scmagnify.partial_ordering

scmagnify.partial_ordering#

scmagnify.partial_ordering(adata, dyn='velocity', lag=5)#

Computes the partial ordering of cells using diffusion operators from RNA velocity or pseudotime kernels.

Parameters:

  • adata (AnnData) – Annotated data object.

  • dyn (Literal['velocity', 'pseudotime'] (default: 'velocity')) – Dynamics used to orient and/or weight edges in the DAG of cells. Default is ‘velocity’.

  • lag (int (default: 5)) – Number of diffusion lags to use when computing partial ordering of cells. Default is 5.

Return type:

FloatTensor

Returns:

torch.FloatTensor Diffusion operator tensor aggregating lagged transitions.

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