BrownianSpatialDataSimulator.py

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High-level description

The BrownianSpatialDataSimulator 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.

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Code Structure

The BrownianSpatialDataSimulator 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.

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References

• cassiopeia.data.CassiopeiaTree: The class representing the lineage tree.
• cassiopeia.simulator.SpatialDataSimulator: The parent class for spatial data simulators.

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Symbols

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BrownianSpatialDataSimulator

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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.

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Inputs

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Outputs

This class does not directly return any output. It modifies the input CassiopeiaTree object in-place.

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Internal Logic

1. Initialization: The constructor initializes the simulator with the specified parameters and performs validation checks.
2. overlay_data Method:
   • 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_meta DataFrame of the CassiopeiaTree.

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Side Effects

• Modifies the input CassiopeiaTree object in-place by adding spatial coordinates to the nodes and cell metadata.

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Dependencies

• numpy: Used for numerical operations and random number generation.
• pandas: Used for handling the cell_meta DataFrame.

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Configuration

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Error Handling

Raises DataSimulatorError if:

• dim is less than or equal to zero.
• diffusion_coefficient is negative.