mvmapper: Interactive spatial mapping of genetic structures
File(s)mvmapper_manuscript_20170928.docx (79.22 KB)
Accepted version
Author(s)
Dupuis, Julian R
Bremer, Forest T
Jombart, Thibaut
Sim, Sheina B
Geib, Scott M
Type
Journal Article
Abstract
Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata are not always easily integrated into these methods in a user-friendly fashion. Here, we present a deployable Python-based web-tool, mvmapper, for visualizing and exploring results of multivariate analyses in geographic space. This tool can be used to map results of virtually any multivariate analysis of georeferenced data, and routines for exporting results from a number of standard methods have been integrated in the R package adegenet, including principal components analysis (PCA), spatial PCA, discriminant analysis of principal components, principal coordinates analysis, nonmetric dimensional scaling and correspondence analysis. mvmapper's greatest strength is facilitating dynamic and interactive exploration of the statistical and geographic frameworks side by side, a task that is difficult and time-consuming with currently available tools. Source code and deployment instructions, as well as a link to a hosted instance of mvmapper, can be found at https://popphylotools.github.io/mvMapper/.
Date Issued
2018-03-01
Date Acceptance
2017-10-03
Citation
Molecular Ecology Resources, 2018, 18 (2), pp.362-367
ISSN
1755-098X
Publisher
Wiley
Start Page
362
End Page
367
Journal / Book Title
Molecular Ecology Resources
Volume
18
Issue
2
Copyright Statement
© 2017 John Wiley & Sons Ltd. This is the pre-peer reviewed version of the following article, which has been published in final form at https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12724
Sponsor
Medical Research Council (MRC)
Grant Number
MR/K010174/1B
Subjects
Python
data visualization
multivariate analyses
ordinations in reduced space
population genetics
software
Publication Status
Published
Date Publish Online
2017-10-07