scib.metrics.hvg_overlap

scib.metrics.hvg_overlap(adata_pre, adata_post, batch_key, n_hvg=500, verbose=False)

Highly variable gene overlap

Metric that computes the average percentage of overlapping highly variable genes per batch pre post integration.

Parameters

  • adata_pre – Unintegrated anndata object

  • adata_post – Integrated anndata object

  • batch_key – Batch variable in adata_post.obs

  • n_hvg – Number of hvgs to compute per batch

Returns

Average percentage of overlapping highly variable genes

The score can only be computed on feature spaces. No preprocessing is needed, as the function will perform highly variable gene selection.

Example

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