metacoder0.3.7 package

add_alpha

Get list of usable functions

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

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

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

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

Compare groups of samples

Find complement of sequences

dplyr select_helpers

Converts decimal numbers to other bases

Look up official names from potentially misspelled names

Count capture groups

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

dplyr select_helpers

An example hierarchies object

An example Hierarchy object

An example Hierarchy object

An example Hierarchy object

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

Get data in a taxmap object by name

Get data in a taxonomy or 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

Plot a taxonomic tree

Plot a matrix of heat trees

Make a set of many [hierarchy()] class objects

The Hierarchy class

Highlight taxon ID column

Get ID classifications of taxa

Convert data input for Taxamp

Finds the gap/overlap of circle coordinates

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

Test if taxa are roots

Test if taxa are stems

Bounding box coords for labels

Layout functions

Get leaf taxa

Apply function to leaves of each taxon

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

Make color/size legend

Create a mapping between two variables

Create a mapping without NSE

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

Get number of leaves

Get number of leaves

Count observations in [taxmap()]

Count observation assigned in [taxmap()]

Get number of subtaxa

Get number of subtaxa

Get number of supertaxa

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

Get data indexes associated with taxa

Apply function to observations per taxon

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 Greengenes release

Infer edge list from hierarchies

Parse mothur *.tax.summary Classify.seqs output

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

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

Convert one or more data sets to taxmap

Converts the uBiome file format to taxmap

Parse UNITE general release FASTA

Makes coordinates for a regular polygon

Print a object with a prefix

Use EMBOSS primersearch for in silico PCR

Test if primersearch is installed

Use EMBOSS primersearch for in silico PCR

Print a character

Print a data.frame

Print method for unsupported

Print a factor

Print an integer

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

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

Reverse sequences

Get root taxa

Execute EMBOSS Primersearch

Sample a proportion of observations from [taxmap()]

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

List to vector of unique elements

Splits a taxonomy at a specific level or rank

dplyr select_helpers

Return startup message

Get stem taxa

Get subtaxa

Apply function to subtaxa of each taxon

Get all supertaxa of a taxon

Apply function to supertaxa of each taxon

A class for multiple taxon objects

Taxmap class

Taxon class

Taxonomy database class

Taxon ID class

Get taxon IDs

Get taxon indexes

Taxon name class

Get taxon names

Taxon rank class

Get taxon ranks

Taxonomy class

Convert taxonomy info to a table

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 parameters

Verify size range parameters

Check that an object is a taxmap

Verify transformation function parameters

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

Write an imitation of the UNITE general FASTA database

Replace low counts with zero