Select one Visium slide from anndata object¶
select_slide(adata, s, batch_key='sample')[source]¶
This function selects the data for one slide from the spatial anndata object.
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¶
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).
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¶
Sum X_data values across neighbours.
coords – numpy.ndarray with variable measurements for each observation (observations * variables)
neighbours – numpy.ndarray with neigbour indices for each observation (observations * neigbours)