title: Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.
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.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Zachary S L
authors.initials: ZS
authors.lastname: Foster
authors.affiliation: Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America.|Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Sharpton
authors.affiliation: Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, Oregon, United States of America.
authors.forename: Niklaus J
authors.identifier: 0000-0003-1656-7602
authors.initials: NJ
authors.lastname: Grünwald
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D004247:DNA / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D011381:Programming Languages; D014584:User-Computer Interface
chemical_list: D004247:DNA