moscot.problems.cross_modality.TranslationProblem

class moscot.problems.cross_modality.TranslationProblem(adata_src, adata_tgt, **kwargs)

Class for integrating single-cell multi-omics data, based on [Demetci et al., 2022].

Parameters:

• adata_src (AnnData) – Annotated data object containing the source modality.

• adata_tgt (AnnData) – Annotated data object containing the target modality.

• kwargs (Any) – Keyword arguments for CompoundProblem.

Methods

add_problem(key, problem, *[, overwrite])	Add a subproblem.
cell_transition(source[, target, ...])	Aggregate the transport matrix.
compute_feature_correlation(obs_key[, ...])	Compute correlation of push-forward or pull-back distribution with features.
load(path)	Load the model from a file.
prepare(src_attr, tgt_attr[, joint_attr, ...])	Prepare the translation problem.
pull(*args, **kwargs)	Pull mass from target to source.
push(*args, **kwargs)	Push mass from source to target.
remove_problem(key)	Remove a subproblem.
save(path[, overwrite])	Save the problem to a file.
solve([alpha, epsilon, tau_a, tau_b, rank, ...])	Solve the translation problem.
translate(source, target[, forward, ...])	Translate the source modality to the target modality.

Attributes

adata	Annotated data object.
adata_src	Source data.
adata_tgt	Target data.
batch_key	Batch key in obs.
problem_kind	Kind of the underlying problem.
problems	OT subproblems that define the biological problem.
solutions	Solutions to the problems.
stage	Problem stage.