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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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F1000 Research Limited
2018
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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. |
format | Online Article Text |
id | pubmed-6124381 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT quinnthomasp visualizingbalancesofcompositionaldataanewalternativetobalancedendrograms |