The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

The itol.toolkit is an R package that provides helper functions for the Interactive Tree Of Life (iTOL). This package has been selected as a third-party tool in iTOL documentation and is recommended as one of the Top 40 New CRAN packages in January 2023 by the R Views channel of RStudio.

First version published in Bioinformatics journal, Please cite:

Tong Zhou, Kuidong Xu, Feng Zhao et. al. itol.toolkit accelerates working with iTOL (Interactive Tree Of Life) by an automated generation of annotation files, Bioinformatics, 2023;, btad339, https://doi.org/10.1093/bioinformatics/btad339

Features

Installation

Based on the dependence packages from CRAN and Bioconductor source. We recommend to use pak to install itol.toolkit package automatically to avoid problems.

install.packages("pak")

# from CRAN
pak::pak('itol.toolkit')

# from GitHub
pak::pak('TongZhou2017/itol.toolkit')
If you prefer not to use the pak method, you can still use the traditional installation method.

[Click to view] Traditional method To install the stable versions, you can use the CRAN official repository. For development versions, you can use the GitHub repository. However, if you need to install packages from Bioconductor, you’ll need to use the BiocManager package.

# install Biostrings
# install.packages("BiocManager")
BiocManager::install("Biostrings")

# from CRAN
install.packages("itol.toolkit")

# from GitHub
# install.packages("devtools") # if you have not installed "devtools" package
devtools::install_github("TongZhou2017/itol.toolkit")
Please note that in order to use this software, you will need to manually install the required dependencies from Bioconductor. A complete list of the necessary packages and installation instructions can be found in the supplementary materials.

If you encounter any issues during the installation process, such as problems caused by other systems, R versions, or dependency packages, please refer to the supplementary materials for a solution.

Quickstart

# load package
library(itol.toolkit)

# read data
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
data("template_groups")
df_group <- data.frame(id = unique(template_groups$group), 
                       data = unique(template_groups$group))

# create hub
hub <- create_hub(tree = tree)

## create unit
unit <- create_unit(data = df_group, 
                    key = "Quickstart", 
                    type = "DATASET_COLORSTRIP", 
                    tree = tree)

## add unit into hub
hub <- hub + unit

## write template file
write_hub(hub,getwd())

Documents

We have documents for every single function and some important tips for users. We also provided a ChatBot to help users learn the package interactively on Chat Thing.

Single functions

Tips

Video

Watch the video

We collected reproducible plots into a gallery page.

Support

Please open an issue to report bugs, propose new functions, or ask for help.

License

MIT License

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.