OmicVerse Cross-Modal Cell Type Transfer

Goal

Transfer cell labels from a reference AnnData to a query AnnData using a shared latent space such as X_glue, then write predicted labels and uncertainty scores back to the query object. Keep this as one skill: the notebook's plots are optional presentation on top of the same transfer job, not a separate capability.

Quick Workflow

1. Confirm the query and reference expose the same embedding basis in .obsm, or fall back to X.
2. Confirm the reference has the target label column in .obs.
3. Train ov.utils.weighted_knn_trainer(...) on the reference embedding.
4. Transfer labels with ov.utils.weighted_knn_transfer(...).
5. Store the first label column and uncertainty column in query_adata.obs.
6. Plot on an existing basis for smoke validation; use mde only if pymde is available.

Interface Summary