High-level description
TheBrownianSpatialDataSimulator class simulates spatial data for a lineage tree using a Brownian motion process. This simulator assigns spatial coordinates to each cell in a CassiopeiaTree, mimicking the movement of cells in a spatial context.
Code Structure
TheBrownianSpatialDataSimulator class inherits from the SpatialDataSimulator class. It primarily implements the overlay_data method, which is responsible for assigning spatial coordinates to the nodes of a CassiopeiaTree based on a Brownian motion model.
References
cassiopeia.data.CassiopeiaTree: The class representing the lineage tree.cassiopeia.simulator.SpatialDataSimulator: The parent class for spatial data simulators.
Symbols
BrownianSpatialDataSimulator
Description
This class simulates spatial data for a lineage tree using a Brownian motion process. It takes the dimensionality of the space, a diffusion coefficient, and optional scaling and random seed parameters as input.Inputs
| Name | Type | Description |
|---|---|---|
| dim | int | The number of spatial dimensions. |
| diffusion_coefficient | float | The diffusion coefficient for the Brownian motion process. |
| scale_unit_area | bool | Whether to scale the spatial coordinates to a unit area. Defaults to True. |
| random_seed | Optional[int] | A random seed for reproducibility. Defaults to None. |
Outputs
This class does not directly return any output. It modifies the inputCassiopeiaTree object in-place.
Internal Logic
- Initialization: The constructor initializes the simulator with the specified parameters and performs validation checks.
overlay_dataMethod:- Traverses the tree from root to leaves.
- Assigns the root cell to the origin (0, 0, …) in the spatial space.
- For each edge (parent-child relationship) in the tree:
- Calculates the branch length (time since last cell division).
- Samples a random displacement vector from a normal distribution with mean 0 and variance proportional to the branch length and diffusion coefficient.
- Adds the displacement vector to the parent’s coordinates to obtain the child’s coordinates.
- Optionally scales the spatial coordinates to a unit area.
- Sets the spatial coordinates as a node attribute and in the
cell_metaDataFrame of theCassiopeiaTree.
Side Effects
- Modifies the input
CassiopeiaTreeobject in-place by adding spatial coordinates to the nodes and cell metadata.
Dependencies
numpy: Used for numerical operations and random number generation.pandas: Used for handling thecell_metaDataFrame.
Configuration
| Option | Type | Default | Description |
|---|---|---|---|
| scale_unit_area | bool | True | Whether to scale the spatial coordinates to a unit area. |
Error Handling
RaisesDataSimulatorError if:
dimis less than or equal to zero.diffusion_coefficientis negative.