moscot.problems.time.LineageProblem#

class moscot.problems.time.LineageProblem(adata, **kwargs)[source]#

Estimator for modelling time series single cell data based on [Lange et al., 2023].

Parameters:

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_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 Wasserstein distance between OT-interpolated and intermediate cells.

compute_random_distance(source, ...[, ...])

Compute Wasserstein distance between randomly interpolated and intermediate cells.

compute_time_point_distances(source, ...[, ...])

Compute Wasserstein distance between time points.

load(path)

Load the model from a file.

prepare(time_key[, lineage_attr, ...])

Prepare the lineage 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 lineage problem.

Attributes

adata

Annotated data object.

apoptosis_key

Key in obs where cell apoptosis is stored.

cell_costs_source

Cell cost obtained by the first dual potential.

cell_costs_target

Cell cost obtained by the second dual potential.

posterior_growth_rates

Posterior estimate of the source growth rates.

prior_growth_rates

Prior estimate of the source growth rates.

problem_kind

Kind of the underlying problem.

problems

OT subproblems that define the biological problem.

proliferation_key

Key in obs where cell proliferation is stored.

solutions

Solutions to the problems.

stage

Problem stage.

temporal_key

Temporal key in obs.