mira.tl.get_cell_pointwise_mutual_information

mira.tl.get_cell_pointwise_mutual_information(adata1, adata2, *, key='X_topic_compositions', colname='pointwise_mutual_information')

For each cell, calculate the pointwise mutual information between RNA and ATAC topic compositions. This compares the joint distribution of topic compositions against the marginal distributions over all cells. High values for pointwise mutual information suggest that the topic compositions in one mode statistically support the compositions in the other.

Parameters

expr_adataanndata.AnnData

AnnData object with expression features, must have “X_topic_compositions” in .obsm.

atac_adataanndata.AnnData

AnnData object with accessibility features, must have “X_topic_compositions” in .obsm.

Returns

adataanndata.AnnData

.obs[‘pointwise_mutual_information’]np.ndarray[float] of shape (n_cells,)

Pointwise mutual information between expression and accessibility topoics for each cell