popari.simulation_framework.SyntheticDataset

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popari.simulation_framework.SyntheticDataset#

class popari.simulation_framework.SyntheticDataset(replicate_name, parameters, random_state=None, verbose=0)[source]#

Simulated spatial transcriptomics dataset.

Uses AnnData as a base class, with additional methods for simulation.

Attributes

Methods

annotate_domain([points])

assign_domain_labels()

sample_noisy_expression([...])

Samples gene expression from Negative Binomial distribution according to SyntheticDataset attributes.

simulate_expression([predefined_metagenes, ...])

Simulate expression using parameters.

simulate_metagene_based_expression([...])

Simulate metagenes and embeddings following metagene-based SpiceMix model.

simulate_nsf_expression(...[, ...])

Simulate metagenes and embeddings following metagene-based NSF model.

synthesize_cell_embeddings([signal_sigma_x, ...])

Generate synthetic cell embeddings.

synthesize_metagenes([original_metagenes, ...])

Synthesize related metagenes according to the metagene_variation_probabilities vector.
Parameters:

  • replicate_name (int | str)

  • parameters (SimulationParameters)

  • random_state (int | Generator)

  • verbose (int)

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