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

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

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,
  inverseValuesAsWeights = FALSE
)

Arguments

mat	input matrix
graphdensity	fraction of edges to keep
communityMethod	see igraph's community detection
getEfficiency	boolean, this is slow to compute
inverseValuesAsWeights	if TRUE, high correlations produce small edge weights. This detail is important when using igraph algorithms as different methods use weights in different ways. See igraph for its is_weighted documentation which notes that weights are used as distances in shortest path calculations and as strength (similar to degree) for community methods.

Value

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

Author(s)

Avants BB

Examples

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)

stnava/ANTsR documentation built on April 13, 2025, 4:10 a.m.