# Helper Functions for 'Interactive Tree Of Life'

## Documentation for package ‘itol.toolkit’ version 1.1.12

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

+-method | plus method add method for S4 class itol.hub and itol.unit
color_distance | Color distance
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
correct_type | Correct type parameter
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
df_tree | Data frame tree
dt_transpose_header | Transpose a data.table using the first column as new header
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
gradient_color | Generate gradient colors
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
longest_continuous_match | Calculate longest continuous match between input and target strings
merge_unit | Merge units
search_tree_file | Search tree file
show-method | show method for S4 class itol.hub
sort_color | Sort colors
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
vector_tree | Vector tree
write_hub | Write all data object into files
write_raw | Write raw data into files
write_unit | Write unit object into file