phylojunction.interface package

Subpackages

• phylojunction.interface.cmdbox package
  • Submodules
  • phylojunction.interface.cmdbox.cmd_parse module
    • cmdline2dag()
    • parse_deterministic_function_assignment()
    • parse_samp_dn_assignment()
    • parse_variable_assignment()
    • script2dag()
  • phylojunction.interface.cmdbox.cmd_parse_utils module
    • parse_spec()
    • parse_val_vector()
    • tokenize_fn_spec()
    • val_or_obj()
  • Module contents
• phylojunction.interface.grammar package
  • Submodules
  • phylojunction.interface.grammar.ct_fn_grammar module
    • PJCtFnGrammar
      • PJCtFnGrammar.create_ct_fn_obj()
      • PJCtFnGrammar.ct_fn_grammar_dict
      • PJCtFnGrammar.grammar_check()
      • PJCtFnGrammar.init_return_ann_tr()
  • phylojunction.interface.grammar.ct_fn_treereader_makers module
    • make_tree_reader()
  • phylojunction.interface.grammar.det_fn_branch_count_makers module
    • make_n_rec_branches()
  • phylojunction.interface.grammar.det_fn_clock_makers module
    • make_gamma_spike_clock_tree()
  • phylojunction.interface.grammar.det_fn_discrete_sse_makers module
    • make_DiscreteStateDependentProbability()
    • make_DiscreteStateDependentRate()
    • make_SSEStash()
  • phylojunction.interface.grammar.det_fn_grammar module
    • PJDetFnGrammar
      • PJDetFnGrammar.create_det_fn_obj()
      • PJDetFnGrammar.det_fn_grammar_dict
      • PJDetFnGrammar.grammar_check()
      • PJDetFnGrammar.init_return_gamma_spike_clock_tree()
      • PJDetFnGrammar.init_return_n_rec_branches()
      • PJDetFnGrammar.init_return_sse_stash()
      • PJDetFnGrammar.init_return_state_dep_prob()
      • PJDetFnGrammar.init_return_state_dep_rate()
      • PJDetFnGrammar.init_return_tree_mapped_with_attr()
  • phylojunction.interface.grammar.det_fn_map_attribute module
    • make_mapped_ann_tree()
  • phylojunction.interface.grammar.dn_discrete_sse_makers module
    • make_discrete_SSE_dn()
  • phylojunction.interface.grammar.dn_grammar module
    • PJDnGrammar
      • PJDnGrammar.create_dn_obj()
      • PJDnGrammar.dn_grammar_dict
      • PJDnGrammar.grammar_check()
      • PJDnGrammar.init_return_discrete_SSE_dn()
      • PJDnGrammar.init_return_parametric_dn()
  • Module contents
• phylojunction.interface.pjcli package
  • Submodules
  • phylojunction.interface.pjcli.cli_plotting module
    • call_node_plot_cli()
    • selected_node_plot_cli()
    • start_fig_and_axes()
  • phylojunction.interface.pjcli.pj_cli module
    • call_cli()
    • execute_pj_script()
  • Module contents
• phylojunction.interface.pysidegui package
  • Subpackages
    • phylojunction.interface.pysidegui.pjguipages package
      • Submodules
      • phylojunction.interface.pysidegui.pjguipages.gui_pages module
      • Module contents
    • phylojunction.interface.pysidegui.pjguiwidgets package
      • Submodules
      • phylojunction.interface.pysidegui.pjguiwidgets.matplotlibwidget module
      • phylojunction.interface.pysidegui.pjguiwidgets.pj_buttons module
      • Module contents
  • Submodules
  • phylojunction.interface.pysidegui.content_main_window module
    • ContentGUIMainWindow
      • ContentGUIMainWindow.setup_ui()
  • phylojunction.interface.pysidegui.pj_gui module
    • GUIMainWindow
      • GUIMainWindow.all_samples_clicked()
      • GUIMainWindow.avg_repl_check()
      • GUIMainWindow.clean_disable_everything()
      • GUIMainWindow.coverage_df
      • GUIMainWindow.do_selected_node_compare_page()
      • GUIMainWindow.do_selected_node_coverage_page()
      • GUIMainWindow.do_selected_node_dag_page()
      • GUIMainWindow.draw_cov()
      • GUIMainWindow.draw_node_dag()
      • GUIMainWindow.draw_violin()
      • GUIMainWindow.gui_modeling
      • GUIMainWindow.hpd_df
      • GUIMainWindow.init_and_refresh_radio_spin()
      • GUIMainWindow.init_top_menus()
      • GUIMainWindow.input_script_filepath
      • GUIMainWindow.is_avg_repl_check
      • GUIMainWindow.load_model()
      • GUIMainWindow.one_sample_clicked()
      • GUIMainWindow.other_comparison_df
      • GUIMainWindow.parse_cmd_update_gui()
      • GUIMainWindow.pj_comparison_df
      • GUIMainWindow.print_about()
      • GUIMainWindow.quit_app_button_clicked()
      • GUIMainWindow.read_compare_csv()
      • GUIMainWindow.read_coverage_hpd_csv()
      • GUIMainWindow.read_execute_script()
      • GUIMainWindow.read_log_files_dir_build_hpd()
      • GUIMainWindow.redraw_selected_node()
      • GUIMainWindow.refresh_cmd_history()
      • GUIMainWindow.refresh_node_lists()
      • GUIMainWindow.refresh_selected_node_display_plot_radio()
      • GUIMainWindow.refresh_selected_node_display_plot_spin()
      • GUIMainWindow.reset_selection()
      • GUIMainWindow.selected_node_display()
      • GUIMainWindow.selected_node_plot()
      • GUIMainWindow.selected_node_read()
      • GUIMainWindow.show_cmd_log_page()
      • GUIMainWindow.show_compare_page()
      • GUIMainWindow.show_coverage_page()
      • GUIMainWindow.show_pgm_page()
      • GUIMainWindow.show_settings_page()
      • GUIMainWindow.show_warnings_page()
      • GUIMainWindow.staticMetaObject
      • GUIMainWindow.toggle_button_animation()
      • GUIMainWindow.write_data_to_dir()
      • GUIMainWindow.write_model_to_file()
      • GUIMainWindow.write_plot_to_file()
      • GUIMainWindow.write_smaps_to_dir()
    • GUIModeling
      • GUIModeling.clear()
      • GUIModeling.cmd_log()
      • GUIModeling.cmd_log_list
      • GUIModeling.dag_obj
      • GUIModeling.parse_cmd_update_pgm()
      • GUIModeling.update_dag_random_seed()
    • call_gui()
  • Module contents

