stereo.algorithm.spa_track.SpaTrack.get_ot_matrix¶

SpaTrack.get_ot_matrix(data_type, alpha1=0.5, alpha2=0.5, spatial_key=None, n_pcs=50, pca_res_key=None)[source]¶

Calculate transfer probabilities between cells.

Using optimal transport theory based on gene expression and/or spatial location information.

Parameters:

data_type (str) – The type of sequencing data. * - spatial: for the spatial transcriptome data. * - single-cell: for the single-cell sequencing data.
alpha1 (int) – The proportion of spatial location information, defaults to 0.5.
alpha2 (int) – The proportion of gene expression information, defaults to 0.5.
spatial_key (Optional[str]) – The key to get position information of cells, by default, the data.spatial_key will be used.
n_pcs (int) – _description_, defaults to 50
pca_res_key (Optional[str]) – The number of used pcs to be calculated, defaults to None

The transfer matrix stored with the key trans in data.tl.result.