Helper Functions for Interactive Tree Of Life (iTOL)
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
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')
pak
method, you can still use the traditional installation 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")
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.
# 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())
We have documents for every single function and some important tips for users:
Please open an issue to report bugs, propose new functions, or ask for help.