inst/GENT/imap_characteristics.R

In SAFE-ICU/GeneExpressionNetworkToolkit: Gene Expression Network Toolkit

## ------INFOMAP community detection-------
#setwd("E:\\RShinyapp\\networksanalysis\\code")
#setwd("C://Networks//code//")
require(igraph)
edgelist_el <- read.csv("Edgelist_top_10prcnt_genes.csv")
#edgelist <- edgelist_table()


# edgelist_el["abs_value"] <- abs(edgelist_el[,3])
# edgelist_el = edgelist_el[,-3]

graph_obj <- graph.data.frame(edgelist_el)
imap_comm_det <- cluster_infomap(graph_obj, e.weights = edgelist_el[,3], v.weights = edgelist_el[,1], nb.trials = 10,
                                 modularity = F)
#total number of communities
comm_list = cbind(imap_comm_det$names,imap_comm_det$membership)
colnames(comm_list) <- c("Gene Name","Community number")