Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of colo...
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| creator | Foster, Zachary S L Sharpton, Thomas J Grünwald, Niklaus J |
| description | Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual. |
| doi_str_mv | 10.1371/journal.pcbi.1005404 |
| format | Article |
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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 13(2): e1005404. doi:10.1371/journal.pcbi.1005404</rights><rights>2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. 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| subjects | Algorithms Bias Biology and Life Sciences Colleges & universities Computer and Information Sciences Computer Graphics DNA - genetics DNA Barcoding, Taxonomic - methods Documentation Earth Sciences Funding Gene expression Genetic engineering Genetic research Genetic Variation - genetics High-Throughput Nucleotide Sequencing Methods Ontology Programming Languages Research and Analysis Methods Scientific software Software Taxonomy Technology application Trees User-Computer Interface |
| title | Metacoder: An R package for visualization and manipulation of community taxonomic diversity data |
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