TongZhou2017/itol.toolkit

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

• Support all 114 themes among all 23 template types in iTOL v6

• High throughput generate templates in one command

• Learn published template themes and use theme

• Save all-in-one reproducible data locally

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.

# 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")

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 and Slack.

Single functions

• COLLAPSE: collapse branches by range id or node id.

• PRUNE: drop out branches.

• SPACING: adjust branch spacing.

• TREE_COLORS: set branch style at range, clade, branch, label, and background level.

• DATASET_STYLE: set branch style at branch and label level.

• LABELS: change node name.

• DATASET_TEXT: add text by HTML.

• DATASET_COLORSTRIP: add color strip with text.

• DATASET_BINARY: multi columns with one shape symbol.

• DATASET_GRADIENT: one column heatmap.

• DATASET_HEATMAP: heatmap with field tree.

• DATASET_SYMBOL: internal tree one column with multi shape symbol.

• DATASET_EXTERNALSHAPE: outside multi column with multi shape symbol.

• DATASET_DOMAINS: strucutre with multi shape symbol.

• DATASET_SIMPLEBAR: bar plot.

• DATASET_MULTIBAR: multi bar plot.

• DATASET_BOXPLOT: box plot.

• DATASET_LINECHART: line plot.

• DATASET_PIECHART: pie plot.

• DATASET_ALIGNMENT: sequence alignment.

• DATASET_CONNECTIONS: network between braches.

• DATASET_IMAGE: add image.

• POPUP_INFO: interactive external information.

Tips

• Overview: overview for all functions.

• Installation: FAQ about installation.

• Datasets: overview of 5 example datasets for demo.

• Colors: buildin color palette.

• Data reproduction: learn data from template files.

• VS table2itol: compare with the other iTOL helper tool, table2itol.

• Tree construction: create a tree by different data and methods.

Video

Gallery

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