cell2clone.compute_sample_celltype_clonality

cell2clone.compute_sample_celltype_clonality(adata, class_col, sample_col='sample_id', celltype_col='cell_type', state_labels=('TRBC1', 'TRBC2'), min_cells=20, out_prefix=None, eps=1e-06, clone_score_method='per_celltype', clone_score_col='clone_size_score', clone_score_clip_eps=1e-06, add_clone_score_center=True)

Compute sample-by-cell-type clonality metrics from two-state receptor classifications.

Calculates state fractions, entropy, log-ratio, clonality, and a clone-size score for each sample-cell type combination.

Parameters

adataAnnData

AnnData object containing cell annotations.

class_colstr

Column containing receptor-chain classifications.

…

Returns

pandas.DataFrame

Sample × cell type clonality metrics.

Adds:

• {out_prefix}_log2_ratio = log2((state1 + eps) / (state2 + eps))

• {out_prefix}_log2_ratio_scaled = median-centered log2 ratio

• clonality = abs({out_prefix}_log2_ratio_scaled)

• frac_{state1} (e.g. frac_TRBC1)

• clone_size_score (bias-centered distance of frac_{state1} to median, scaled to [0,1])