dendroNetwork (version 0.5.5)

cyto_create_cpm_style: Create CPM style in Cytoscape

Description

Function to create a style in Cytoscape to visualise the communities in a network using clique percolation method (CPM: Palla et al., 2005). See also: find_all_cpm_com() Each node is filled with the colour of the community. If a node is part of several communities a pie chart is used to show the various community colours. The function uses a graph as input and the number of cliques (default = 3). The style can be specified or automatically named based on the name of the network an the number of cliques. Before starting this function, Cytoscape must be up and running!

Usage

cyto_create_cpm_style(graph_input, k = 3, com_k = NULL, style_name = "auto")

Value

The style applied in Cytoscape, no objects in R as return.

Arguments

graph_input

the graph with the CPM communities

k

clique size for the visualisation. This should be an integer with the value 3 or higher

com_k

data_frame with the communities for the specific clique size (two columns: node and com_name). This is the result of clique_community_names_par() or clique_community_names()

style_name

name of the output style in Cytoscape. If set to "auto", the style is derived from the name of the network and value for k

Examples

if (FALSE) {
data(hol_rom)
sim_table_hol <- sim_table(hol_rom)
g_hol <- dendro_network(sim_table_hol)
hol_com_cpm_k3 <- clique_community_names(g_hol, k = 3)
cyto_create_graph(g_hol)
cyto_create_cpm_style(g_hol, k = 3, com_k = hol_com_cpm_k3)
}