run_motif_embedding | R Documentation |
Calculate a motif adjacency matrix for a given motif and motif type, restrict it to its largest connected component, and then run Laplace embedding with specified Laplacian type and number of eigenvalues and eigenvectors.
run_motif_embedding( 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 )
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. |
A list with 7 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.
adj_mat <- matrix(c(1:9), nrow = 3) run_motif_embedding(adj_mat, "M1", "func")
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