cellrank.external.kernels.StationaryOTKernel

class cellrank.external.kernels.StationaryOTKernel(adata, g, terminal_states=None, **kwargs)[source]

Stationary optimal transport kernel from [Zhang et al., 2021].

This class requires the statOT package, which can be installed as pip install statot POT.

Parameters

Attributes

adata

Annotated data object.

backward

Direction of the process.

condition_number

Condition number of the transition matrix.

kernels

Get the kernels of the kernel expression, except for constants.

params

Parameters which are used to compute the transition matrix.

shape

(n_cells, n_cells).

transition_matrix

Return row-normalized transition matrix.

Methods

compute_projection([basis, key_added, copy])

Compute a projection of the transition matrix in the embedding.

compute_transition_matrix(eps, dt[, basis, ...])

Compute transition matrix using stationary OT [Zhang et al., 2021].

copy()

Return a copy of itself.

plot_random_walks(n_sims[, max_iter, seed, ...])

Plot random walks in an embedding.

plot_single_flow(cluster, cluster_key, time_key)

Visualize outgoing flow from a cluster of cells [Mittnenzweig et al., 2021].

read(fname[, adata, copy])

Deserialize self from a file.

write(fname[, write_adata, ext])

Serialize self to a file.

write_to_adata([key])

Write the transition matrix and parameters used for computation to the underlying adata object.