scHopfield.dynamics.get_top_affected_genes

scHopfield.dynamics.get_top_affected_genes(adata: AnnData, n_genes: int = 20, cluster: str | None = None, cluster_key: str = 'cell_type', exclude_perturbed: bool = True) → DataFrame[source]

Get the top genes most affected by the perturbation.

Parameters:

  • adata (AnnData) – Annotated data object with simulation results

  • n_genes (int, optional (default: 20)) – Number of top genes to return

  • cluster (str, optional) – If specified, analyze only cells in this cluster

  • cluster_key (str, optional (default: 'cell_type')) – Key in adata.obs for cluster labels

  • exclude_perturbed (bool, optional (default: True)) – If True, exclude the perturbed genes from the results

Returns:

DataFrame with top affected genes and their mean delta_X values

Return type:

pd.DataFrame