scimap.tl.spatial_distance

Short description

The spatial_distance function enables users to compute the shortest distance between all cells and every phenotype defined in the dataset. This can be used to understand the average distance between two cell-types of interest. For example the average distance between Tumor cell and activated T-cells. In the event of multiple images present within the dataset, one can compare and contrast these distances to understand the distribution of cellular proximity in various biological situations.

The resultant distance matrix is saved with adata.uns.

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.

phenotype : string, required (The default is 'phenotype')
Column name of the column containing the phenotype information. It could also be any categorical assignment given to single cells.

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_distance')
Key for the returned data, stored in adata.uns.

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

Example

# Spatial distance
adata = sm.tl.spatial_distance (adata,x_coordinate='X_position',y_coordinate='Y_position',imageid='ImageId')