skills/bioskills/bio-tcr-bcr-analysis-repertoire-visualization/scripts/repertoire_plots.py

• plot_spectratype · function · L22-L34 — def plot_spectratype(clone_df, length_col='cdr3_length')
• plot_clonal_space · function · L37-L49 — def plot_clonal_space(clone_df, sample_col='sample')
• plot_clone_tracking · function · L52-L68 — def plot_clone_tracking(clone_df, top_n=10, clone_col='cdr3_aa', time_col='timepoint')
• rarefaction_curve · function · L71-L88 — def rarefaction_curve(counts, depths, reps=20, rng=None)
• plot_rarefaction · function · L91-L104 — def plot_rarefaction(sample_counts, rng=None)
• plot_overlap_heatmap · function · L107-L113 — def plot_overlap_heatmap(overlap_matrix, metric='Morisita-Horn')
• plot_vj_heatmap · function · L116-L123 — def plot_vj_heatmap(clone_df)
• _levenshtein · function · L126-L135 — def _levenshtein(a, b)
• plot_similarity_network · function · L138-L156 — def plot_similarity_network(clone_df, max_norm_dist=0.2, clone_col='cdr3_aa')
• _synthetic_repertoire · function · L159-L175 — def _synthetic_repertoire(rng)