get_taxmap_data

NOTE: This will be replaced by the function `get_dataset` in the `taxa`
package. Get a data set from a taxmap object and complain if it does not
exist. This is intended to be used to parse options in other functions.

internal

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>.

Zachary Foster

metacoder

Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data

Niklaus Grunwald

Kamil Slowikowski

Scott Chamberlain

Rob Gilmore

get_taxmap_data function

<dl><dt>obj</dt>
<dd>A taxmap object</dd>
<dt>data</dt>
<dd>Which data set to use. Can be any of the following:<dl>
 <dt>Name</dt>
<dd>The name of the data set to use.</dd></dl></dd> <dt>Index</dt>
<dd>The index of the data set to use.</dd> <dt>TRUE/FALSE vector</dt>
<dd>A TRUE/FALSE vector the same length as the
 number of datasets, with exactly one TRUE corresponding to the
 selected data set.</dd>
</dl>

Arguments

Get a data set from a taxmap object — get_taxmap_data

<dl>

<dt>obj</dt>
<dd>A taxmap object</dd>


<dt>data</dt>
<dd>Which data set to use. Can be any of the following:<dl>
 <dt>Name</dt>
<dd>The name of the data set to use.</dd>

 <dt>Index</dt>
<dd>The index of the data set to use.</dd>

 <dt>TRUE/FALSE vector</dt>
<dd>A TRUE/FALSE vector the same length as the
 number of datasets, with exactly one TRUE corresponding to the
 selected data set.</dd>


</dl></dd>

</dl>

get_taxmap_data: Get a data set from a taxmap object

Description

Usage

Arguments

See Also