moscot.problems.cross_modality.TranslationProblem.prepare

TranslationProblem.prepare(src_attr, tgt_attr, joint_attr=None, batch_key=None, cost='sq_euclidean', cost_kwargs=mappingproxy({}), a=None, b=None, xy_callback=None, x_callback=None, y_callback=None, xy_callback_kwargs=mappingproxy({}), x_callback_kwargs=mappingproxy({}), y_callback_kwargs=mappingproxy({}), marginal_kwargs=mappingproxy({}), subset=None, reference=None)

Prepare the translation problem.

See also

• See Translating multiomics single-cell data on how to prepare the translation problem.

Parameters:

• src_attr (Union[str, Mapping[str, Any]]) –

  How to get the data for the source modality:

  • str - a key in obsm where the data is stored.

  • dict - it should contain 'attr' and 'key', the attribute and the key in AnnData, and optionally 'tag', one of Tag.

  By default, tag = 'point_cloud' is used.

• tgt_attr (Union[str, Mapping[str, Any]]) –

  How to get the data for the target modality:

  • str - a key in obsm where the data is stored.

  • dict - it should contain 'attr' and 'key', the attribute and the key in AnnData, and optionally 'tag', one of Tag.

  By default, tag = 'point_cloud' is used.

• joint_attr (Union[str, Mapping[str, Any], None]) –

  How to get the data for the linear term in the fused case:

  • None - the pure Gromov-Wasserstein case is used.

  • str - a key in obsm where the data is stored.

  • dict - it should contain 'attr' and 'key', the attribute and key in AnnData, and optionally 'tag' from the tags.

  By default, tag = 'point_cloud' is used.

• batch_key (Optional[str]) – Key in obs specifying the batch.

• cost (Union[Literal['euclidean', 'sq_euclidean', 'cosine', 'pnorm_p', 'sq_pnorm', 'geodesic'], Mapping[Literal['xy', 'x', 'y'], Literal['euclidean', 'sq_euclidean', 'cosine', 'pnorm_p', 'sq_pnorm', 'geodesic']]]) –

  Cost function to use. Valid options are:

  • str - name of the cost function for all terms, see get_available_costs().

  • dict - a dictionary with the following keys and values:

    • 'xy' - cost function for the linear term.

    • 'x' - cost function for the source modality.

    • 'y' - cost function for the target modality.

• cost_kwargs (Union[Mapping[str, Any], Mapping[Literal['x', 'y', 'xy'], Mapping[str, Any]]]) – Keyword arguments for the BaseCost or any backend-specific cost.

• a (Union[bool, str, None]) –

  Source marginals. Valid options are:

  • str - key in obs where the source marginals are stored.

  • bool - if True, estimate the marginals, otherwise use uniform marginals.

  • None - uniform marginals.

• b (Union[bool, str, None]) –

  Target marginals. Valid options are:

  • str - key in obs where the target marginals are stored.

  • bool - if True, estimate the marginals, otherwise use uniform marginals.

  • None - uniform marginals.

• xy_callback (Union[Literal['local-pca'], Callable[[Literal['xy', 'x', 'y'], AnnData, Optional[AnnData]], Optional[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]], Optional[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]], Optional[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.

• marginal_kwargs (Mapping[str, Any]) – Keyword arguments for the estimate_marginals() method.

• 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'.

Return type:

TranslationProblem[TypeVar(K, bound= Hashable)]

Returns:

: Returns self and updates the following fields:

• problems - the prepared subproblems.

• solutions - set to an empty dict.

• batch_key - key in obs where batches are stored.

• stage - set to 'prepared'.

• problem_kind - set to 'quadratic'.