spac

• spac package
  • Submodules
  • spac.data_utils module
    • add_pin_color_rules()
    • add_rescaled_features()
    • append_annotation()
    • bin2cat()
    • calculate_centroid()
    • combine_annotations()
    • combine_dfs()
    • concatinate_regions()
    • downsample_cells()
    • ingest_cells()
    • load_csv_files()
    • rescale_features()
    • select_values()
    • subtract_min_per_region()
    • subtract_min_quantile()
  • spac.phenotyping module
    • apply_phenotypes()
    • assign_manual_phenotypes()
    • combine_phenotypes()
    • decode_phenotype()
    • generate_phenotypes_dict()
    • is_binary_0_1()
  • spac.spatial_analysis module
    • calculate_nearest_neighbor()
    • neighborhood_profile()
    • ripley_l()
    • spatial_interaction()
  • spac.transformations module
    • apply_per_batch()
    • arcsinh_transformation()
    • arcsinh_transformation_core()
    • batch_normalize()
    • get_cluster_info()
    • normalize_features()
    • normalize_features_core()
    • phenograph_clustering()
    • rename_annotations()
    • run_umap()
    • run_utag_clustering()
    • tsne()
    • z_score_normalization()
  • spac.utag_functions module
    • add_probabilities_to_centroid()
    • custom_message_passing()
    • low_variance_filter()
    • sparse_matrix_dstack()
    • utag()
    • z_score()
  • spac.utils module
    • annotation_category_relations()
    • check_annotation()
    • check_column_name()
    • check_distances()
    • check_feature()
    • check_label()
    • check_list_in_list()
    • check_table()
    • color_mapping()
    • regex_search_list()
    • spell_out_special_characters()
    • text_to_others()
  • spac.visualization module
    • boxplot()
    • dimensionality_reduction_plot()
    • heatmap()
    • hierarchical_heatmap()
    • histogram()
    • interative_spatial_plot()
    • plot_ripley_l()
    • relational_heatmap()
    • sankey_plot()
    • spatial_plot()
    • threshold_heatmap()
    • tsne_plot()
    • visualize_2D_scatter()
    • visualize_nearest_neighbor()
  • Module contents