stlearn.tl.cci.permutation

stlearn.tl.cci.permutation(adata: anndata._core.anndata.AnnData, n_pairs: int = 200, distance: int = None, use_lr: str = 'cci_lr', use_het: str = None) → anndata._core.anndata.AnnData

Permutation test for merged result :param adata: :type adata: AnnData The data object including the cell types to count :param n_pairs: :type n_pairs: int Number of gene pairs to run permutation test (default: 1000) :param distance: :type distance: int Distance between spots (default: 30) :param use_lr: :type use_lr: str LR cluster used for permutation test (default: ‘lr_neighbours_louvain_max’) :param use_het: :type use_het: str cell type diversity counts used for permutation test (default ‘het’)

Returns

adata – Final significant merged scores stored in adata.uns[‘merged_sign’]

Return type

AnnData Data Frame of p-values from permutation test for each window stored in adata.uns[‘merged_pvalues’]