Package: metacoder 0.3.8

Zachary Foster

metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Authors:Zachary Foster [aut, cre], Niklaus Grunwald [ths], Kamil Slowikowski [ctb], Scott Chamberlain [ctb], Rob Gilmore [ctb]

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metacoder.pdf |metacoder.html
metacoder/json (API)
NEWS

# Install 'metacoder' in R:
install.packages('metacoder', repos = c('https://grunwaldlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/grunwaldlab/metacoder/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp

9.61 score 138 stars 328 scripts 188 downloads 32 mentions 128 exports 139 dependencies

Last updated 5 days agofrom:e881d1bc67. Checks:1 OK, 10 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 12 2025
R-4.5-win-x86_64NOTEFeb 12 2025
R-4.5-mac-x86_64NOTEFeb 12 2025
R-4.5-mac-aarch64NOTEFeb 12 2025
R-4.5-linux-x86_64NOTEFeb 12 2025
R-4.4-win-x86_64NOTEFeb 12 2025
R-4.4-mac-x86_64NOTEFeb 12 2025
R-4.4-mac-aarch64NOTEFeb 12 2025
R-4.3-win-x86_64NOTEFeb 12 2025
R-4.3-mac-x86_64NOTEFeb 12 2025
R-4.3-mac-aarch64NOTEFeb 12 2025

Exports:%>%all_namesambiguous_synonymsarrange_obsarrange_taxaas_phyloseqbranchescalc_diff_abund_deseq2calc_group_meancalc_group_mediancalc_group_rsdcalc_group_statcalc_n_samplescalc_obs_propscalc_prop_samplescalc_taxon_abundclassificationscompare_groupscomplementcontainscounts_to_presencedatabase_listdiverging_paletteends_witheverythingextract_tax_datafilter_ambiguous_taxafilter_obsfilter_taxaget_dataget_data_frameget_datasetheat_treeheat_tree_matrixhierarchieshierarchyid_classificationsidsinternodesis_ambiguousis_branchis_internodeis_leafis_rootis_stemlayout_functionsleavesleaves_applylookup_tax_datamake_dada2_asv_tablemake_dada2_tax_tablemap_datamap_data_matchesmutate_obsn_leavesn_leaves_1n_obsn_obs_1n_subtaxan_subtaxa_1n_supertaxan_supertaxa_1ncbi_taxon_samplenmsnum_rangeobsobs_applyone_ofparse_dada2parse_edge_listparse_greengenesparse_mothur_tax_summaryparse_mothur_taxonomyparse_newickparse_phyloparse_phyloseqparse_primersearchparse_qiime_biomparse_rdpparse_silva_fastaparse_tax_dataparse_ubiomeparse_unite_generalprimersearchprimersearch_rawprint_treequalitative_palettequantative_paletteranksrarefy_obsread_fastaremove_redundant_namesreplace_taxon_idsrev_compreverserootssample_frac_obssample_frac_taxasample_n_obssample_n_taxaselect_obsstarts_withstemssubtaxasubtaxa_applysupertaxasupertaxa_applytaxataxmaptaxontaxon_databasetaxon_idtaxon_idstaxon_indexestaxon_nametaxon_namestaxon_ranktaxon_rankstaxonomytaxonomy_tabletransmute_obswrite_greengeneswrite_mothur_taxonomywrite_rdpwrite_silva_fastawrite_unite_generalzero_low_counts

Dependencies:ade4apeaskpassassertthatbackportsbase64encbitbit64bitopsbslibcachemcheckmateclicliprclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsGAgenericsggfittextggplot2gluegridExtragridtextgtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrmarkdownMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplypermutephangornpillarpixmappkgconfigplyrpngprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloRCurlreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessegmentedseqinrshadessolriumspstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsveganviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo

Documentation for metacoder

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Feb 12 2025.

