_mode)}{

Controls how edge weights map to visual widths:
\describe{
\item{\strong{linear}}{Width proportional to weight. Best for similar-magnitude weights.}
\item{\strong{log}}{Logarithmic scaling. Best for weights spanning orders of magnitude.}
\item{\strong{sqrt}}{Square root scaling. Moderate compression for skewed data.}
\item{\strong{rank}}{Rank-based scaling. Equal visual spacing regardless of values.}
}
}

\subsection{Donut Visualization}{

The donut system visualizes proportions (0-1) as filled rings around nodes:
\describe{
\item{\strong{donut_fill}}{Proportion filled (0-1). Can be scalar or per-node vector.}
\item{\strong{donut_color}}{Fill color. Single color, c(fill, bg), or per-node vector.}
\item{\strong{donut_shape}}{Base shape: "circle", "square", "hexagon", etc.}
\item{\strong{donut_show_value}}{Show numeric value in center.}
}
}
}
\examples{
adj <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
# With cograph()
cograph(adj) |> soplot()

# Direct matrix input with all options
adj |> soplot(
  layout = "circle",
  node_fill = "steelblue",
  node_size = 0.08,
  edge_width = 2
)
mat <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
sn_render(mat)
}
\seealso{
\code{\link{splot}} for base R graphics rendering (alternative engine),
\code{\link{cograph}} for creating network objects,
\code{\link{sn_nodes}} for node customization,
\code{\link{sn_edges}} for edge customization,
\code{\link{sn_layout}} for layout algorithms,
\code{\link{sn_theme}} for visual themes,
\code{\link{from_qgraph}} and \code{\link{from_tna}} for converting external objects
}
