plot_network_core: Core Network Plotting Function

In scNPM: Single-Cell Network Propensity Matching

Core Network Plotting Function

Description

Generates publication-quality gene regulatory network plots from adjacency matrices.

Usage

plot_network_core(
  adj_matrix,
  mode = "undirected",
  layout_fun = igraph::layout_nicely,
  node_id_col = "gene",
  size_var = "degree",
  color_var = "degree",
  size_range = c(1, 5),
  color_palette = c("steelblue", "white", "orangered"),
  label_size = 2,
  edge_color = "#ADD8E6",
  edge_alpha = 0.6,
  edge_size = 0.3,
  curvature = 0,
  edge_linetype = "solid",
  legend_position = "right"
)

Arguments

adj_matrix	Square adjacency matrix (rows/columns = gene names).
mode	Network type: "undirected" (default) or "directed".
layout_fun	Igraph layout function (default = igraph::layout_nicely; currently informational).
node_id_col	Column name for node IDs (default = "gene").
size_var	Node attribute for size mapping (default = "degree").
color_var	Node attribute for color mapping (default = "degree").
size_range	Numeric vector (length 2) for node size range (default = c(1,5)).
color_palette	Color gradient for nodes (default = c("steelblue", "white", "orangered")).
label_size	Font size for node labels (default = 2).
edge_color	Edge color (default = "#ADD8E6").
edge_alpha	Edge transparency (default = 0.6).
edge_size	Edge thickness (default = 0.3).
curvature	Edge curvature (0 = straight, default = 0).
edge_linetype	Edge line type ("solid" (default) or "dashed").
legend_position	Legend position ("right" (default), "bottom", "none").

Value

ggplot object (network plot) or NULL if no edges exist.

scNPM documentation built on Oct. 19, 2026, 5:10 p.m.