cellrank.tl.kernels.PrecomputedKernel

class cellrank.tl.kernels.PrecomputedKernel(transition_matrix=None, adata=None, backward=False, compute_cond_num=False)[source]

Kernel which contains a precomputed transition matrix.

Parameters
  • transition_matrix (Union[ndarray, spmatrix, KernelExpression, str, None]) – Row-normalized transition matrix or a key in adata .obsp or a cellrank.tl.kernels.KernelExpression with the computed transition matrix. If None, try to determine the key based on backward.

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

  • backward (bool) – Direction of the process.

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_transition_matrix(*args, **kwargs)

Return self.

copy()

Return a copy of self.

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.