General utils¶
Select one Visium slide from anndata object¶

cell2location.utils.
select_slide
(adata, s, batch_key='sample')[source]¶ 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)[source]¶ 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 spatiallyadjacent 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 spatiallyadjacent 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)[source]¶ 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)