scimap.tl.spatial_expression

Short description

The spatial_expression function allows users to compute a proximity based weighted expression scoring.
The function generates a neighbourhood for each cell and computes a score for all markers based on its proximity to cells within it's neighbourhood.

The function supports two methods to define a local neighbourhood
Radius method: Can be used to identifies the neighbours within a user defined radius for every cell. KNN method: Can be used to identifies the neighbours based on K nearest neigbours for every cell

The resultant proportion matrix is saved with adata.uns. This can be further clustered to identify similar neighbourhoods.

Parameters

adata : AnnData Object

x_coordinate : float, required (The default is 'X_centroid')
Column name containing the x-coordinates values.

y_coordinate : float, required (The default is 'Y_centroid')
Column name containing the y-coordinates values.

method : string, optional (The default is 'radius')
Two options are available: a) 'radius', b) 'knn'. a) radius - Identifies the neighbours within a given radius for every cell. b) knn - Identifies the K nearest neigbours for every cell.

radius : int, optional (The default is 30)
The radius used to define a local neighbhourhood.

knn : int, optional (The default is 10)
Number of cells considered for defining the local neighbhourhood.

use_raw : boolina, optional (The default is True)
Argument to denote whether to use the raw data or scaled data (sm.pp.rescale).

imageid : string, optional (The default is 'imageid')
Column name of the column containing the image id.

subset : string, optional (The default is None)
imageid of the image to be subsetted for analyis.

label : string, optional (The default is 'spatial_expression')
Key for the returned data, stored in adata.uns.

Returns AnnData object with the results stored in adata.uns['spatial_expression'].

Example

# Running the radius method
adata = sm.tl.spatial_expression (adata, x_coordinate='X_centroid',y_coordinate='Y_centroid',
                                  method='radius', radius=30, imageid='imageid', 
                                  use_raw=True,subset=None,label='spatial_expression_radius')
# Running the knn method
adata = sm.tl.spatial_expression (adata, x_coordinate='X_centroid',y_coordinate='Y_centroid',
                                  method='knn', knn=10, imageid='imageid', 
                                  use_raw=True,subset=None,label='spatial_expression_knn')