plot_network_diff: Plot the difference between two networks
In tgrimes/SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description Usage Arguments Value Examples

This function plots the difference in connectivity between two networks. For two identical networks, the graph will be empty. For non-identical networks, black edges are shared by both networks but differ in magnitude or direction (if the networks are weighted), tan edges are in network_1 but not network_2, and red edges are in network_2 but not network_1. All edges are scaled according to the strongest association in either network.

plot_network_diff(network_1, network_2, compare_graph = NULL,
  as_subgraph = FALSE, node_scale = 4, edge_scale = 1,
  node_color = adjustcolor("orange", 0.5), edge_colors = c("black",
  "wheat", "red"), generate_layout = igraph::nicely,
  include_vertex_labels = TRUE, ...)

`network_1`	A 'network' or 'matrix' object.
`network_2`	A 'network' 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.
`edge_colors`	A vector of three colors used for edges; the first colors edges common to both network, the second colors edges in network_1 but not network_2, and the third colors edges that are in network_2 but not network_1. Default is c("black", "wheat", "red").
`generate_layout`	A function to generate the layout of a graph; used if coords is NULL. See ?igraph::layout_ for details. Other options include 'igraph::as_star', 'igraph::in_circle', and 'igraph::with_fr', among many others.
`include_vertex_labels`	If TRUE, the verticies will be labeled.
`...`	Additional arguments passed to plot.igraph().

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()', 'plot_network_diff()' or 'plot_network_sim()' through the 'compare_edge' argument, which will setup the plot for easier comparison between the old graph and the graph of 'network'.

# Create two networks, the second being a perturbation of the first.
nw1 <- random_network(20)
nw2 <- perturb_network(nw1, n_nodes = 5)
# Can compare networks by plotting each using the same layout.
g <- plot(nw1)
plot(nw2, g)
# Or, the differential network can be plotted.
plot_network_diff(nw1, nw2, g)