plot_network: Plot network adjacency matrix

In kpj/dce: Pathway Enrichment Based on Differential Causal Effects

Plot network adjacency matrix

Description

Generic function which plots any adjacency matrix (assumes DAG)

Usage

plot_network(
  adja_matrix,
  nodename_map = NULL,
  edgescale_limits = NULL,
  nodesize = 17,
  labelsize = 3,
  node_color = "white",
  node_border_size = 0.5,
  arrow_size = 0.05,
  scale_edge_width_max = 1,
  show_edge_labels = FALSE,
  visualize_edge_weights = TRUE,
  use_symlog = FALSE,
  highlighted_nodes = c(),
  legend_title = "edge weight",
  value_matrix = NULL,
  shadowtext = FALSE,
  ...
)

Arguments

adja_matrix	Adjacency matrix of network
nodename_map	node names
edgescale_limits	Limits for scale_edge_color_gradient2 (should contain 0). Useful to make plot comparable to others
nodesize	Node sizes
labelsize	Node label sizes
node_color	Which color to plot nodes in
node_border_size	Thickness of node's border stroke
arrow_size	Size of edge arrows
scale_edge_width_max	Max range for 'scale_edge_width'
show_edge_labels	Whether to show edge labels (DCEs)
visualize_edge_weights	Whether to change edge color/width/alpha relative to edge weight
use_symlog	Scale edge colors using dce::symlog
highlighted_nodes	List of nodes to highlight
legend_title	Title of edge weight legend
value_matrix	Optional matrix of edge weights if different from adjacency matrix
shadowtext	Draw white outline around node labels
...	additional parameters

Value

plot of dag and dces

Author(s)

Martin Pirkl, Kim Philipp Jablonski

Examples

adj <- matrix(c(0,0,0,1,0,0,0,1,0),3,3)
plot_network(adj)

kpj/dce documentation built on Oct. 29, 2022, 1:40 a.m.