cellrank.external.kernels.OTKernel

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

Stationary optimal transport kernel from [Zhang21].

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

Parameters

  • adata (anndata.AnnData) – Annotated data object.

  • terminal_states (Union[str, Series, None]) – Categorical pandas.Series where non-NaN values mark terminal states. If None, terminal states are assumed to be already present in adata ['terminal_states'].

  • g (Union[str, ndarray]) – Key in anndata.AnnData.obs containing relative growth rates for cells or the array itself.

  • cluster_key (Optional[str]) – If a key to cluster labels is given, terminal_states will be associated with these for naming and colors.

  • kwargs (Any) – Additional keyword arguments.

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.

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 [Zhang21].

copy()

Return a copy of itself.

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

Plot random walks in an embedding.

read(fname)

Deserialize self from a file.

write(fname[, ext])

Serialize self to a file.

write_to_adata([key])

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