Skip to contents

Graph motifs

Source: R/motifs.R
motifs.Rd

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

Usage

motifs(graph, size = 3, cut.prob = NULL, callback = NULL)

Arguments

graph

Graph object, the input graph.

size

The size of the motif, currently sizes 3 and 4 are supported in directed graphs and sizes 3 to 6 in undirected graphs.

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). If NULL, the default, no cuts are made.

callback

Optional callback function to call for each motif found. The function should accept two arguments: vids (integer vector of vertex IDs in the motif) and isoclass (the isomorphism class of the motif). The function should return FALSE to continue the search or TRUE to stop it. If NULL (the default), motif counts are returned as a numeric vector.

Important limitation: Callback functions must NOT call any igraph functions (including simple queries like vcount() or ecount()). Doing so will cause R to crash due to reentrancy issues. Extract any needed graph information before calling the function with a callback, or use collector mode (the default) and process results afterward.

Value

When callback is NULL, motifs() returns a numeric vector, the number of occurrences 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.

When callback is provided, the function returns NULL invisibly and calls the callback function for each motif found.

Details

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 isomorphism_class().

motifs_randesu, motifs_randesu_callback_closure()

See also

isomorphism_class()

Other graph motifs: count_motifs(), dyad_census(), sample_motifs()

Examples

g <- sample_pa(100)
motifs(g, 3)
#>  [1]  NA  NA 266  NA  80   0   0   0   0   0   0   0   0   0   0   0
count_motifs(g, 3)
#> [1] 346
sample_motifs(g, 3)
#> [1] 60

# Using callback to stop search after finding 5 motifs
count <- 0
motifs(g, 3, callback = function(vids, isoclass) {
  count <<- count + 1
  count < 5  # stop after 5 motifs
})