{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T15:15:38Z","timestamp":1777043738240,"version":"3.51.4"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:00:00Z","timestamp":1774396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM152744"],"award-info":[{"award-number":["R01GM152744"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Stacked barplots, though widely used in microbiome studies, can obscure important patterns in microbiome data. They omit rare taxa and can mask shifts that emerge at finer taxonomic levels. To address this issue, we introduce phylobar, an R package that interactively links stacked barplots with overview phylogenetic or taxonomic hierarchies. The interface allows users to collapse or expand subtrees, paint color palettes interactively, and search for specific taxa. This allows comparison across taxonomic resolutions that are hidden in static overviews. phylobar works with any omics data with hierarchical organization, including cell type hierarchies, as we demonstrate in a case study of immune cell composition in COVID-19 patients.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>phylobar is available as an R package on GitHub. It uses the htmlwidgets library to link interactive D3 visualizations with R. The interactive plots can be embedded within R Markdown or Quarto notebooks, and views can be exported as vector graphics files. The package is open source and documented at https:\/\/mkdiro-O.github.io\/phylobar.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag151","type":"journal-article","created":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T12:40:41Z","timestamp":1774356041000},"source":"Crossref","is-referenced-by-count":0,"title":["phylobar: an R package for multiresolution compositional barplots in omics studies"],"prefix":"10.1093","volume":"42","author":[{"given":"Megan","family":"Kuo","sequence":"first","affiliation":[{"name":"University of Wisconsin-Madison Department of Statistics, , Madison, WI 53703,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3923-1116","authenticated-orcid":false,"given":"Kim-Anh","family":"L\u00ea Cao","sequence":"additional","affiliation":[{"name":"University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saritha","family":"Kodikara","sequence":"additional","affiliation":[{"name":"University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3818-1981","authenticated-orcid":false,"given":"Jiadong","family":"Mao","sequence":"additional","affiliation":[{"name":"University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9415-1971","authenticated-orcid":false,"given":"Kris","family":"Sankaran","sequence":"additional","affiliation":[{"name":"University of Wisconsin-Madison Department of Statistics, , Madison, WI 53703,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,3,25]]},"reference":[{"key":"2026042409470047300_btag151-B1","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D\u00b3 data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"2026042409470047300_btag151-B2","doi-asserted-by":"publisher","first-page":"914","DOI":"10.12688\/f1000research.151662.1","article-title":"Stackbarextended: a user-friendly stacked bar-plot representation incorporating phylogenetic information and microbiota differential abundance analysis","volume":"13","author":"Cuisiniere","year":"2024","journal-title":"F1000Res"},{"key":"2026042409470047300_btag151-B3","doi-asserted-by":"publisher","first-page":"11060","DOI":"10.1073\/pnas.1502875112","article-title":"Temporal and spatial variation of the human microbiota during pregnancy","volume":"112","author":"DiGiulio","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026042409470047300_btag151-B4","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1093\/biostatistics\/kxac018","article-title":"Multiscale analysis of count data through topic alignment","volume":"24","author":"Fukuyama","year":"2023","journal-title":"Biostatistics"},{"key":"2026042409470047300_btag151-B5","volume-title":"Reproducible Research with R and RStudio","author":"Gandrud","year":"(3 ). , :  & \/, 2020."},{"key":"2026042409470047300_btag151-B6","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.12688\/f1000research.26669.1","article-title":"TreeSummarizedExperiment: a s4 class for data with hierarchical structure","volume":"9","author":"Huang","year":"2020","journal-title":"F1000Res"},{"key":"2026042409470047300_btag151-B7","doi-asserted-by":"publisher","first-page":"2966","DOI":"10.1101\/689547","article-title":"Poincar\u00e9 maps for analyzing complex hierarchies in single-cell data","volume":"11","author":"Klimovskaia","year":"2019","journal-title":"Nat. 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