Plot the graph of average state differences (visNetwork)

This function uses the visNetwork package to plot a network of nodes. The nodes are positioned by default in a hierarchical layout and their colors are derived using the diff values and the get_node_colors function. The color of each node indicates how much more inhibited or active that node is, when comparing the average model classified in the 'good' category vs the average 'bad' one.

plot_avg_state_diff_graph_vis(net, diff, nodes.size = 20, title)

Arguments

net	igraph graph object (to be translated to a visNetwork object)
diff	numeric vector. Every value must be in the [-1,1] interval and represents the average activity difference of each node. The node names have to be specified in the names attribute of the given vector. For example, diff could be the result of using the function get_avg_activity_diff_based_on_specific_synergy_prediction
nodes.size	an integer specifying the size of the nodes. Default value: 20.
title	string. The title of the visNetwork plot.

See also

Other network plotting functions: plot_avg_link_operator_diff_graphs(), plot_avg_link_operator_diff_graph(), plot_avg_state_diff_graphs(), plot_avg_state_diff_graph()

Examples

topology.file = system.file("extdata", "example.sif", package = "emba", mustWork = TRUE)
net = construct_network(topology.file)
diff = c(-0.95,-0.05,0.46,0.39,-0.04,0.72,-0.12,-0.51,-0.86,-0.80)
names(diff) = c("A","C","B","D","W","I","E","J","F","K")
plot_avg_state_diff_graph_vis(net, diff, title = "TEST")