R: Graph motifs

graph-motifs {igraph}

R Documentation

Graph motifs

Description

Graph motifs are small connected subgraphs with a well-defined structure. These functions search a graph for various motifs.

Usage

graph.motifs(graph, size = 3, cut.prob = rep(0, size)) 
graph.motifs.no(graph, size = 3, cut.prob = rep(0, size)) 
graph.motifs.est(graph, size = 3, cut.prob = rep(0, size), sample.size =
    vcount(graph)/10, sample = NULL)

Arguments

`graph`	Graph object, the input graph.
`size`	The size of the motif, currently 3 and 4 are supported only.
`cut.prob`	Numeric vector giving the probabilities that the search graph is cut at a certain level. Its length should be the same as the size of the motif (the `size` argument). By default no cuts are made.
`sample.size`	The number of vertices to use as a starting point for finding motifs. Only used if the `sample` argument is `NULL`.
`sample`	If not `NULL` then it specifies the vertices to use as a starting point for finding motifs.

Details

graph.motifs searches a graph for motifs of a given size and returns a numeric vector containing the number of different motifs. The order of the motifs is defined by their isomorphism class, see graph.isoclass.

graph.motifs.no calculates the total number of motifs of a given size in graph.

graph.motifs.est estimates the total number of motifs of a given size in a graph based on a sample.

Value

graph.motifs returns a numeric vector, the number of occurences of each motif in the graph. The motifs are ordered by their isomorphism classes. Note that for unconnected subgraphs, which are not considered to be motifs, the result will be NA.

graph.motifs.no and graph.motifs.est return a numeric constant.

Author(s)

Gabor Csardi csardi.gabor@gmail.com

Examples

g <- barabasi.game(100)
graph.motifs(g, 3)
graph.motifs.no(g, 3)
graph.motifs.est(g, 3)

[Package igraph version 0.7.0 Index]