diff --git a/stereo/algorithm/time_series_analysis.py b/stereo/algorithm/time_series_analysis.py index ebbd6fdd..51dabefc 100644 --- a/stereo/algorithm/time_series_analysis.py +++ b/stereo/algorithm/time_series_analysis.py @@ -39,14 +39,14 @@ def main( All the parameters below are key word arguments and only for `other` `run_method`. - :param spatial_weight: the weight to combine spatial feature - :param n_spatial_feature: n top features to combine of spatial feature - :param temporal_mean_threshold: filter out genes of which mean absolute temporal feature <= temporal_mean_threshold - :param temporal_top_threshold: filter out genes of which top absolute temporal feature < temporal_top_threshold - :param Epsilon: max value to finish iteration - :param w_size: window size to rasterizing spatial expression, see also data.tl.gene_spatial_feature - :param use_col: the col in obs representing celltype or clustering - :param branch: celltypes order in use_col + :param spatial_weight: the weight to combine spatial feature, defaults to 1. + :param n_spatial_feature: n top features to combine of spatial feature, defaults to 2. + :param temporal_mean_threshold: filter out genes of which mean absolute temporal feature <= temporal_mean_threshold, defaults to 0.85. + :param temporal_top_threshold: filter out genes of which top absolute temporal feature < temporal_top_threshold, defaults to 1. + :param Epsilon: max value to finish iteration, defaults to 1e-7. + :param w_size: window size to rasterizing spatial expression, default to 20. + :param use_col: the col in obs representing celltype or clustering, default to None. + :param branch: celltypes order in use_col, default to None. """ # noqa if run_method == RunMethodType.tvg_marker.value: @@ -199,7 +199,7 @@ def gene_spatial_feature(self, w_size=20): self.stereo_exp_data.genes_matrix['spatial_feature'] = X_pca def fuzzy_C_gene_pattern_cluster(self, cluster_number, spatial_weight=1, n_spatial_feature=2, - temporal_mean_threshold=0.85, temporal_top_threshold=1, Epsilon=1e7, w_size=None, + temporal_mean_threshold=0.85, temporal_top_threshold=1, Epsilon=1e-7, w_size=None, use_col=None, branch=None): """ Use fuzzy C means cluster method to cluster genes based on 1-p_value of celltypes in branch