get_taxmap_cols

Convert logical, names, or indexes to column names and check that they exist.

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_cols function

<dl><dt>obj</dt>
<dd>A taxmap object</dd>
<dt>data</dt>
<dd>The name of a table in <code>obj</code> that contains counts.</dd>
<dt>cols</dt>
<dd>The columns in the data set to use. Takes one of
the following inputs:<dl>
 <dt>TRUE/FALSE:</dt>
<dd>All non-target columns will be preserved or not.</dd></dl></dd> <dt>Vector of TRUE/FALSE of length equal to the number of columns:</dt>
<dd>Preserve the columns
corresponding to <code>TRUE</code> values.</dd> <dt>Character vector:</dt>
<dd>The names of columns to preserve</dd> <dt>Numeric vector:</dt>
<dd>The indexes of columns to preserve</dd>
</dl>

Arguments

Get a column subset — get_taxmap_cols

<dl>

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


<dt>data</dt>
<dd>The name of a table in <code>obj</code> that contains counts.</dd>


<dt>cols</dt>
<dd>The columns in the data set to use. Takes one of
the following inputs:<dl>
 <dt>TRUE/FALSE:</dt>
<dd>All non-target columns will be preserved or not.</dd>

 <dt>Vector of TRUE/FALSE of length equal to the number of columns:</dt>
<dd>Preserve the columns
corresponding to <code>TRUE</code> values.</dd>

 <dt>Character vector:</dt>
<dd>The names of columns to preserve</dd>

 <dt>Numeric vector:</dt>
<dd>The indexes of columns to preserve</dd>


</dl></dd>

</dl>

get_taxmap_cols: Get a column subset

Description

Usage

Arguments

See Also