stereo.algorithm.ms_spa_track.MSSpaTrack.transfer_matrix

MSSpaTrack.transfer_matrix(data1_index=None, data2_index=None, spatial_key='spatial', alpha=0.1, epsilon=0.01, rho=inf, G_1=None, G_2=None, **kwargs)[source]

Calculates transfer matrix between two time.

Parameters:

  • data1_index (Union[int, str, None]) – The index in the ms_data of the first data.

  • data2_index (Union[int, str, None]) – The index in the ms_data of the second data.

  • spatial_key (str) – The key to get position information of cells, defaults to ‘spatial’

  • alpha (float) – Alignment tuning parameter. Note:0 <= alpha <= 1. When alpha = 0 only the gene expression data is taken into account, while alpha =1 only the spatial coordinates are taken into account.

  • epsilon (float) – Weight for entropy regularization term, defaults to 0.01

  • rho (float) – Weight for KL divergence penalizing unbalanced transport, defaults to np.inf

  • G_1 (Optional[float]) – Distance matrix within spatial data 1 (spots, spots), defaults to None

  • G_2 (Optional[float]) – Distance matrix within spatial data 2 (spots, spots), defaults to None