- 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).
Connectivities between data points (sparse matrix).
Distances between data points (sparse matrix).
DPT distances (on-fly matrix).
Eigen basis of transition matrix (numpy array).
Eigen values of transition matrix (numpy array).
Transition matrix (sparse matrix).
Symmetrized transition matrix (sparse matrix).
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 transition matrix.
Generate igraph from connectiviies.