scanpy.Neighbors

class scanpy.Neighbors(adata, n_dcs=None, neighbors_key=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 : AnnData

Annotated data object.

n_dcs : Optional[int] (default: None)

Number of diffusion components to use.

neighbors_key : Optional[str] (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 (on-fly matrix).
eigen_basis	Eigen basis of transition matrix (numpy array).
eigen_values	Eigen values of transition matrix (numpy array).
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, knn, n_pcs, ...])	Compute distances and connectivities of neighbors.
compute_transitions([density_normalize])	Compute transition matrix.
getdoc()
to_igraph()	Generate igraph from connectiviies.