API Reference

This section contains the complete API reference for PLASTRO.

• Plasticity Module
  • Core Functions
  • Utility Functions
  • Function Details
• Overlap Module
  • Core Functions
  • Utility Functions
  • Function Details
• Lineage Simulation Module
  • Core Functions
  • Utility Functions
  • Function Details
• Phenotype Simulation Module
  • Core Functions
  • Utility Functions
  • Function Details
• Phylo Module
  • Core Functions
  • Utility Functions
  • Function Details

Main Functions

The most commonly used functions are available directly from the main package:

random_walk_plasticity(full_simulated_ad, ...)	Simulate random walk plasticity in single cells.
PLASTRO_score(character_matrix, ad[, ...])	Compute the PLASTRO overlap plasticity score.
simulate_lineage_tracing(sim_ad, terminal_ad)	Simulate lineage tracing using Cassiopeia on single-cell data.
neighbor_joining(distance_matrix[, outgroup])	Construct phylogenetic tree using neighbor-joining algorithm.
generate_ad(sample_structure, n_dim[, ...])	Generate a complete AnnData object with simulated single-cell data.
simulate_realistic_dataset([n_cell_types, ...])	Generate a realistic single-cell dataset for plasticity testing.