publication . Article . Other literature type . Preprint . 2017

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.

Zachary S. L. Foster; Thomas J. Sharpton; Niklaus J. Grünwald;
Open Access
  • Published: 01 Feb 2017 Journal: PLOS Computational Biology, volume 13, page e1005404 (eissn: 1553-7358, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
<jats:title>Abstract</jats:title><jats:p>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 <jats:italic>metacoder</jats:italic>, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. <jats:italic>Metacoder</jats:italic> includes a dynamic and flexible function that can parse most text-based formats that contain taxon...
Subjects
free text keywords: Data mining, computer.software_genre, computer, Bar chart, law.invention, law, Parsing, Computer graphics, Bioinformatics, Barcode, Identifier, Visualization, Computer science, Hierarchical database model, Data visualization, business.industry, business, Taxon, R package, Tree visualization, Research Article, Biology and Life Sciences, Taxonomy, Computer and Information Sciences, Data Management, Research and Analysis Methods, Database and Informatics Methods, Biological Databases, Sequence Databases, Sequence Analysis, Evolutionary Biology, Evolutionary Systematics, Phylogenetics, Phylogenetic Analysis, Infographics, Graphs, Molecular Biology, Molecular Biology Techniques, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Computational Biology, Genome Analysis, Gene Ontologies, Genetics, Genomics, Earth Sciences, Marine and Aquatic Sciences, Bodies of Water, Oceans, Biology (General), QH301-705.5
Related Organizations
25 references, page 1 of 2

1 Cristescu ME. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol. 2014;29(10):566–571. 10.1016/j.tree.2014.08.001 25175416 [OpenAIRE] [PubMed] [DOI]

2 De Vargas C, Audic S, Henry N, Decelle J, MahéF, Logares R, et al Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348(6237):1261605 10.1126/science.1261605 25999516 [OpenAIRE] [PubMed] [DOI]

3 Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, et al Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 2016;209(2):798–811. 10.1111/nph.13697 26467257 [OpenAIRE] [PubMed] [DOI]

4 Yu DW, Ji Y, Emerson BC, Wang X, Ye C, Yang C, et al Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol. 2012;3(4):613–623. 10.1111/j.2041-210X.2012.00198.x [OpenAIRE] [DOI]

5 Consortium HMP, et al Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–214. 10.1038/nature11234 22699609 [OpenAIRE] [PubMed] [DOI]

6 Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol. 2014;12(1):1 10.1186/s12915-014-0069-1 24417977 [OpenAIRE] [PubMed] [DOI]

7 Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods. 2012;9(8):811–814. 10.1038/nmeth.2066 22688413 [OpenAIRE] [PubMed] [DOI]

8 Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–7541. 10.1128/AEM.01541-09 19801464 [OpenAIRE] [PubMed] [DOI]

9 Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughe y MJ, Woese CR. The ribosomal database project (RDP). Nucleic Acids Res. 1996;24(1):82–85. 10.1093/nar/24.1.82 8594608 [OpenAIRE] [PubMed] [DOI]

10 Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al GenBank. Nucleic Acids Res. 2013;41(D1):D36–D42. 10.1093/nar/gks1195 23193287 [OpenAIRE] [PubMed] [DOI]

11 Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, et al Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 2013;22(21):5271–5277. 10.1111/mec.12481 24112409 [OpenAIRE] [PubMed] [DOI]

12 Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2012;41:D597–D604. 10.1093/nar/gks1160 23193267 [OpenAIRE] [PubMed] [DOI]

13 DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environn Microbiol. 2006;72(7):5069–5072. 10.1128/AEM.03006-05 16820507 [OpenAIRE] [PubMed] [DOI]

14 Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–D596. 10.1093/nar/gks1219 23193283 [OpenAIRE] [PubMed] [DOI]

15 Foster ZSL, Grünwald NJ. Metacoder user documentation; 2016. Available from: http://grunwaldlab.github.io/metacoder_documentation.

25 references, page 1 of 2
Abstract
<jats:title>Abstract</jats:title><jats:p>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 <jats:italic>metacoder</jats:italic>, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. <jats:italic>Metacoder</jats:italic> includes a dynamic and flexible function that can parse most text-based formats that contain taxon...
Subjects
free text keywords: Data mining, computer.software_genre, computer, Bar chart, law.invention, law, Parsing, Computer graphics, Bioinformatics, Barcode, Identifier, Visualization, Computer science, Hierarchical database model, Data visualization, business.industry, business, Taxon, R package, Tree visualization, Research Article, Biology and Life Sciences, Taxonomy, Computer and Information Sciences, Data Management, Research and Analysis Methods, Database and Informatics Methods, Biological Databases, Sequence Databases, Sequence Analysis, Evolutionary Biology, Evolutionary Systematics, Phylogenetics, Phylogenetic Analysis, Infographics, Graphs, Molecular Biology, Molecular Biology Techniques, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Computational Biology, Genome Analysis, Gene Ontologies, Genetics, Genomics, Earth Sciences, Marine and Aquatic Sciences, Bodies of Water, Oceans, Biology (General), QH301-705.5
Related Organizations
25 references, page 1 of 2

1 Cristescu ME. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol. 2014;29(10):566–571. 10.1016/j.tree.2014.08.001 25175416 [OpenAIRE] [PubMed] [DOI]

2 De Vargas C, Audic S, Henry N, Decelle J, MahéF, Logares R, et al Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348(6237):1261605 10.1126/science.1261605 25999516 [OpenAIRE] [PubMed] [DOI]

3 Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, et al Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 2016;209(2):798–811. 10.1111/nph.13697 26467257 [OpenAIRE] [PubMed] [DOI]

4 Yu DW, Ji Y, Emerson BC, Wang X, Ye C, Yang C, et al Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol. 2012;3(4):613–623. 10.1111/j.2041-210X.2012.00198.x [OpenAIRE] [DOI]

5 Consortium HMP, et al Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–214. 10.1038/nature11234 22699609 [OpenAIRE] [PubMed] [DOI]

6 Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol. 2014;12(1):1 10.1186/s12915-014-0069-1 24417977 [OpenAIRE] [PubMed] [DOI]

7 Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods. 2012;9(8):811–814. 10.1038/nmeth.2066 22688413 [OpenAIRE] [PubMed] [DOI]

8 Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–7541. 10.1128/AEM.01541-09 19801464 [OpenAIRE] [PubMed] [DOI]

9 Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughe y MJ, Woese CR. The ribosomal database project (RDP). Nucleic Acids Res. 1996;24(1):82–85. 10.1093/nar/24.1.82 8594608 [OpenAIRE] [PubMed] [DOI]

10 Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al GenBank. Nucleic Acids Res. 2013;41(D1):D36–D42. 10.1093/nar/gks1195 23193287 [OpenAIRE] [PubMed] [DOI]

11 Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, et al Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 2013;22(21):5271–5277. 10.1111/mec.12481 24112409 [OpenAIRE] [PubMed] [DOI]

12 Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2012;41:D597–D604. 10.1093/nar/gks1160 23193267 [OpenAIRE] [PubMed] [DOI]

13 DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environn Microbiol. 2006;72(7):5069–5072. 10.1128/AEM.03006-05 16820507 [OpenAIRE] [PubMed] [DOI]

14 Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–D596. 10.1093/nar/gks1219 23193283 [OpenAIRE] [PubMed] [DOI]

15 Foster ZSL, Grünwald NJ. Metacoder user documentation; 2016. Available from: http://grunwaldlab.github.io/metacoder_documentation.

25 references, page 1 of 2
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