lynx.io.filter_cells

lynx.io.filter_cells(adata_ref, adata_query, by='map', filter_ref=True)

Filter common cells across 2 spatial modalities

Parameters:

• adata_ref (sc.AnnData) – Expression matrix of ref modality

• adata_query (sc.AnnData) – Expression matrix of query modality

• by (str) – Filtering option (by barcode / map)

• filter_ref (bool)

Both adata objects contains mapped coordinates [x_centroids, y_centroids] under adata.obsm

Return type:

(adata_ref_filtered, adata_query_filtered)

Parameters:

• adata_ref (scanpy.AnnData)

• adata_query (scanpy.AnnData)

• by (str)

• filter_ref (bool)