Visualizing balances of compositional data: A new alternative to balance dendrograms

F1000Research
Thomas P Quinn

Abstract

Balances have become a cornerstone of compositional data analysis. However, conceptualizing balances is difficult, especially for high-dimensional data. Most often, investigators visualize balances with the balance dendrogram, but this technique is not necessarily intuitive and does not scale well for large data. This manuscript introduces the 'balance' package for the R programming language. This package visualizes balances of compositional data using an alternative to the balance dendrogram. This alternative contains the same information coded by the balance dendrogram, but projects data on a common scale that facilitates direct comparisons and accommodates high-dimensional data. By stripping the branches from the tree, 'balance' can cleanly visualize any subset of balances without disrupting the interpretation of the remaining balances. As an example, this package is applied to a publicly available meta-genomics data set measuring the relative abundance of 500 microbe taxa.

References

Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Oct 3, 2012·PLoS Computational Biology·Jonathan Friedman, Eric J Alm
Jul 12, 2013·PloS One·Andrew D FernandesGregory B Gloor
Mar 17, 2015·PLoS Computational Biology·David LovellJürg Bähler
May 8, 2015·PLoS Computational Biology·Zachary D KurtzRichard A Bonneau
Jun 2, 2015·Microbial Ecology in Health and Disease·Siddhartha MandalShyamal D Peddada
Jun 18, 2016·International Journal of Obesity : Journal of the International Association for the Study of Obesity·M R YeomansL Chambers
Oct 11, 2016·Nature Microbiology·Anna Heintz-BuschartPaul Wilmes
Feb 2, 2017·MSystems·James T MortonRob Knight
Feb 16, 2017·ELife·Justin D SilvermanLawrence A David
Apr 3, 2018·Bioinformatics·Thomas P QuinnTamsyn M Crowley
Jul 24, 2018·MSystems·J Rivera-PintoM L Calle

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Citations

Mar 3, 2020·Global Change Biology·Julie VercelloniKerrie Mengersen
Aug 20, 2019·Journal of the National Cancer Institute. Monographs·Jean-Luc C MougeotFarah B Mougeot
Feb 13, 2021·NAR Genomics and Bioinformatics·Mohammad H Norouzi-BeiramiKaveh Kavousi
Feb 13, 2021·NAR Genomics and Bioinformatics·Thomas P Quinn, Ionas Erb

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Software Mentioned

propr
R
EASI
ALDEx2
ggplot2
GPL
zCompositions
CoDaDendrogram
SPIEC
philr

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