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Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data

View ORCID ProfileZachary S. L. Foster, View ORCID ProfileThomas J. Sharpton, View ORCID ProfileNiklaus J. Grünwald
doi: https://doi.org/10.1101/071019
Zachary S. L. Foster
1Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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  • ORCID record for Zachary S. L. Foster
Thomas J. Sharpton
2Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
3Department of Statistics, Oregon State University, Corvallis, OR, 97331, USA
4Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
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Niklaus J. Grünwald
1Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
4Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
5Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR, 97330, USA
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  • For correspondence: nik.grunwald@ars.usda.gov
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Abstract

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.

Note: This article was previously submitted as a pre-print: Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald. 2016. Metacoder: An R package for manipulation and heat tree visualization of community taxonomic data from metabar-coding. BioRxiv 071019; doi: http://dx.doi.org/10.1101/071019.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 07, 2016.
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Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data
Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald
bioRxiv 071019; doi: https://doi.org/10.1101/071019
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Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data
Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald
bioRxiv 071019; doi: https://doi.org/10.1101/071019

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