API for Rclade
Automated Deep-Time Phylogenetic Tree Collapsing and Visualization
| Global functions | |
|---|---|
| .acquire_log_lock | Man page Source code |
| .onAttach | Source code |
| .rclade_extract_config | Man page Source code |
| .release_log_lock | Man page Source code |
| RCLADE_HADEAN_END | Man page |
| RCLADE_X_MARGIN_FACTOR | Man page |
| RCLADE_X_MIN_FLOOR | Man page |
| SUPPORTED_TREE_EXTENSIONS | Man page |
| add_clip_off | Man page Source code |
| add_geo_events | Man page Source code |
| add_geo_timescale | Man page Source code |
| add_hpd_range | Man page Source code |
| add_smart_legend | Man page Source code |
| add_support_labels | Man page Source code |
| annotate_clade | Man page Source code |
| batch_plot | Man page Source code |
| batch_with_interrupt | Man page Source code |
| build_base_tree | Man page Source code |
| build_full_taxa_df | Man page Source code |
| build_group_vec | Man page Source code |
| build_path | Man page Source code |
| build_plot_timetree_params | Man page Source code |
| build_taxonomy_lookup | Man page Source code |
| check_dependency | Man page Source code |
| check_example_tree | Man page Source code |
| check_input_validation | Man page Source code |
| check_malicious_chars | Man page Source code |
| check_monophyly | Man page Source code |
| check_monophyly_logic | Man page Source code |
| check_special_monophyly | Man page Source code |
| check_taxonomy_extraction | Man page Source code |
| cleanup_on_interrupt | Man page Source code |
| collapse_by_groups | Source code |
| compute_collapse_segments | Source code |
| compute_collapse_vertices | Source code |
| compute_legend_layout | Man page Source code |
| compute_mrca_map | Man page Source code |
| compute_time_breaks | Man page Source code |
| compute_x_min | Man page Source code |
| convert_unit | Man page Source code |
| detect_alphabet | Man page Source code |
| detect_encoding | Man page Source code |
| detect_sequence_format | Man page Source code |
| detect_taxonomy_format | Man page Source code |
| detect_tree_format | Man page Source code |
| ensure_dir | Man page Source code |
| escape_regex | Man page Source code |
| example_tree | Man page |
| find_rank_cycles | Man page Source code |
| format_elapsed | Man page Source code |
| format_step | Man page Source code |
| format_timestamp | Man page Source code |
| generate_colors | Man page Source code |
| geom_polygon_straight | Source code |
| geom_segment_straight | Source code |
| get_dependency_versions | Man page Source code |
| get_git_hash | Man page Source code |
| get_level_prefix | Man page Source code |
| get_progress_summary | Man page Source code |
| get_rank_name | Man page Source code |
| get_supported_extensions | Man page Source code |
| get_taxonomy_levels | Man page Source code |
| get_version_string | Man page Source code |
| highlight_clades | Man page Source code |
| init_progress_tracking | Man page Source code |
| init_steps | Man page Source code |
| level_to_num | Man page Source code |
| log_critical | Man page Source code |
| log_debug | Man page Source code |
| log_error | Man page Source code |
| log_info | Man page Source code |
| log_keyvalue | Man page Source code |
| log_memory | Man page Source code |
| log_message | Man page Source code |
| log_progress | Man page Source code |
| log_section | Man page Source code |
| log_stats | Man page Source code |
| log_subsection | Man page Source code |
| log_table | Man page Source code |
| log_warning | Man page Source code |
| managed_tempdir | Man page Source code |
| managed_tempfile | Man page Source code |
| next_step | Man page Source code |
| normalize_file_newlines | Man page Source code |
| normalize_newlines | Man page Source code |
| normalize_rank | Man page Source code |
| parse_custom_rank | Man page Source code |
| parse_custom_regex | Man page Source code |
| parse_embedded | Man page Source code |
| parse_gtdb | Man page Source code |
| parse_ncbi | Man page Source code |
| parse_plot_params | Man page Source code |
| parse_semicolon_delimited | Man page Source code |
| parse_silva | Man page Source code |
| parse_taxonomy | Man page Source code |
| parse_taxonomy_with_file | Man page Source code |
| plot_timetree | Man page Source code |
| polytomy_tree | Man page |
| prepare_geo_timescales | Man page Source code |
| print.rclade_options | Man page Source code |
| print_version | Man page Source code |
| pt_single_tree | Man page Source code |
| pt_step1_prepare_inputs | Man page Source code |
| pt_step2_resolve_taxonomy | Man page Source code |
| pt_step3_compute_mrca | Man page Source code |
| pt_step4_generate_colors | Man page Source code |
| pt_step5_render_and_collapse | Man page Source code |
| pt_step6_add_annotations | Man page Source code |
| pt_step7_finalize_plot | Man page Source code |
| rclade_logger | Man page |
| rclade_logo | Man page Source code |
| rclade_options | Man page Source code |
| read_file_utf8 | Man page Source code |
| read_taxonomy_file | Man page Source code |
| read_tree_auto | Man page Source code |
| resolve_group | Man page Source code |
| resolve_special_identifier | Man page Source code |
| resolve_target_domains | Man page Source code |
| resolve_taxonomy_source_priority | Man page Source code |
| run_rclade_cli | Man page Source code |
| run_rclade_selftest | Man page Source code |
| run_rclade_shiny | Man page Source code |
| save_session_info | Man page Source code |
| save_timetree | Man page Source code |
| selftest_report | Man page Source code |
| set_log_enabled | Man page Source code |
| set_log_file | Man page Source code |
| set_log_level | Man page Source code |
| sort_by_depth | Man page Source code |
| split_legend | Man page Source code |
| strip_tree_annotations | Man page Source code |
| summarize_multi_trees | Man page Source code |
| summarize_taxonomy_quality | Man page Source code |
| summarize_taxonomy_quality_with_file | Man page Source code |
| summarize_timetree | Man page Source code |
| theme_timetree | Man page Source code |
| timer_start | Man page Source code |
| timer_stop | Man page Source code |
| truncate_long_newick_labels | Source code |
| update_progress | Man page Source code |
| validate_cli_params | Man page Source code |
| validate_collapse_plan | Man page Source code |
| validate_custom_groups | Man page Source code |
| validate_fasta_content | Man page Source code |
| validate_fastq_content | Man page Source code |
| validate_file_exists | Man page Source code |
| validate_file_not_empty | Man page Source code |
| validate_inputs | Man page Source code |
| validate_newick_syntax | Man page Source code |
| validate_sequence_deep | Man page Source code |
| validate_sequence_file | Man page Source code |
| validate_taxonomy_no_cycles | Man page Source code |
| validate_tree_deep | Man page Source code |
| validate_tree_sequence_match | Man page Source code |
| validate_tree_structure | Man page Source code |
| with_graceful_interrupt | Man page Source code |
| write_file_utf8 | Man page Source code |
