tidygenclust

tidygenclust provides functions and methods to run genetic clustering in R, using the commonly used ADMIXTURE program as we as the python package fastmixture. It also help to align and compare multiple runs of the same or different K using the functionalities of the python package clumppling. tidygenclust builds on tidypopgen, enhancing the grammar of population genetics with a focus on genetic clustering.

Installation

Currently installation is limited to Linux and OSX, but NOT Windows (you can use the WSL). You can install the development version of tidygenclust from GitHub with:

# install.packages("pak")
pak::pak("EvolEcolGroup/tidygenclust")

Note for MacOS user

We use reticulate to seamlessly integrate the required python packages and dependencies into R without additional installation steps for the user. However, for this to work correctly for MacOS users, you need llvm installed in the first place. In bash, you will need:

# llvm can be installed via brew
brew install llvm libomp

# correct paths need to be specified
export PATH="/opt/homebrew/opt/llvm/bin:$PATH" 
export CC="/opt/homebrew/opt/llvm/bin/clang"
export CXX="/opt/homebrew/opt/llvm/bin/clang++"

Overview of functionality

On overview of the functionality of tidygenclust and its integration with tidypopgen is provided in the “Get Started”” vignette. This also includes a detailed description of how to align multiple runs of clustering and compare them.