Skip to contents

Create networks in Cytoscape

Source: R/cyto_create_graph.R
cyto_create_graph.Rd

Function to create a network in cytoscape (https://cytoscape.org/) Cytoscape must be running before executing this function

Usage

cyto_create_graph(
  graph_input,
  network_name = substitute(graph_input),
  collection_name = "default",
  style_name = "default",
  CPM_table = NULL,
  GN_table = NULL
)

Arguments

graph_input

igraph network used to create network in Cytoscape

network_name

name of the network in Cytoscape, defaults to the name of variable that is the network in R

collection_name

name of the collection in Cytoscape (default = default)

style_name

name of the style in Cytoscape (default = default)

CPM_table

table with the name of the nodes in the first column and the CPM-communities in other columns. This is the result of find_all_cpm_com()

GN_table

two column table with the name of the nodes in the first column and the Girvan-Newman-communities in other columns

Value

a graph in Cytoscape

Examples

if (FALSE) { # \dontrun{
data(hol_rom)
sim_table_hol <- sim_table(hol_rom)
g_hol <- dendro_network(sim_table_hol)
hol_com_cpm_all <- find_all_cpm_com(g_hol)
g_hol_gn <- gn_names(g_hol)
cyto_create_graph(g_hol, CPM_table = hol_com_cpm_all, GN_table = g_hol_gn)
} # }