CelLink.model.Cellink.alignment

Cellink.alignment(wt1, wt2, n_neighbors=10, lambd=5e-3, matching_ratio=1, reg=5e-3, reg_m1=(20, 0.1), reg_m2=(0.1, 20), numItermax=1000, iterative=True, sparse=False, BOT=True, verbose=True)

Perform cell-cell alignment (stage I and stage II).

Parameters:

• wt1 (float, default=0.3) – The shrinkage weight to put on the raw data for arr1.

• wt2 (float, default=0.3) – The shrinkage weight to put on the raw data for arr2.

• n_neighbors (int) – Number of neighbors desired

• verbose (bool, default=True) – Whether to print the progress.

• matching_ratio (int) – The mass ratio of cells in arr1 compared with arr2

• lambd (float, default = 1e-1) – The penalty coefficient of entropy regularization of BOT

• reg (float, default = 0.05) – The penalty coefficient of entropy regularization of UOT

• reg_m (tuple) – Each element in the tuple is the penalty coefficient of the KL divergence of the transported mass from one modality and the initial mass from another

• numItermax (int) – Max number of iterations of sinkhorn algorithms

• iterative (bool) – If True, utilize iterative OT, otherwise only balanced OT.

Returns:

None