scib.metrics.pcr

scib.metrics.pcr(adata, covariate, embed=None, n_comps=50, recompute_pca=True, verbose=False)

Principal component regression for anndata object

Wraps pc_regression() while checking whether to:

• compute PCA on embedding or expression data (set embed to name of embedding matrix e.g. embed='X_emb')

• use existing PCA (only if PCA entry exists)

• recompute PCA on expression matrix (default)

Parameters

• adata – Anndata object

• covariate – Key for adata.obs column to regress against

• embed – Embedding to use for principal components. If None, use the full expression matrix (adata.X), otherwise use the embedding provided in adata_post.obsm[embed].

• n_comps – Number of PCs, if PCA is recomputed

Returns

Variance contribution of regression