diff --git a/src/find_interaction_cluster/clip_figures/__main__.py b/src/find_interaction_cluster/clip_figures/__main__.py index 122674490a4d8228fb6ebb7341088b946c6710f7..e3c9fffceba7c11d9d8599bde92d1bda37fc96b8 100644 --- a/src/find_interaction_cluster/clip_figures/__main__.py +++ b/src/find_interaction_cluster/clip_figures/__main__.py @@ -19,9 +19,8 @@ def clip_analysis(clip_folder: str, weight: int = -1, project: str = "GSM1018963_GSM1018964", test_type: str = "permutation", iteration: int = 10000, display_size: bool=False, - community_file: str = "", - ps: int = 1, - logging_level: str = "DEBUG") -> None: + community_file: str = "", sl_reg: bool = False, + ps: int = 1, logging_level: str = "DEBUG") -> None: """ Create the final figure. @@ -43,6 +42,8 @@ def clip_analysis(clip_folder: str, weight: int = -1, :param community_file: A file containing custom communities. If \ it equals to '' then weight, global weight and same genes parameter are \ used to find the community files computed with ChIA-PET data. + :param sl_reg: True to display the FaRLine regulation of the \ + same factor, False to not display it. :param ps: The number of processes to create (default 1) :param logging_level: The level of data to display (default 'DISABLE') :return: The final dataframe that can be used to create clip figures @@ -57,7 +58,8 @@ def clip_analysis(clip_folder: str, weight: int = -1, raise NotADirectoryError(f"{clip_folder} is not an existing directory") clip_folder_analysis(clip_folder, project, weight, global_weight, same_gene, feature, test_type, iteration, - display_size, community_file, ps, logging_level) + display_size, community_file, sl_reg, ps, + logging_level) clip_analysis() \ No newline at end of file