moscot.problems.space.MappingProblem¶
- class moscot.problems.space.MappingProblem(adata_sc, adata_sp)[source]¶
Class for mapping single cell omics data onto spatial data, based on [Nitzan et al., 2019].
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, device, ...])Correlate true and predicted gene expression.
impute([var_names, device, batch_size])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