topographical_correlation_map

topographical_correlation_map(domain, population_A, population_B, include_boundaries=None, exclude_boundaries=None, boundary_exclude_distance=0, radius_of_interest=50, kernel_radius=150, kernel_sigma=50, kernel_function=None, mesh_step=10, max_correlation_threshold=5, remain_within_connected_component=False, add_contribution_as_labels=False, contribution_label_name='TCM contributions', visualise_output=False, visualise_tcm_kwargs={})

Compute the topographical correlation map (TCM) between two populations within a given domain.

The TCM is a measure of spatial heterogeneity in the correlation between pairs of points across the domain and is computed as the ratio of the number of points in population B within a radius of interest to the expectation under complete spatial randomness from each point in population A.

The TCM provides a quantitative summary of colocalisation between the populations up to a specific length scale.

Parameters:

domainDomain

A muspan domain.

population_Alist or np.ndarray or query-like

The first population of objects or a query to select objects.

population_Blist or np.ndarray or query-like

The second population of objects or a query to select objects.

include_boundariesarray-like, query-like, or None, optional

Boundaries to include in the analysis. Defaults to None.

exclude_boundariesarray-like, query-like, or None, optional

Boundaries to exclude from the analysis. Defaults to None.

boundary_exclude_distancefloat, optional

Distance from the boundary to exclude objects, by default 0.

radius_of_interestfloat, optional

The radius within which to consider objects for correlation. Default is 50.

kernel_radiusfloat, optional

The radius of the kernel used for smoothing. Default is 150.

kernel_sigmafloat, optional

The standard deviation of the default Gaussian kernel used for smoothing. Default is 50.

kernel_functioncallable, optional

Custom kernel function. If None, a Gaussian kernel is used. Defaults to None.

mesh_stepfloat, optional

The step size for the mesh grid. Default is 10.

max_correlation_thresholdfloat, optional

The maximum correlation threshold for normalization. Default is 5.

remain_within_connected_componentbool, optional

Whether to remain within the connected component of the boundary. Default is False.

visualise_outputbool, optional

Whether to visualize the output TCM. Default is False.

visualise_tcm_kwargsdict, optional

Additional keyword arguments for visualise.visualise_topographical_correlation_map.

Returns:

topographicalCorrelationMapnp.ndarray

The computed topographical correlation map.

Raises:

ValueError

If the provided queries are not of the correct type.

Notes

For more information on the topographical correlation map, see the following reference.