Least action path

spaTrack.VectorField(adata: AnnData, basis: Union[None, str] = None, normalize: bool = False, result_key: Union[None, str] = None, **kwargs)[source]

Learn the function of vector filed.

Parameters:

  • adata – An AnnData object.

  • basis – The label of cell coordinates, for example, umap or spatial. (Default: None)

  • normalize – Logic flag to determine whether to normalize the data to have zero means and unit covariance. (Default: False)

Returns:

A vector field class object.

Return type:

BaseVectorfield

spaTrack.least_action(adata: AnnData, init_cells: Union[str, list], target_cells: Union[str, list], basis: str = 'umap', vf_key: str = 'VecFld', vecfld: Union[None, Callable] = None, adj_key: str = 'pearson_transition_matrix', n_points: int = 25, n_neighbors: int = 100, **kwargs)[source]

Calculate the optimal paths between any two cell states.

Parameters:

  • adata – An AnnData object.

  • init_cells – Cell name or indices of the initial cell states.

  • target_cells – Cell name or indices of the terminal cell states.

  • basis – The embedding data used to predict the least action path. (Default: “umap”)

  • vf_key – A key to the vector field functions in adata.uns. (Default: “VecFld”)

  • vecfld – The vector field function. (Default: None)

  • adj_key – The key to the adjacency matrix in adata.obsp. (Default: “pearson_transition_matrix”)

  • n_points – The number of points on the least action path. (Default: 25)

  • n_neighbors – The number of neighbors. (Default: 100)

Returns:

A trajectory class containing the least action paths information.

Return type:

LeastActionPath

spaTrack.map_cell_to_LAP(adata, basis='spatial', cell_neighbors=150)[source]

Assign a new pseudotime value to each of these cells based on their position along the LAP.

Parameters:

  • adata – An AnnData object.

  • basis – The embedding data. (Default: ‘spatial’)

  • cell_neighbors – The number of cell neighbors. (Default: 150)

Returns:

The ptime of cells map to the LAP and selected neighbor cells.

Return type:

tuple

spaTrack.plot_least_action_path(adata, basis='spatial', ax=None, linewidth=3, point_size=6, linestyle='solid')[source]

Plot the LAP and selected subset of cells.

Parameters:

  • adata – An AnnData object.

  • basis – The embedding data used to predict the least action path. (Default: ‘spatial’)

  • ax – Figure axes. (Default: None)

  • linewidth – Linewidth of the LAP. (Default: 3)

  • point_size – Point size of the LAP. (Default: 6)

  • linestyle – Linestyple of the LAP. (Default: ‘solid’)

Returns:

The plot of the LAP and cells.

Return type:

ax