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

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 f...

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Detalles Bibliográficos
Autor principal: Quinn, Thomas P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124381/
https://www.ncbi.nlm.nih.gov/pubmed/30228880
http://dx.doi.org/10.12688/f1000research.15858.1
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author Quinn, Thomas P.
author_facet Quinn, Thomas P.
author_sort Quinn, Thomas P.
collection PubMed
description 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.
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spelling pubmed-61243812018-09-17 Visualizing balances of compositional data: A new alternative to balance dendrograms Quinn, Thomas P. F1000Res Software Tool Article 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. F1000 Research Limited 2018-08-14 /pmc/articles/PMC6124381/ /pubmed/30228880 http://dx.doi.org/10.12688/f1000research.15858.1 Text en Copyright: © 2018 Quinn TP http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Quinn, Thomas P.
Visualizing balances of compositional data: A new alternative to balance dendrograms
title Visualizing balances of compositional data: A new alternative to balance dendrograms
title_full Visualizing balances of compositional data: A new alternative to balance dendrograms
title_fullStr Visualizing balances of compositional data: A new alternative to balance dendrograms
title_full_unstemmed Visualizing balances of compositional data: A new alternative to balance dendrograms
title_short Visualizing balances of compositional data: A new alternative to balance dendrograms
title_sort visualizing balances of compositional data: a new alternative to balance dendrograms
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124381/
https://www.ncbi.nlm.nih.gov/pubmed/30228880
http://dx.doi.org/10.12688/f1000research.15858.1
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