plot_network_sim: Plot the similarity between two networks

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

Description

This function plots the similarity of connections between two networks. Both networks must be weighted. The width of each edge corresponds to the strength of similarity and is calculated by sqrt(abs((s1 + s2)s1s2)), where s1 and s2 are the weights for a particular connection in network_1 and network_2, respectively

Usage

plot_network_sim(network_1, network_2, compare_graph = NULL, ...)

Arguments

network_1	A weighted 'network' or 'matrix' object.
network_2	A weighted 'network' or 'matrix' object.
compare_graph	The plot of another network to use for comparison.
...	Additional arguments passed to plot_network.

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, 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.

Examples

# Create two networks, the second being a perturbation of the first.
nw1 <- random_network(20)
nw2 <- perturb_network(nw1, n_nodes = 5)
nw1 <- gen_partial_correlations(nw1)
nw2 <- gen_partial_correlations(nw2)
# Can compare networks by plotting each using the same layout.
g <- plot(nw1)
plot(nw2, g)
# Or, plot the differential network or similarity network
plot_network_diff(nw1, nw2, g)
plot_network_sim(nw1, nw2, g)
# Note the behavior when both networks are the same.
plot_network_diff(nw1, nw1, g) # No differences produces an empty network
plot_network_sim(nw1, nw1, g) # Edge widths are still scaled by connection strength.

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