plot_network: Visualize a network

In SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description

This function is used to plot a network. The network argument can be a network object, network module, an adjacency matrix, or an association matrix. If the result of another plot is provided using the compare_graph argument, then the layout of this network will be based on that plot.

Usage

plot_network(
  network,
  compare_graph = NULL,
  as_subgraph = FALSE,
  node_scale = 4,
  edge_scale = 1,
  node_color = adjustcolor("orange", 0.5),
  generate_layout = igraph::nicely,
  include_vertex_labels = TRUE,
  display_plot = TRUE,
  ...
)

Arguments

network	A 'network', 'network_module', or 'matrix' object.
compare_graph	The plot of another network to use for comparison.
as_subgraph	If TRUE, only nodes of positive degree will be shown.
node_scale	Used for scaling of nodes.
edge_scale	Used for scaling of edges.
node_color	The color used for the nodes.
generate_layout	A function to generate the layout of a graph; used if coords is NULL. See layout_ from igraph for details. Other options include as_star, in_circle, and with_fr, among many others.
include_vertex_labels	If TRUE, the verticies will be labeled.
display_plot	If TRUE (default), the plot will be generated and displayed.
...	Additional arguments passed to plot.igraph.

Value

Creates a plot of the network and returns a graph object. The graph object can be passed back into a future call of plot.network through the compare_edge argument, which will setup the plot for easier comparison between the old graph and the graph of network.

Examples

set.seed(0)
# Basic plotting for networks, modules, and matricies
nw <- random_network(10)
plot(nw)
module <- random_module(1:10)
plot(module)
adj_mat <- get_adjacency_matrix(nw)
plot_network(adj_mat)
# To compare multiple networks, the layout from the first plot can be used
# in subsequent plots using the second argument, `compare_graph`.
nw1 <- random_network(10)
nw2 <- remove_connections_to_node(nw1, 6, prob_remove = 1)
g <- plot(nw1)
plot(nw2, g)
# If the network contains many nodes of degree 0, plotting as subgraph
# may be preferred.
nw <- random_network(100, n_modules = 1)
plot(nw)
plot(nw, as_subgraph = TRUE)
# Networks can be plotted with modules highlighted.
nw <- random_network(100)
g <- plot_network(nw)
plot_modules(nw, g)
# For large networks, the vertex labels can clutter the graph; these can
# be removed using the `include_vertex_labels` argument.
nw <- random_network(250)
g <- plot(nw)
plot(nw, g, include = FALSE)

SeqNet documentation built on July 9, 2021, 9:08 a.m.