Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Documentation for package ‘metacoder’ version 0.3.7

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-- 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 --

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_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 --

Replace low counts with zero