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

None.

kernels

Underlying base kernels.

params

Parameters which are used to compute the transition matrix.

shape

(n_cells, n_cells).

transition_matrix

Row-normalized transition matrix.

Methods

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

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

copy([deep])

Not implemented.

plot_projection([basis, key_added, ...])

Plot transition_matrix as a stream or a grid plot.

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, copy])

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