# cellrank.external.kernels.WOTKernel.compute_transition_matrix

WOTKernel.compute_transition_matrix(cost_matrices=None, lambda1=1, lambda2=50, epsilon=0.05, growth_iters=1, solver='duality_gap', growth_rate_key=None, use_highly_variable=True, last_time_point=LastTimePoint.UNIFORM, threshold='auto', conn_kwargs=mappingproxy({}), **kwargs)[source]

Compute transition matrix using Waddington OT .

Computes transport maps linking together pairs of time points for time-series single cell data using unbalanced optimal transport, taking into account cell birth and death rates. From the sequence of transition maps linking pairs of sequential time points, we construct one large transition matrix which contains the normalized transport maps as blocks on the 1st upper diagonal.

Parameters
Return type

WOTKernel

Returns

cellrank.external.kernels.WOTKernel Makes transition_matrix, transport_maps and growth_rates available. Also modifies anndata.AnnData.obs with the following key:

• ’estimated_growth_rates’ - the estimated final growth rates.

Notes