stlearn.spatial.trajectory.set_root

stlearn.spatial.trajectory.set_root(adata: AnnData, use_label: str, cluster: str, use_raw: bool = False)[source]

Automatically set the root index for trajectory analysis.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • use_label (str) – Use label result of cluster method.

  • cluster (str) – Cluster identifier to use as the root cluster. Must exist in adata.obs[use_label].

  • use_raw (bool, default False) – If True, use adata.raw.X for calculations; otherwise use adata.X.

Returns:

Index of the selected root cell in the AnnData object

Return type:

int

Raises:

  • ValueError – If the specified cluster is not found in the clustering results.

  • ZeroDivisionError – If the specified cluster contains no cells.