ANTsR (version 1.0)

makeGraph: Simple function to create and measure a graph from a square input matrix.

Description

Creates an igraph object from a square input correlation matrix - only positive correlations are used. Based on the graph.adjacency function of igraph. gplot is helpful for visualization.

Usage

makeGraph(mat, graphdensity = 1, communityMethod = NA,
  getEfficiency = FALSE)

Arguments

mat

input matrix

graphdensity

fraction of edges to keep

communityMethod

see igraph's community detection

getEfficiency

boolean, this is slow to compute

Value

a named list is output including the graph object, adjacency matrix and several graph metrics

Examples

# NOT RUN {
mat <- matrix(c(rep(1,100)),ncol=10)
gobj<-makeGraph( mat )
mat <- matrix(  c( 1, 0.5, 0.2, -0.1, 1, 0.3, -0.2, 0.6, 1 ) , ncol= 3 )
gobj<-makeGraph( mat , 0.5 )
# gplot( gobj$adjacencyMatrix ) # need sna library for this
# }