Draft:Mapmixture
mapmixture R package
From Wikipedia, the free encyclopedia
mapmixture is an open-source R package and accompanying Shiny web application developed by Tom Jenkins for the spatial visualization of population genetic structure and admixture results.[1] The package was formally described in Molecular Ecology Resources in February 2024. The software is designed to facilitate the geographic representation of ancestry coefficients generated by programs such as STRUCTURE[2], ADMIXTURE[3], and related clustering or ordination approaches. By integrating admixture proportion data with geographic coordinates, mapmixture produces publication-quality maps displaying pie charts at sampling locations, enabling researchers to visualize spatial patterns of genetic structure.
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| mapmixture | |
|---|---|
| Developer | Tom Jenkins |
| Initial release | 2024 |
| Written in | R |
| Platform | Cross-platform |
| Type | Population genetics software |
| License | Open-source |
| Website | https://github.com/Tom-Jenkins/mapmixture |
Functionality
The primary function of the package, mapmixture(), generates spatial maps of admixture proportions using input data provided in .csv or .tsv formats. These input files typically contain individual- or population-level ancestry coefficients alongside latitude and longitude coordinates. Maps can be generated using base geographic layers or custom map objects produced with other R spatial packages.
In addition to spatial mapping, mapmixture includes several supplementary visualization functions:
structure_plot()produces traditional STRUCTURE-style bar plots or faceted bar plots of ancestry proportions.scatter_plot()enables visualization of ordination analyses, including principal component analysis (PCA) and discriminant analysis of principal components (DAPC).launch_mapmixture()launches the associated Shiny web application.
The package integrates with widely used R visualization packages such as ggplot2[4] and gridExtra[5], allowing users to customize map aesthetics, adjust figure layouts, and generate composite publication figures.
Shiny application
The mapmixture Shiny application provides a graphical user interface for users who prefer not to write R scripts. Through the interface, users can upload admixture and coordinate data, adjust visualization parameters, and export figures. This functionality increases accessibility for researchers without extensive programming experience.
Applications
mapmixture is primarily used in population genetics, phylogeography, and conservation genetics. By displaying admixture proportions directly on geographic maps, the software supports interpretation of spatial patterns of gene flow, hybridization, and population differentiation.
Availability
The package is distributed via GitHub (https://github.com/tom-jenkins/mapmixture), where example scripts and demonstration outputs are provided. The accompanying peer-reviewed publication documents its implementation and example applications.