scanpy.Neighbors

Contents

scanpy.Neighbors#

class scanpy.Neighbors(adata, *, n_dcs=None, neighbors_key=None)[source]#

Data represented as graph of nearest neighbors.

Represent a data matrix as a graph of nearest neighbor relations (edges) among data points (nodes).

Parameters:
adata AnnData

Annotated data object.

n_dcs int | None (default: None)

Number of diffusion components to use.

neighbors_key str | None (default: None)

Where to look in .uns and .obsp for neighbors data

Attributes

connectivities

Connectivities between data points (sparse matrix).

distances

Distances between data points (sparse matrix).

distances_dpt

DPT distances.

eigen_basis

Eigen basis of transition matrix.

eigen_values

Eigen values of transition matrix.

rp_forest

transitions

Transition matrix (sparse matrix).

transitions_sym

Symmetrized transition matrix (sparse matrix).

Methods

compute_eigen([n_comps, sym, sort, random_state])

Compute eigen decomposition of transition matrix.

compute_neighbors([n_neighbors, n_pcs, ...])

Compute distances and connectivities of neighbors.

compute_transitions([density_normalize])

Compute transition matrix.

getdoc()

to_igraph()

Generate igraph from connectiviies.