Last update: 2021-06-23
Started: 2016-04-11

Readme and manuals

Help Manual

Help pageTopics
Return names of data in [taxonomy()] or [taxmap()]all_names
Get patterns for ambiguous taxaambiguous_synonyms
Sort user data in [taxmap()] objectsarrange_obs
Sort the edge list of [taxmap()] objectsarrange_taxa
Convert taxmap to phyloseqas_phyloseq
Get "branch" taxabranches
Differential abundance with DESeq2calc_diff_abund_deseq2
Calculate means of groups of columnscalc_group_mean
Calculate medians of groups of columnscalc_group_median
Relative standard deviations of groups of columnscalc_group_rsd
Apply a function to groups of columnscalc_group_stat
Count the number of samplescalc_n_samples
Calculate proportions from observation countscalc_obs_props
Calculate the proportion of samplescalc_prop_samples
Get classifications of taxaclassifications
Compare groups of samplescompare_groups
Find complement of sequencescomplement
Apply a function to groups of columnscounts_to_presence
Database listdatabase_list
The default diverging color palettediverging_palette
An example hierarchies objectex_hierarchies
An example Hierarchy objectex_hierarchy1
An example Hierarchy objectex_hierarchy2
An example Hierarchy objectex_hierarchy3
An example taxmap objectex_taxmap
Extracts taxonomy info from vectors with regexextract_tax_data
Filter ambiguous taxon namesfilter_ambiguous_taxa
Filter observations with a list of conditionsfilter_obs
Filter taxa with a list of conditionsfilter_taxa
Taxonomic filtering helpersfiltering-helpers ids nms ranks
Get data in a taxmap object by nameget_data
Get data in a taxonomy or taxmap object by nameget_data_frame
Get a data set from a taxmap objectget_dataset
Plot a taxonomic treeheat_tree heat_tree.default heat_tree.Taxmap
Plot a matrix of heat treesheat_tree_matrix
Make a set of many [hierarchy()] class objectshierarchies
The Hierarchy classhierarchy
Highlight taxon ID columnhighlight_taxon_ids
A HMP subsethmp_otus
Sample information for HMP subsethmp_samples
Get ID classifications of taxaid_classifications
Get "internode" taxainternodes
Find ambiguous taxon namesis_ambiguous
Test if taxa are branchesis_branch
Test if taxa are "internodes"is_internode
Test if taxa are leavesis_leaf
Test if taxa are rootsis_root
Test if taxa are stemsis_stem
Layout functionslayout_functions
Get leaf taxaleaves
Apply function to leaves of each taxonleaves_apply
Convert one or more data sets to taxmaplookup_tax_data
Make a imitation of the dada2 ASV abundance matrixmake_dada2_asv_table
Make a imitation of the dada2 taxonomy matrixmake_dada2_tax_table
Create a mapping between two variablesmap_data
Create a mapping without NSEmap_data_
Metacodermetacoder
Add columns to [taxmap()] objectsmutate_obs
Get number of leavesn_leaves
Get number of leavesn_leaves_1
Count observations in [taxmap()]n_obs
Count observation assigned in [taxmap()]n_obs_1
Get number of subtaxan_subtaxa
Get number of subtaxan_subtaxa_1
Get number of supertaxan_supertaxa
Get number of supertaxan_supertaxa_1
Download representative sequences for a taxonncbi_taxon_sample
Get data indexes associated with taxaobs
Apply function to observations per taxonobs_apply
Convert the output of dada2 to a taxmap objectparse_dada2
Parse Greengenes releaseparse_greengenes
Parse mothur *.tax.summary Classify.seqs outputparse_mothur_tax_summary
Parse mothur Classify.seqs *.taxonomy outputparse_mothur_taxonomy
Parse a Newick fileparse_newick
Parse a phylo objectparse_phylo
Convert a phyloseq to taxmapparse_phyloseq
Parse EMBOSS primersearch outputparse_primersearch
Parse a BIOM output from QIIMEparse_qiime_biom
Parse RDP FASTA releaseparse_rdp
Parse SILVA FASTA releaseparse_silva_fasta
Convert one or more data sets to taxmapparse_tax_data
Converts the uBiome file format to taxmapparse_ubiome
Parse UNITE general release FASTAparse_unite_general
Use EMBOSS primersearch for in silico PCRprimersearch
Use EMBOSS primersearch for in silico PCRprimersearch_raw
Print a text treeprint_tree
The default qualitative color palettequalitative_palette
The default quantative color palettequantative_palette
Lookup-table for IDs of taxonomic ranksranks_ref
Calculate rarefied observation countsrarefy_obs
Read a FASTA fileread_fasta
Remove redundant parts of taxon namesremove_redundant_names
Replace taxon idsreplace_taxon_ids
Revere complement sequencesrev_comp
Reverse sequencesreverse
Get root taxaroots
Sample a proportion of observations from [taxmap()]sample_frac_obs
Sample a proportion of taxa from [taxonomy()] or [taxmap()]sample_frac_taxa
Sample n observations from [taxmap()]sample_n_obs
Sample n taxa from [taxonomy()] or [taxmap()]sample_n_taxa
Subset columns in a [taxmap()] objectselect_obs
Get stem taxastems
Get subtaxasubtaxa
Apply function to subtaxa of each taxonsubtaxa_apply
Get all supertaxa of a taxonsupertaxa
Apply function to supertaxa of each taxonsupertaxa_apply
A class for multiple taxon objectstaxa
Taxmap classtaxmap
Taxon classtaxon
Taxonomy database classtaxon_database
Taxon ID classtaxon_id
Get taxon IDstaxon_ids
Get taxon indexestaxon_indexes
Taxon name classtaxon_name
Get taxon namestaxon_names
Taxon rank classtaxon_rank
Get taxon rankstaxon_ranks
Taxonomy classtaxonomy
Convert taxonomy info to a tabletaxonomy_table
Replace columns in [taxmap()] objectstransmute_obs
Write an imitation of the Greengenes databasewrite_greengenes
Write an imitation of the Mothur taxonomy filewrite_mothur_taxonomy
Write an imitation of the RDP FASTA databasewrite_rdp
Write an imitation of the SILVA FASTA databasewrite_silva_fasta
Write an imitation of the UNITE general FASTA databasewrite_unite_general
Replace low counts with zerozero_low_counts