Helper Functions for Interactive Tree Of Life (iTOL)
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Support all 114 themes among all 23 template types in iTOL v6
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High throughput generate templates in one command
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Learn published template themes and use theme
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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.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.
# 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())Please open an issue to report bugs, propose new functions, or ask for help.