scib.metrics.cell_cycle

scib.metrics.cell_cycle(adata_pre, adata_post, batch_key, embed=None, agg_func=<function mean>, organism='mouse', n_comps=50, recompute_cc=True, precompute_pcr_key=None, verbose=False)

Cell cycle conservation score

Compare the variance contribution of S-phase and G2/M-phase cell cycle scores before and after integration. Cell cycle scores are computed per batch on the unintegrated data set, eliminating the batch effect confounded by the batch_key variable.

\[CC \, conservation = 1 - \frac { |Var_{after} - Var_{before}| } {Var_{before}}\]

Variance contribution is obtained through principal component regression using pc_regression().

Parameters:

  • adata_pre – adata before integration

  • adata_post – adata after integration

  • batch_key – Batch key in adata_post.obs

  • embed – Name of embedding in adata_post.obsm. If embed=None, use the full expression matrix (adata_post.X), otherwise use the embedding provided in adata_post.obsm[embed]

  • agg_func – any function that takes a list of numbers and aggregates them into a single value. If agg_func=None, all results will be returned

  • organism – ‘mouse’ or ‘human’ for choosing cell cycle genes

  • n_comps – number of principle components

  • recompute_cc – If True, force recompute cell cycle score, otherwise use precomputed scores if available as ‘S_score’ and ‘G2M_score’ in adata_post.obs

  • precompute_pcr_key – Key in adata_pre for precomputed PCR values for cell cycle scores. Ignores cell cycle scores in adata_pre if present.

Returns:

A score between 1 and 0. The larger the score, the stronger the cell cycle variance is conserved.

The function can be computed on full corrected feature spaces and latent embeddings for both integrated and unintegrated anndata.Anndata objects. No preprocessing is needed, as the function will perform PCA directly on the feature or embedding space.

Examples

# full feature output
scib.me.cell_cycle(adata_unintegrated, adata, batch_key="batch")

# embedding output
scib.me.cell_cycle(adata_unintegrated, adata, batch_key="batch", embed="X_emb")