Introduction

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.

Publications

  1. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.
    Cite this
    Foster ZS, Sharpton TJ, Grünwald NJ, 2017-02-01 - PLoS computational biology

Credits

  1. Zachary S L Foster
    Developer

    Department of Botany and Plant Pathology, Oregon State University, United States of America

  2. Thomas J Sharpton
    Developer

    Center for Genome Research and Biocomputing, Oregon State University, United States of America

  3. Niklaus J Grünwald
    Investigator

    Horticultural Crops Research Laboratory, USDA-ARS, United States of America

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Summary
AccessionBT006959
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByNiklaus J Grünwald