Some useful igraph commands (R) for converting weighted adjacency matrices to graph files

matrix2graph.r

# Load adjacency matrix as a graph object
library(igraph)

Load adjacency matrix:
dat=read.csv(file.choose(),header=TRUE,row.names=1,check.names=FALSE)

m=as.matrix(dat)

g=graph.adjacency(m,mode="undirected",weighted=TRUE)

# Print a weighted adjacency matrix with names as columns and rows, just the upper half
get.adjacency(g, type=c("upper"),attr=NULL, names=TRUE, edges=TRUE)

# Write to .net file
write.graph(g, file="filename.net", format=c("pajek"))

# To write graphs to other formats see: http://igraph.sourceforge.net/doc/R/write.graph.html
# Edgelists are not weighted, as far I as know


# Community structure detection based on edge betweenness - Girvan and Newman 2004
gn=edge.betweenness.community (g, weights=E(g)$weight,directed=FALSE,edge.betweenness=TRUE,merges=TRUE,bridges=TRUE,modularity=TRUE,membership=TRUE)

# Community strucure via short random walks - Pons and Latapy 2005
w=walktrap.community(g, weights = E(g)$weight, steps = 4, merges =
          TRUE, modularity = TRUE, membership = TRUE)