moscot.problems.space.MappingProblem

class moscot.problems.space.MappingProblem(adata_sc, adata_sp)

Class for mapping single cell omics data onto spatial data, based on [Nitzan et al., 2019].

Parameters:

• adata_sc (AnnData) – Annotated data object containing the single-cell data.

• adata_sp (AnnData) – Annotated data object containing the spatial data.

Methods

add_problem(key, problem, *[, overwrite])	Add a subproblem.
annotation_mapping(mapping_mode, ...[, ...])	Transfer annotations between distributions.
cell_transition(source[, target, ...])	Aggregate the transport matrix.
compute_entropy(source, target[, forward, ...])	Compute the conditional entropy per cell.
compute_feature_correlation(obs_key[, ...])	Compute correlation of push-forward or pull-back distribution with features.
correlate([var_names, corr_method])	Correlate true and predicted gene expression.
impute([var_names, device])	Impute the expression of specific genes.
load(path)	Load the model from a file.
prepare(sc_attr[, batch_key, spatial_key, ...])	Prepare the mapping problem 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 mapping problem.
spatial_correspondence([interval, max_dist, ...])	Compute structural correspondence between spatial and molecular distances.

Attributes

adata	Annotated data object.
adata_sc	Single-cell data.
adata_sp	Spatial data, alias for adata.
batch_key	Batch key in obs.
filtered_vars	Filtered variables.
problem_kind	Kind of the underlying problem.
problems	OT subproblems that define the biological problem.
solutions	Solutions to the problems.
spatial_key	Spatial key in obsm.
stage	Problem stage.