Plot Cograph Network

Plots a network with grid graphics. Node and edge aesthetics can be passed as arguments or set beforehand with sn_nodes and sn_edges.

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

network: A cograph_network object, matrix, data.frame, igraph or tna object. Other inputs are converted with as_cograph(); tna objects are converted with from_tna().
title: Optional plot title.
title_size: Title font size.
margins: Plot margins as c(bottom, left, top, right).
layout_margin: Margin around the network layout (proportion of viewport). Default 0.15.
newpage: Logical. Start a new graphics page? Default TRUE.
background: Background color for the plot. Default "white".
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. NULL (default) keeps the layout stored in a cograph_network and uses "oval" for inputs without stored coordinates.
theme: Theme name: "classic", "dark", "minimal", etc.
seed: Random seed for deterministic layouts. Default 42. Set NULL for random.
labels: Node labels. Can be a character vector to set custom labels.
threshold: Minimum absolute edge weight to display. Edges with abs(weight) < threshold are hidden. Similar to qgraph's threshold.
maximum: Maximum edge weight for width scaling. Weights above this are capped. Similar to qgraph's maximum parameter.
node_size: Node size.
node_shape: Node shape: "circle", "square", "triangle", "diamond", "ellipse", "heart", "star", "pie", "donut", "cross".
node_fill: Node fill color.
node_border_color: Node border color.
node_border_width: Node border width.
node_alpha: Node transparency (0-1).
label_size: Node label text size.
label_color: Node label text color.
label_position: Label position: "center", "above", "below", "left", "right".
show_labels: Logical. Show node labels?
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.
pie_colors: For pie/donut/donut_pie nodes: colors for pie segments.
pie_border_width: Border width for pie chart segments.
donut_values: For donut_pie nodes: vector of values (0-1) for outer ring proportion.
donut_border_width: Border width for donut ring.
donut_inner_ratio: For donut nodes: inner radius ratio (0-1). Default 0.5.
donut_bg_color: For donut nodes: background color for unfilled portion.
donut_show_value: For donut nodes: show value in center? Default FALSE.
donut_value_size: For donut nodes: font size for center value.
donut_value_color: For donut nodes: color for center value text.
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.
donut_color: Fill color(s) for the donut ring. Simplified API: single color for fill, or c(fill, background) for both.
donut_colors: Deprecated. Use donut_color instead.
donut_shape: Base shape for donut: "circle", "square", "hexagon", "triangle", "diamond", "pentagon". The default "circle" takes the base shape from node_shape when that is one of these shapes.
donut_value_fontface: Font face for donut center value: "plain", "bold", "italic", "bold.italic". Default "bold".
donut_value_fontfamily: Font family for donut center value. Default "sans".
donut_value_digits: Decimal places for donut center value. Default 2.
donut_value_prefix: Text before donut center value (e.g., "$"). Default "".
donut_value_suffix: Text after donut center value (e.g., "%"). Default "".
donut2_values: List of values for inner donut ring (for double donut).
donut2_colors: List of color vectors for inner donut ring segments.
donut2_inner_ratio: Inner radius ratio for inner donut ring. Default 0.4.
edge_width: Edge width. If NULL, scales by weight using edge_size and edge_width_range.
edge_size: Maximum edge width for weight scaling. It replaces the upper bound of edge_width_range. NULL (default) uses edge_width_range unchanged.
esize: Deprecated. Use edge_size instead.
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.
edge_scale_mode: Scaling mode for edge weights: "linear" (default), "log" (for wide weight ranges), "sqrt" (moderate compression), or "rank" (equal visual spacing).
edge_cutoff: Accepted for compatibility with splot(). The grid renderer keeps width scaling continuous and does not use the value.
cut: Deprecated. Use edge_cutoff instead.
edge_width_scale: Scale factor for edge widths. Values > 1 make edges thicker.
edge_color: Edge color.
edge_alpha: Edge transparency (0-1).
edge_style: Line style: "solid", "dashed", "dotted", "longdash", "twodash".
curvature: Edge curvature amount.
arrow_size: Size of arrow heads.
show_arrows: Logical. Show arrows?
edge_positive_color: Color for positive edge weights.
positive_color: Deprecated. Use edge_positive_color instead.
edge_negative_color: Color for negative edge weights.
negative_color: Deprecated. Use edge_negative_color instead.
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.
edge_labels: Edge labels. Can be TRUE to show weights, or a vector.
edge_label_size: Edge label text size.
edge_label_color: Edge label text color.
edge_label_position: Position along edge (0 = source, 0.5 = middle, 1 = target).
edge_label_offset: Perpendicular offset from edge line.
edge_label_bg: Background color for edge labels (default "white"). Set to NA for transparent.
edge_label_fontface: Font face: "plain", "bold", "italic", "bold.italic".
edge_label_border: Border style: NULL, "rect", "rounded", "circle".
edge_label_border_color: Border color for label border.
edge_label_underline: Logical. Underline the label text?
bidirectional: Logical. Show arrows at both ends of edges?
loop_rotation: Angle in radians for self-loop direction (default: pi/2 = top).
curve_shape: Spline tension for curved edges (-1 to 1, default: 0).
curve_pivot: Pivot position along edge for curve control point (0-1, default: 0.5).
curves: Curve mode. NULL (default) or "mutual" keeps single edges straight and curves reciprocal edges as two opposing arcs; FALSE plots all edges straight; "force" curves all edges. TRUE is rejected with an error.
node_names: Alternative names for legend (separate from display labels).
legend: Logical. Show legend?
legend_position: Legend position: "topright", "topleft", "bottomright", "bottomleft".
scaling: Scaling mode: "default" for qgraph-matched scaling where node_size=6 looks similar to qgraph vsize=6, or "legacy" for the earlier cograph scaling constants.
weight_digits: Number of decimal places to which a matrix input is rounded before conversion, so that entries rounding to zero are not plotted as edges. Other inputs are not rounded. Default 2. Set NULL to disable rounding.

Value

The updated cograph_network object, invisibly. The function is called for the plot it produces.

Details

soplot and splot

soplot() uses grid graphics and splot() uses base R graphics. The two functions share argument names for the common aesthetics, and splot() has a larger set of arguments.

Edge Curve Behavior

With the default curves, reciprocal edge pairs (A->B and B->A) curve in opposite directions and single edges remain straight. curves = FALSE plots all edges as straight lines, and curves = "force" curves every edge.

Weight Scaling Modes

edge_scale_mode sets how edge weights map to widths. "linear" makes width proportional to weight, "log" compresses weights that span orders of magnitude, "sqrt" gives moderate compression, and "rank" spaces widths evenly by weight rank.

Donut Visualization

Donuts show proportions (0-1) as filled rings around nodes. donut_fill sets the filled proportion per node, donut_color sets the fill color (or fill and background), donut_shape sets the base shape and donut_show_value prints the value in the center.

Examples

soplot(regulation_net, layout = "circle")