run_motif_clustering {motifcluster} | R Documentation |
Run motif-based clustering
Description
Run motif-based clustering on the adjacency matrix of a (weighted directed) network, using a specified motif, motif type, weighting scheme, embedding dimension, number of clusters and Laplacian type.
Usage
run_motif_clustering(
adj_mat,
motif_name,
motif_type = c("struc", "func"),
mam_weight_type = c("unweighted", "mean", "product"),
mam_method = c("sparse", "dense"),
num_eigs = 2,
type_lap = c("comb", "rw"),
restrict = TRUE,
num_clusts = 2
)
Arguments
adj_mat |
Adjacency matrix to be embedded. |
motif_name |
Motif used for the motif adjacency matrix. |
motif_type |
Type of motif adjacency matrix to use.
One of |
mam_weight_type |
Weighting scheme for the motif adjacency matrix.
One of |
mam_method |
The method to use for building the motif adjacency matrix.
One of |
num_eigs |
Number of eigenvalues and eigenvectors for the embedding. |
type_lap |
Type of Laplacian for the embedding.
One of |
restrict |
Whether or not to restrict the motif adjacency matrix to its largest connected component before embedding. |
num_clusts |
The number of clusters to find. |
Value
A list with 8 entries:
-
adj_mat
: the original adjacency matrix. -
motif_adj_mat
: the motif adjacency matrix. -
comps
: the indices of the largest connected component of the motif adjacency matrix (if restrict = TRUE). -
adj_mat_comps
: the original adjacency matrix restricted to the largest connected component of the motif adjacency matrix (if restrict = TRUE). -
motif_adj_mat_comps
: the motif adjacency matrix restricted to its largest connected component (if restrict = TRUE). -
vals
: a length-num_eigs
vector containing the eigenvalues associated with the Laplace embedding of the (restricted) motif adjacency matrix. -
vects
: a matrix containing the eigenvectors associated with the Laplace embedding of the (restricted) motif adjacency matrix. -
clusts
: a vector containing integers representing the cluster assignment of each vertex in the (restricted) graph.
Examples
adj_mat <- matrix(c(1:16), nrow = 4)
run_motif_clustering(adj_mat, "M1", "func")