moscot.base.problems.CompoundProblem.prepare#

CompoundProblem.prepare(policy, key, subset=None, reference=None, xy_callback=None, x_callback=None, y_callback=None, xy_callback_kwargs=mappingproxy({}), x_callback_kwargs=mappingproxy({}), y_callback_kwargs=mappingproxy({}), **kwargs)#

Prepare the individual OT subproblems.

See also

See Subset policy on how to use different policies.

Parameters:

policy (Literal['sequential', 'star', 'external_star', 'explicit', 'triu', 'tril']) – Rule which defines how to construct the subproblems.
key (Optional[str]) – Key in obs for the SubsetPolicy.
subset (Optional[Sequence[Tuple[TypeVar(K, bound= Hashable), TypeVar(K, bound= Hashable)]]]) – Subset of obs['{key}'] for the ExplicitPolicy. Only used when policy = 'explicit'.
reference (Optional[Any]) – Reference for the SubsetPolicy. Only used when policy = 'star'.
xy_callback (Union[Literal['local-pca'], Callable[[Literal['xy', 'x', 'y'], AnnData, Optional[AnnData]], Mapping[Literal['xy', 'x', 'y'], TaggedArray]], None]) – Callback function used to prepare the data in the linear term.
x_callback (Union[Literal['local-pca'], Callable[[Literal['xy', 'x', 'y'], AnnData, Optional[AnnData]], Mapping[Literal['xy', 'x', 'y'], TaggedArray]], None]) – Callback function used to prepare the data in the source quadratic term.
y_callback (Union[Literal['local-pca'], Callable[[Literal['xy', 'x', 'y'], AnnData, Optional[AnnData]], Mapping[Literal['xy', 'x', 'y'], TaggedArray]], None]) – Callback function used to prepare the data in the target quadratic term.
xy_callback_kwargs (Mapping[str, Any]) – Keyword arguments for the xy_callback.
x_callback_kwargs (Mapping[str, Any]) – Keyword arguments for the x_callback.
y_callback_kwargs (Mapping[str, Any]) – Keyword arguments for the y_callback.
kwargs (Any) – Keyword arguments for the subproblems’ prepare() method.

Return type:

BaseCompoundProblem[TypeVar(K, bound= Hashable), TypeVar(B, bound= OTProblem)]

Returns:

: Returns self and updates the following fields:

problems - the prepared subproblems.
solutions - set to an empty dict.
stage - set to 'prepared'.
problem_kind - kind of the OT problem.