Helper Functions for 'Interactive Tree Of Life'
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Documentation for package ‘itol.toolkit’ version 1.1.7
Help Pages
| +-method | plus method add method for S4 class itol.hub and itol.unit |
| complex_html_text | Complex HTML text |
| convert_01 | Convert character data to 0/1 |
| convert_01_to_connect | Convert 0/1 data to connection pairs |
| convert_range_to_node | Convert range to node id |
| correct_get_color | correct_get_color |
| count_to_tree | Calculate tree based on count matrix |
| create_hub | Create itol.hub Object |
| create_theme | Create itol.theme Object |
| create_unit | Create itol.unit |
| df_merge | Merge two data frame |
| fa_read | Read fasta file |
| fa_write | Write fasta file |
| file_get_dir | Get file dir |
| file_get_name | Get file name |
| file_to_unit | Create itol.unit Object from file |
| get_color | get_color |
| head_line | head line |
| hub_to_unit | Create itol.unit Object from object |
| inbuilt_themes | inbuilt themes |
| itol.hub | The itol.hub Class |
| itol.hub-class | The itol.hub Class |
| itol.theme | The itol.theme Class |
| itol.theme-class | The itol.theme Class |
| itol.unit | The itol.unit Class |
| itol.unit-class | The itol.unit Class |
| learn_data | Learn data from template file |
| learn_data_from_file | Learn object data from file |
| learn_data_from_files | Learn object data from files |
| learn_data_from_unit | Learn object data from unit |
| learn_data_from_unit_list | Learn object data from units |
| learn_df | Learn from tree |
| learn_field | Learn field |
| learn_legend | Learn legend |
| learn_line | Learn paramter |
| learn_profile | Learn profile |
| learn_separator | Learn separator |
| learn_subdf | Learn sub data frame |
| learn_theme_align | Learn align |
| learn_theme_alignment | Learn alignment |
| learn_theme_bar | Learn bar |
| learn_theme_basic_plot | Learn basic plot |
| learn_theme_basic_theme | Learn basic theme |
| learn_theme_binary | Learn binary |
| learn_theme_border | Learn border |
| learn_theme_common_themes | Learn common themes |
| learn_theme_connection | Learn connection |
| learn_theme_domain | Learn domain |
| learn_theme_externalshape | Learn externalshape |
| learn_theme_heatmap | Learn heatmap |
| learn_theme_image | Learn image |
| learn_theme_label | Learn label |
| learn_theme_linechart | Learn linechart |
| learn_theme_piechart | Learn piechart |
| learn_theme_specific_themes | Learn specific themes |
| learn_theme_strip_label | Learn strip label |
| learn_type | Learn template type |
| line_clean | Filter out comments and empty lines |
| line_split | Split lines into two parts |
| merge_unit | Merge units |
| search_tree_file | Search tree file |
| show-method | show method for S4 class itol.hub |
| template_groups | template groups |
| template_parameters_count | template parameters count |
| train_theme | Train inbuilt theme |
| unite_rows | Paste rows |
| use.theme | Extract theme from inbuilt_themes |
| write_hub | Write all data object into files |
| write_raw | Write raw data into files |
| write_unit | Write unit object into file |