moscot.problems.spatiotemporal.SpatioTemporalProblem¶
- class moscot.problems.spatiotemporal.SpatioTemporalProblem(adata, **kwargs)[source]¶
Class for analyzing time series spatial single-cell data.
Methods
add_problem
(key, problem, *[, overwrite])Add a subproblem.
align
([reference, mode, spatial_key, key_added])Align the spatial data.
annotation_mapping
(mapping_mode, ...[, ...])Transfer annotations between distributions.
cell_transition
(source, target, ...[, ...])Aggregate the transport matrix.
compute_batch_distances
(time, batch_key[, ...])Compute the average Wasserstein distance between batches for a specific time point.
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.
compute_interpolated_distance
(source, ...[, ...])compute_random_distance
(source, ...[, ...])compute_time_point_distances
(source, ...[, ...])load
(path)Load the model from a file.
prepare
(time_key[, spatial_key, joint_attr, ...])Prepare the spatiotemporal problem problem.
pull
(source, target[, data, subset, ...])Pull mass from target to source.
push
(source, target[, data, subset, ...])Push mass from source to target.
remove_problem
(key)Remove a subproblem.
sankey
(source, target, source_groups, ...[, ...])Compute a Sankey diagram between cells across time points.
save
(path[, overwrite])Save the problem to a file.
score_genes_for_marginals
([...])Compute gene scores to obtain prior knowledge about proliferation and apoptosis.
solve
([alpha, epsilon, tau_a, tau_b, rank, ...])Solve the spatiotemporal problem.
Attributes
Annotated data object.
Key in
obs
where cell apoptosis is stored.Batch key in
obs
.Cell cost obtained by the first dual potential.
Cell cost obtained by the second dual potential.
Posterior estimate of the source growth rates.
Prior estimate of the source growth rates.
Kind of the underlying problem.
OT subproblems that define the biological problem.
Key in
obs
where cell proliferation is stored.Solutions to the
problems
.Spatial key in
obsm
.Problem stage.
Temporal key in
obs
.