cell2clone.leiden_chain_clones_sampleaware

cell2clone.leiden_chain_clones_sampleaware(adata, class_col, valid_states, sample_col='sample_uid_tpd', use_rep='X_pca', n_neighbors=30, resolution=0.8, purity_cutoff=0.8, key_added='clone_call', ignore_ambiguous=True, min_cells_in_cluster=10, random_state=0)

Detect clonal populations independently within each sample.

Cells are clustered using Leiden, and clusters are labelled as clonal when a receptor-chain state exceeds the specified purity threshold.

Parameters

adataAnnData

AnnData object containing cells.

class_colstr

Column containing receptor-chain classifications.

valid_statessequence of str

States considered valid for clone calling.

…

Returns

AnnData

AnnData object annotated with clone assignments and cluster summaries.