General utils

Select one Visium slide from anndata object

cell2location.utils.select_slide(adata, s, batch_key='sample')

This function selects the data for one slide from the spatial anndata object.

Parameters

• adata – Anndata object with multiple spatial experiments

• s – name of selected experiment

• batch_key – column in adata.obs listing experiment name for each location

Compute KNN graph using spatial coordinates

cell2location.utils.spatial_neighbours(coords, n_sp_neighbors=7, radius=None, include_source_location=True, sample_id=None)

Find spatial neighbours using the number of neighbours or radius (KDTree approach).

Parameters

• coords – numpy.ndarray with x,y positions of spots.

• n_sp_neighbors – how many spatially-adjacent neighbors to report for each spot (including the source spot). Use 7 for hexagonal grid.

• radius – Supersedes n_sp_neighbors - radius within which to report spatially-adjacent neighbors for each spot. Pick radius based on spot size.

• include_source_location – include the observation itself into the list of neighbours.

• sample_id – pd.Series or np.array listing sample membership for each observation (each row of coords).

Add the values of neighbours in a KNN graph for each index node

cell2location.utils.sum_neighbours(X_data, neighbours)

Sum X_data values across neighbours.

Parameters

• coords – numpy.ndarray with variable measurements for each observation (observations * variables)

• neighbours – numpy.ndarray with neigbour indices for each observation (observations * neigbours)