scanpy.Neighbors

class scanpy.Neighbors(adata, n_dcs=None)

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 : AnnDataAnnData

Annotated data object.

n_dcs : int, NoneOptional[int] (default: None)

Number of diffusion components to use.

Attributes

connectivities

Connectivities between data points (sparse matrix).

distances

Distances between data points (sparse matrix).

distances_dpt

DPT distances (on-fly matrix).

eigen_basis

Eigen basis of transition matrix (numpy array).

eigen_values

Eigen values of transition matrix (numpy array).

getdoc

rp_forest

rtype

Mapping, NoneOptional[Mapping[str, Mapping[str, ndarray]]]

transitions

Transition matrix (sparse matrix).

transitions_sym

Symmetrized transition matrix (sparse matrix).

Methods

compute_eigen([n_comps, sym, sort])

Compute eigen decomposition of transition matrix.

compute_neighbors([n_neighbors, knn, n_pcs, …])

Compute distances and connectivities of neighbors.

compute_transitions([density_normalize])

Compute transition matrix.

to_igraph()

Generate igraph from connectiviies.