Build a graph object from a graph object

Usage

build_graph_from_igraph(
  igraph,
  use_existing_modules = TRUE,
  module.method = c("Fast_greedy", "Walktrap", "Edge_betweenness", "Spinglass"),
  module_attr = NULL,
  node_annotation = NULL,
  top_modules = 15,
  seed = 1115
)

Arguments

igraph: a igraph object
use_existing_modules: Logical (default = TRUE). If TRUE, reuse module information already stored on igraph vertices when available.
module.method: Character. Network community detection (module identification) method. Options include "Fast_greedy", "Walktrap", "Edge_betweenness", and "Spinglass".
module_attr: Character or NULL (default = NULL). Optional vertex attribute name containing precomputed module labels. When NULL, the function will auto-detect one of "Modularity", "modularity2", "modularity3", or "modularity".
node_annotation: Data Frame The annotation file of nodes in network
top_modules: Integer. Number of top-ranked modules to select.
seed: Integer (default = 1115). Random seed for reproducibility.

Value

An graph object

Examples

data(ppi_example)
ig <- igraph::graph_from_data_frame(
  d        = ppi_example$ppi,
  vertices = ppi_example$annotation,
  directed = FALSE
)
obj <- build_graph_from_igraph(igraph = ig, module.method = "Fast_greedy")
levels(get_graph_nodes(obj)$Modularity)
#>  [1] "1"      "10"     "11"     "12"     "13"     "14"     "15"     "16"    
#>  [9] "17"     "18"     "19"     "2"      "20"     "21"     "22"     "Others"