scRL.GridCore.align_pseudotime

scRL.GridCore.align_pseudotime(gres, early_cluster, n_sample_cells=10, key_add='pseudotime', boundary=True, early_cell=None, n_jobs=8)[source]

This function aligns pseudotime across a grid-based representation of data. It can start from a predefined early cell or a cluster, optionally restricting start points to grid boundaries. Pseudotime is calculated using Dijkstra’s algorithm for shortest paths in a graph constructed from the grid adjacency matrix. The function handles multiple graph components by connecting them and adjusting pseudotime accordingly. The result is normalized and stored.

Parameters:

  • gres – Grids results

  • early_cluster – User defined early cluster which must be matched to the grids cluster name, ignored if early cell is set.

  • n_sample_cells – Number of cells to sample in early cluster (Default: 10)

  • key_add – The added key for pseudo-time (Default: ‘pseudotime’)

  • boundary – Whether restrict the starting points to the grid boundary (Default: True)

  • early_cell – User defined starting cell (Default: None)

  • n_jobs – Number of cores to use (Default: 8)

Return type:

None