itol.toolkit

Helper Functions for Interactive Tree Of Life (iTOL)

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.package automatically to avoid problems.

install.packages("pak")

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

# from GitHub
pak::pak('TongZhou2017/itol.toolkit')

If you do not want to install pak package, you can use the most traditional installation method. However, pay attention to the installation of dependency packages. For a complete list of dependency packages and how to install them, see supplementary materials.

There are two options available:

Stable versions can be installed from CRAN official or development versions can be installed from GitHub, but dependency packages from BioConductor need to be installed using BiocManager.

# 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 have installation problems caused by other systems, R versions, or dependency packages, go to 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())

Support

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

License

MIT License