Zonation & utilities

Discretizing trajectories into tissue zones, binning expression along the gradient, and summarizing cell-type dynamics.

utils.get_zonations	Discretize trajectory gradient assignment via Jenks Breaks Save clustering assignment under adata.obs['zone']
utils.get_zonation_features	Compute zonation (discrete) enriched features
utils.get_binned_expr	Smooth P x N (feature-first) matrix => P x K bins with sliding-window average - For computing trajectory dynamics (adata.obs['t']), return scaled values to [0, 1] - For computing feature expressions, return log-normalized values
utils.get_celltype_dynamics	Compute cell-type dynamics along the binned trajectory (sliding window)
utils.get_cluster_dynamics
utils.sort_fitted_expr	Sort expression by both cells (along pseudotime) & features (along peak expression location across pseudotime)