Submodules

phylojunction.interface.pj_sandbox module

phylojunction.interface.pj_sandbox.run_example_geosse_file() → DirectedAcyclicGraph

Run example 2.

This example reads script examples/bisse.pj. The tree is a sample from a geographic state-dependent speciation extinction (GeoSSE) process.

phylojunction.interface.pj_sandbox.run_example_manual_incomplete_sampling_bisse() → DirectedAcyclicGraph

Run example 3.

This example manually builds a BiSSE distribution with incomplete sampling, assigns it to a stochastic DAG node, and adds the node to a DAG.

phylojunction.interface.pj_sandbox.run_example_manual_tree_building(ax: Axes) → None

Run example 4.

This example manually builds an AnnotatedTree instance manually and plots it on provided Axes object.

phylojunction.interface.pj_sandbox.run_example_map_attr(ax: Axes) → None

Run example 6.

Returns:

phylojunction.interface.pj_sandbox.run_example_read_tree_function(ax: Axes) → None

Run example 5.

This example reads a newick string into an AnnotatedTree instance, and plots it in the provided Axes object.

phylojunction.interface.pj_sandbox.run_example_yule_string() → DirectedAcyclicGraph

Run example 1.

This example sets up a simple Yule model with two samples, and two Yule tree replicates per sample.

Module contents