Core Function Descriptions

Below is a live table of contents that will bring you to a summary of each core function within SOM_Seq_Sim. Note that the structure of the table of contents follows the repo structure; SOM and Seq_Sim functions are separated.

• SOM Core Functions
  • Module contents
    • Self-Organizing Maps (SOMs) Module
      • What is a Self-Organizing Map?
      • How Does a SOM Work?
      • How Does a SOM Compare to Other Clustering Methods?
    • SOM
      • SOM.calculate_percent_variance_explained()
      • SOM.calculate_topographic_error()
      • SOM.plot_categorical_data()
      • SOM.plot_component_planes()
      • SOM.plot_map_grid()
      • SOM.train_map()
• Seq_Sim Core Functions
  • Module contents
    • add_differential_cell_types()
    • add_rows_for_diff_cells()
    • apply_noise()
    • arg_parser()
    • calculate_abundance()
    • calculate_diff_expression()
    • case_when()
    • combine_features()
    • create_celltype_dataframe()
    • create_directory_if_not_exists()
    • create_new_rows_for_cell_type()
    • encode_categorical_columns()
    • generate_all_features()
    • generate_and_save_features()
    • generate_cell_counts()
    • generate_cell_counts_for_subject()
    • generate_cell_types()
    • generate_cell_types_from_range()
    • generate_cluster_features()
    • generate_diff_cell_types()
    • generate_disease_features()
    • generate_dummy_data_wo_interaction()
    • generate_feature()
    • generate_individual_features()
    • generate_major_cell_counts()
    • generate_pseudo_features()
    • generate_rare_cell_counts()
    • generate_variance()
    • identify_diff_clusters()
    • load_config()
    • process_feature()
    • save_data_to_csv()
    • set_random_seed()
    • validate_arguments()