omicverse.single.AnnotationRef

omicverse.single.AnnotationRef#

class omicverse.single.AnnotationRef(adata_query, adata_ref, celltype_key='celltype')[source]#

Reference-based label transfer helper for single-cell annotation.

Parameters:

  • adata_query (AnnData) – Query AnnData that needs cell-type annotation.

  • adata_ref (AnnData) – Reference AnnData with known cell-type labels.

  • celltype_key (str) – Column name in adata_ref.obs containing reference cell-type labels.

Returns:

Initializes concatenated query/reference data and checks feature overlap.

Return type:

None

__init__(adata_query, adata_ref, celltype_key='celltype')[source]#
Parameters:

  • adata_query (AnnData)

  • adata_ref (AnnData)

  • celltype_key (str (default: 'celltype'))

Methods

__init__(adata_query, adata_ref[, celltype_key])

predict([method, n_neighbors, pred_key, ...])

Transfer reference labels to query cells using weighted kNN.

preprocess([mode, n_HVGs, batch_key])

Preprocess concatenated query/reference data for robust label transfer.

train([method])

Train/compute an integrated embedding used for reference label transfer.
Contents