Simulator

Our simulators for cassiopeia are split up into those that simulate topologies and those that simulate data on top of the topologies.

Tree Simulators

We have several frameworks available for simulating topologies:

sim.BirthDeathFitnessSimulator(...[, ...])	Simulator class for a general forward birth-death process with fitness.
sim.ecDNABirthDeathSimulator(...[, ...])	Simulator class for a forward birth-death process with fitness in a population with ecDNA.
sim.CompleteBinarySimulator([num_cells, depth])	Simulate a complete binary tree.
sim.SimpleFitSubcloneSimulator(...)	Simulates a clonal population which develops one fit subclone.

Data Simulators

These simulators are subclasses of the DataSimulator class and implement the overlay_data method which simulates data according to a given topology.

sim.Cas9LineageTracingDataSimulator([...])

Simulates Cas9-based lineage tracing data.

Spatial Simulators

These simulators are subclasses of the SpatialSimulator class and implement the overlay_data method which adds spatial coordinates to a given topology. SpatialSimulator`s are a special sublcass of `DataSimulator and can be used in addition to other `DataSimulator`s that simulate lineage tracing data.

sim.BrownianSpatialDataSimulator(dim, ...[, ...])	Simulate spatial data with a Brownian motion process.
sim.ClonalSpatialDataSimulator([shape, ...])	Simulate spatial data with a clonal spatial autocorrelation constraint.

Leaf SubSamplers

These are utilities for subsampling lineages for benchmarking purposes. For example, sampling a random proportion of leaves or grouping together cells into clades to model spatial data.

sim.SupercellularSampler([ratio, ...])
sim.SpatialLeafSubsampler([bounding_box, ...])
sim.UniformLeafSubsampler([ratio, ...])