# Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

## Documentation for package ‘metacoder’ version 0.3.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N O P Q R S T W Z

## -- A --

all_names | Return names of data in [taxonomy()] or [taxmap()]
ambiguous_synonyms | Get patterns for ambiguous taxa
arrange_obs | Sort user data in [taxmap()] objects
arrange_taxa | Sort the edge list of [taxmap()] objects
as_phyloseq | Convert taxmap to phyloseq

## -- B --

branches | Get "branch" taxa

## -- C --

calc_diff_abund_deseq2 | Differential abundance with DESeq2
calc_group_mean | Calculate means of groups of columns
calc_group_median | Calculate medians of groups of columns
calc_group_rsd | Relative standard deviations of groups of columns
calc_group_stat | Apply a function to groups of columns
calc_n_samples | Count the number of samples
calc_obs_props | Calculate proportions from observation counts
calc_prop_samples | Calculate the proportion of samples
classifications | Get classifications of taxa
compare_groups | Compare groups of samples
complement | Find complement of sequences
counts_to_presence | Apply a function to groups of columns

## -- D --

database_list | Database list
diverging_palette | The default diverging color palette

## -- E --

extract_tax_data | Extracts taxonomy info from vectors with regex
ex_hierarchies | An example hierarchies object
ex_hierarchy1 | An example Hierarchy object
ex_hierarchy2 | An example Hierarchy object
ex_hierarchy3 | An example Hierarchy object
ex_taxmap | An example taxmap object

## -- F --

filtering-helpers | Taxonomic filtering helpers
filter_ambiguous_taxa | Filter ambiguous taxon names
filter_obs | Filter observations with a list of conditions
filter_taxa | Filter taxa with a list of conditions

## -- G --

get_data | Get data in a taxmap object by name
get_dataset | Get a data set from a taxmap object
get_data_frame | Get data in a taxonomy or taxmap object by name

## -- H --

heat_tree | Plot a taxonomic tree
heat_tree.default | Plot a taxonomic tree
heat_tree.Taxmap | Plot a taxonomic tree
heat_tree_matrix | Plot a matrix of heat trees
hierarchies | Make a set of many [hierarchy()] class objects
hierarchy | The Hierarchy class
highlight_taxon_ids | Highlight taxon ID column
hmp_otus | A HMP subset
hmp_samples | Sample information for HMP subset

## -- I --

ids | Taxonomic filtering helpers
id_classifications | Get ID classifications of taxa
internodes | Get "internode" taxa
is_ambiguous | Find ambiguous taxon names
is_branch | Test if taxa are branches
is_internode | Test if taxa are "internodes"
is_leaf | Test if taxa are leaves
is_root | Test if taxa are roots
is_stem | Test if taxa are stems

## -- L --

layout_functions | Layout functions
leaves | Get leaf taxa
leaves_apply | Apply function to leaves of each taxon
lookup_tax_data | Convert one or more data sets to taxmap

## -- M --

make_dada2_asv_table | Make a imitation of the dada2 ASV abundance matrix
make_dada2_tax_table | Make a imitation of the dada2 taxonomy matrix
map_data | Create a mapping between two variables
map_data_ | Create a mapping without NSE
metacoder | Metacoder
mutate_obs | Add columns to [taxmap()] objects

## -- N --

ncbi_taxon_sample | Download representative sequences for a taxon
nms | Taxonomic filtering helpers
n_leaves | Get number of leaves
n_leaves_1 | Get number of leaves
n_obs | Count observations in [taxmap()]
n_obs_1 | Count observation assigned in [taxmap()]
n_subtaxa | Get number of subtaxa
n_subtaxa_1 | Get number of subtaxa
n_supertaxa | Get number of supertaxa
n_supertaxa_1 | Get number of supertaxa

## -- O --

obs | Get data indexes associated with taxa
obs_apply | Apply function to observations per taxon

## -- P --

parse_dada2 | Convert the output of dada2 to a taxmap object
parse_greengenes | Parse Greengenes release
parse_mothur_taxonomy | Parse mothur Classify.seqs *.taxonomy output
parse_mothur_tax_summary | Parse mothur *.tax.summary Classify.seqs output
parse_newick | Parse a Newick file
parse_phylo | Parse a phylo object
parse_phyloseq | Convert a phyloseq to taxmap
parse_primersearch | Parse EMBOSS primersearch output
parse_qiime_biom | Parse a BIOM output from QIIME
parse_rdp | Parse RDP FASTA release
parse_silva_fasta | Parse SILVA FASTA release
parse_tax_data | Convert one or more data sets to taxmap
parse_ubiome | Converts the uBiome file format to taxmap
parse_unite_general | Parse UNITE general release FASTA
primersearch | Use EMBOSS primersearch for in silico PCR
primersearch_is_installed | Test if primersearch is installed
primersearch_raw | Use EMBOSS primersearch for in silico PCR
print_tree | Print a text tree

## -- Q --

qualitative_palette | The default qualitative color palette
quantative_palette | The default quantative color palette

## -- R --

ranks | Taxonomic filtering helpers
ranks_ref | Lookup-table for IDs of taxonomic ranks
rarefy_obs | Calculate rarefied observation counts
read_fasta | Read a FASTA file
remove_redundant_names | Remove redundant parts of taxon names
replace_taxon_ids | Replace taxon ids
reverse | Reverse sequences
rev_comp | Revere complement sequences
roots | Get root taxa

## -- S --

sample_frac_obs | Sample a proportion of observations from [taxmap()]
sample_frac_taxa | Sample a proportion of taxa from [taxonomy()] or [taxmap()]
sample_n_obs | Sample n observations from [taxmap()]
sample_n_taxa | Sample n taxa from [taxonomy()] or [taxmap()]
select_obs | Subset columns in a [taxmap()] object
stems | Get stem taxa
subtaxa | Get subtaxa
subtaxa_apply | Apply function to subtaxa of each taxon
supertaxa | Get all supertaxa of a taxon
supertaxa_apply | Apply function to supertaxa of each taxon

## -- T --

taxa | A class for multiple taxon objects
taxmap | Taxmap class
taxon | Taxon class
taxonomy | Taxonomy class
taxonomy_table | Convert taxonomy info to a table
taxon_database | Taxonomy database class
taxon_id | Taxon ID class
taxon_ids | Get taxon IDs
taxon_indexes | Get taxon indexes
taxon_name | Taxon name class
taxon_names | Get taxon names
taxon_rank | Taxon rank class
taxon_ranks | Get taxon ranks
transmute_obs | Replace columns in [taxmap()] objects

## -- W --

write_greengenes | Write an imitation of the Greengenes database
write_mothur_taxonomy | Write an imitation of the Mothur taxonomy file
write_rdp | Write an imitation of the RDP FASTA database
write_silva_fasta | Write an imitation of the SILVA FASTA database
write_unite_general | Write an imitation of the UNITE general FASTA database

## -- Z --

zero_low_counts | Replace low counts with zero