Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
Get data in a taxonomy or taxmap object by name
Get data in a taxmap object by name
Return name of database
Get a data set from a taxmap object
Get input from dots or list
get_edge_children
get_edge_parents
Get a data set in as_phyloseq
get_node_children
Get numeric columns from taxmap table
Return numeric values in a character
Find optimal range
Get a vector from a vector/list/table to be used in mapping
Get a column subset
Get a data set from a taxmap object
Parse the other_cols option
Get a table from a taxmap object
Get taxonomy levels
magrittr forward-pipe operator
Test if taxa are stems
Bounding box coords for labels
Apply function to leaves of each taxon
Get number of leaves
Get number of leaves
Get number of supertaxa
Variable name formatting in print methods
Get names of data used in expressions
Downloads sequences from ids
Download representative sequences for a taxon
dplyr select_helpers
Parse Greengenes release
Infer edge list from hierarchies
Parse mothur *.tax.summary Classify.seqs output
Converts the uBiome file format to taxmap
Print a list
Print a logical
Print a matrix
Print a numeric
Print a ordered factor
Print a tibble
Generic vector printer
Print a item
Print a text tree
lappy with progress bars
Punctuation formatting in print methods
The default qualitative color palette
The default quantative color palette
Layout functions
Get root taxa
Execute EMBOSS Primersearch
Sample a proportion of observations from [taxmap()]
Get stem taxa
Taxonomy database class
Taxon ID class
Get taxon IDs
Get taxon indexes
Taxon name class
Get taxon names
Taxon rank class
Get taxon ranks
Extracts taxonomy info from vectors with regex
Get line numbers of FASTA headers
Filter ambiguous taxon names
Filter observations with a list of conditions
Filter taxa with a list of conditions
Taxonomic filtering helpers
Get classification for taxa in edge list
Test if taxa are roots
Compare groups of samples
Reverse sequences
List to vector of unique elements
Splits a taxonomy at a specific level or rank
dplyr select_helpers
Return startup message
Taxmap class
Find complement of sequences
dplyr select_helpers
Convert data input for Taxamp
Finds the gap/overlap of circle coordinates
Converts decimal numbers to other bases
Make color/size legend
Convert one or more data sets to taxmap
Look up official names from potentially misspelled names
add_alpha
Get list of usable functions
Count capture groups
Return names of data in [taxonomy()] or [taxmap()]
Get patterns for ambiguous taxa
Get patterns for ambiguous taxa
Covert numbers to colors
Sort user data in [taxmap()] objects
dplyr select_helpers
An example hierarchies object
An example Hierarchy object
Sort the edge list of [taxmap()] objects
Convert a vector to database IDs
Convert taxmap to phyloseq
Get "branch" taxa
Differential abundance with DESeq2
Calculate means of groups of columns
An example Hierarchy object
Calculate medians of groups of columns
Relative standard deviations of groups of columns
Apply a function to groups of columns
Count the number of samples
Calculate proportions from observation counts
Calculate the proportion of samples
An example Hierarchy object
Sum observation values for each taxon
Test if characters can be converted to numbers
Check that a unknown object can be used with taxmap
Capitalize
Check for name/index in input data
Check length of graph attributes
check for packages
Check option: groups
Check dataset format
Get classifications of taxa
Apply a function to groups of columns
Get values of data used in expressions
Database list
Description formatting in print methods
The default diverging color palette
Converts DNAbin to a named character vector
Run some function to produce new columns.
Run when package loads
Get distance from root of edgelist observations
dplyr select_helpers
Font to indicate an error
Plot a matrix of heat trees
Plot a taxonomic tree
Make a set of many [hierarchy()] class objects
The Hierarchy class
Highlight taxon ID column
Get ID classifications of taxa
Get "internode" taxa
Generate the inverse of a function
Find ambiguous taxon names
Test if taxa are branches
Test if taxa are "internodes"
Test if taxa are leaves
Get leaf taxa
Check length of thing
Print a subset of a character vector
Makes coordinates for a line
Look for NAs in parameters
Convert one or more data sets to taxmap
Make a imitation of the dada2 ASV abundance matrix
Make a imitation of the dada2 taxonomy matrix
Make a temporary file U's replaced with T
Create a mapping without NSE
Create a mapping between two variables
Run a function on unique values of a iterable
dplyr select_helpers
Metacoder
Get all distances between points
Like strsplit, but with multiple separators
Add columns to [taxmap()] objects
Print something
Count observation assigned in [taxmap()]
Count observations in [taxmap()]
Get number of subtaxa
Get number of subtaxa
Get number of supertaxa
Print a factor
Apply function to observations per taxon
Get data indexes associated with taxa
dplyr select_helpers
Convert the output of dada2 to a taxmap object
Parse options specifying datasets
Convert a table with an edge list to taxmap
Parse mothur Classify.seqs *.taxonomy output
Parse a Newick file
Parse a phylo object
Convert a phyloseq to taxmap
used to parse inputs to drop_obs and reassign_obs
Parse EMBOSS primersearch output
Print an integer
Parse a BIOM output from QIIME
Infer edge list from hierarchies composed of character vectors
Parse RDP FASTA release
Read sequences in an unknown format
Parse SILVA FASTA release
Parse summary.seqs output
Parse UNITE general release FASTA
Makes coordinates for a regular polygon
Print a object with a prefix
Test if primersearch is installed
Use EMBOSS primersearch for in silico PCR
Use EMBOSS primersearch for in silico PCR
Print a character
Print a data.frame
Print method for unsupported
Calculate rarefied observation counts
Read a FASTA file
Apply a function to chunks of a file
Remove redundant parts of taxon names
Replace taxon ids
Return github url
Rescale numeric vector to have specified minimum and maximum.
Revere complement sequences
Sample a proportion of taxa from [taxonomy()] or [taxmap()]
Sample n observations from [taxmap()]
Sample n taxa from [taxonomy()] or [taxmap()]
Make scale bar division
Pick labels to show
Subset columns in a [taxmap()] object
Apply function to subtaxa of each taxon
Get subtaxa
Apply function to supertaxa of each taxon
Get all supertaxa of a taxon
A class for multiple taxon objects
Taxon class
Convert taxonomy info to a table
Taxonomy class
Estimate text grob length
Taxon id formatting in print methods
Format a proportion as a printed percent
Transformation functions
Replace columns in [taxmap()] objects
get indexes of a unique set of the input
Check a regex-key pair
Check that all match input
Validate funcs input for Taxamp
Verify color range parameters
Verify label count
Verify size range parameters
Verify size parameters
Check that an object is a taxmap
Verify transformation function parameters
Write an imitation of the UNITE general FASTA database
Replace low counts with zero
Write an imitation of the Greengenes database
Write an imitation of the Mothur taxonomy file
Write an imitation of the RDP FASTA database
Write an imitation of the SILVA FASTA database
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>.
Useful links