thor.analy.get_tf_activity

thor.analy.get_tf_activity(adata: AnnData, layer: str | None = None, net_df: DataFrame | None = None, smooth_radius: float | None = 200) → AnnData

Infer TF activity using the CollecTRI database. This function calculates the pathway score for each cell using Univariate Linear Model.

Parameters:

  • adata (AnnData) – Annotated data matrix

  • layer (str, optional) – Layer to use for the calculation

  • net_df (pd.DataFrame, optional) – Dataframe with the network information. It should contain the following columns: - source: name of the TF - target: name of the regulated gene - weight: weight of the gene

  • smooth_radius (float, optional) – Radius for the smoothing. Default is 200.

Returns:

Annotated data matrix with the TF as the var_names and the score as the X

Return type:

AnnData