scimap.tl.spatial_lda

Short description

The spatial_lda function applies Latent Dirichlet Allocation (LDA) method to identify spatial motifs. First local neighbourhoods are defined and then they are passed togeather through the LDA modelling to identify motifs of neighbourhoods.

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 results of the method are stored in adata.uns
The weights in latent space for each cell which is further used for clustering to identify the motifs are saved under adata.uns['spatial_lda']
The weights each cell-types contribution to the spatial motif is stored under adata.uns['spatial_lda_probability']
The model itself is saved under adata.uns['spatial_lda_model']

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.

num_motifs : int, optional (The default is 10)
The number of requested latent motifs to be extracted from the training corpus.

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.

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.

random_state : int, optional (The default is 0)
Either a randomState object or a seed to generate one. Useful for reproducibility.

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

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

Example

# Running the radius method
adata = spatial_lda (adata, num_motifs=10, radius=100)