Package: itol.toolkit 1.2.2

itol.toolkit: Helper Functions for 'Interactive Tree Of Life'

The 'Interactive Tree Of Life' <https://itol.embl.de/> online server can edit and annotate trees interactively. The 'itol.toolkit' package can support all types of annotation templates.

Authors:Tong Zhou [aut, cre]

itol.toolkit_1.2.2.tar.gz
itol.toolkit_1.2.2.zip(r-4.7)itol.toolkit_1.2.2.zip(r-4.6)itol.toolkit_1.2.2.zip(r-4.5)
itol.toolkit_1.2.2.tgz(r-4.6-any)itol.toolkit_1.2.2.tgz(r-4.5-any)
itol.toolkit_1.2.2.tar.gz(r-4.7-any)itol.toolkit_1.2.2.tar.gz(r-4.6-any)
itol.toolkit_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
itol.toolkit/json (API)

# Install 'itol.toolkit' in R:
install.packages('itol.toolkit', repos = c('https://tongzhou2017.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tongzhou2017/itol.toolkit/issues

Pkgdown/docs site:https://tongzhou2017.github.io

Datasets:

On CRAN:

Conda:

bioinformaticsitolvisualization

7.94 score 182 stars 79 scripts 558 downloads 72 exports 78 dependencies

Last updated from:9c5ecc85bd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK264
source / vignettesOK188
linux-release-x86_64OK174
macos-release-arm64OK153
macos-oldrel-arm64OK168
windows-develOK136
windows-releaseOK119
windows-oldrelOK128
wasm-releaseOK114

Exports:anno_col_groupbinary_data_conversioncolor_distancecomplex_html_textconvert_01convert_01_to_connectconvert_range_to_nodeconvert_to_binarycorrect_get_colorcorrect_typecount_to_treecreate_hubcreate_themecreate_unitdarken_colordf_mergedf_treedt_transpose_headerfa_readfa_writefile_get_dirfile_get_namefile_to_unitget_colorgradient_colorhead_linehub_to_unitlearn_datalearn_data_from_filelearn_data_from_fileslearn_data_from_unitlearn_data_from_unit_listlearn_dflearn_fieldlearn_legendlearn_linelearn_profilelearn_separatorlearn_subdflearn_theme_alignlearn_theme_alignmentlearn_theme_barlearn_theme_basic_plotlearn_theme_basic_themelearn_theme_binarylearn_theme_borderlearn_theme_common_themeslearn_theme_connectionlearn_theme_domainlearn_theme_externalshapelearn_theme_heatmaplearn_theme_imagelearn_theme_labellearn_theme_linechartlearn_theme_piechartlearn_theme_specific_themeslearn_theme_strip_labellearn_typeline_cleanline_splitlongest_continuous_matchmerge_unitsearch_tree_fileshowsort_colortrain_themeunite_rowsuse.themevector_treewrite_hubwrite_rawwrite_unit

Dependencies:ade4apebase64encbslibcachemclicolourpickercommonmarkcpp11data.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2ggscigluegtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSmemoisemimeminiUInlmeotelpillarpixmappkgconfigpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownrstudioapiS7sassscalessegmentedseqinrshinyshinyjssourcetoolsspstringdiststringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewesandersonwithrxfunxtableyaml

Get_Start

Rendered fromGet_Start.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2023-05-04
Started: 2023-01-23

Readme and manuals

Help Manual

Help pageTopics
plus method add method for S4 class itol.hub and itol.unit+,itol.hub,itol.unit-method +,itol.unit,itol.unit-method
Annotate Column Groupsanno_col_group
Binary Data Conversionbinary_data_conversion
Color distancecolor_distance
Complex HTML textcomplex_html_text
Convert character data to 0/1convert_01
Convert 0/1 data to connection pairsconvert_01_to_connect
Convert range to node idconvert_range_to_node
Convert data to binary format for DATASET_BINARYconvert_to_binary
correct_get_colorcorrect_get_color
Correct type parametercorrect_type
Calculate tree based on count matrixcount_to_tree
Create itol.hub Objectcreate_hub
Create itol.theme Objectcreate_theme
Create itol.unitcreate_unit
Darken color while preserving hue and saturationdarken_color
Merge two data framedf_merge
Data frame treedf_tree
Transpose a data.table using the first column as new headerdt_transpose_header
Read fasta filefa_read
Write fasta filefa_write
Get file dirfile_get_dir
Get file namefile_get_name
Create itol.unit Object from filefile_to_unit
get_colorget_color
Generate gradient colorsgradient_color
head linehead_line
Create itol.unit Object from objecthub_to_unit
inbuilt themesinbuilt_themes
The itol.hub Classitol.hub itol.hub-class
The itol.theme Classitol.theme itol.theme-class
The itol.unit Classitol.unit itol.unit-class
Learn data from template filelearn_data
Learn object data from filelearn_data_from_file
Learn object data from fileslearn_data_from_files
Learn object data from unitlearn_data_from_unit
Learn object data from unitslearn_data_from_unit_list
Learn from treelearn_df
Learn fieldlearn_field
Learn legendlearn_legend
Learn paramterlearn_line
Learn profilelearn_profile
Learn separatorlearn_separator
Learn sub data framelearn_subdf
Learn alignlearn_theme_align
Learn alignmentlearn_theme_alignment
Learn barlearn_theme_bar
Learn basic plotlearn_theme_basic_plot
Learn basic themelearn_theme_basic_theme
Learn binarylearn_theme_binary
Learn borderlearn_theme_border
Learn common themeslearn_theme_common_themes
Learn connectionlearn_theme_connection
Learn domainlearn_theme_domain
Learn externalshapelearn_theme_externalshape
Learn heatmaplearn_theme_heatmap
Learn imagelearn_theme_image
Learn labellearn_theme_label
Learn linechartlearn_theme_linechart
Learn piechartlearn_theme_piechart
Learn specific themeslearn_theme_specific_themes
Learn strip labellearn_theme_strip_label
Learn template typelearn_type
Filter out comments and empty linesline_clean
Split lines into two partsline_split
Calculate longest continuous match between input and target stringslongest_continuous_match
Merge unitsmerge_unit
Search tree filesearch_tree_file
show method for S4 class itol.hubshow,itol.hub-method
Sort colorssort_color
template groupstemplate_groups
template parameters counttemplate_parameters_count
Train inbuilt themetrain_theme
Paste rowsunite_rows
Extract theme from inbuilt_themesuse.theme
Vector treevector_tree
Write all data object into fileswrite_hub
Write raw data into fileswrite_raw
Write unit object into filewrite_unit