get_taxmap_other_cols

Parse the other_cols option used in many calculation 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_other_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 names/indexes of columns in <code>data</code> to use. Takes one
of the following inputs:<dl>
 <dt>TRUE/FALSE:</dt>
<dd>All columns will used.</dd></dl></dd> <dt>Vector of TRUE/FALSE of length equal to the number of columns:</dt>
<dd>Use the columns
corresponding to <code>TRUE</code> values.</dd> <dt>Character vector:</dt>
<dd>The names of columns to use</dd> <dt>Numeric vector:</dt>
<dd>The indexes of columns to use</dd>
</dl>
<dt>other_cols</dt>
<dd>Preserve in the output non-target columns present in the
input data. The "taxon_id" column will always be preserved. 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>

Arguments

Parse the other_cols option — get_taxmap_other_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 names/indexes of columns in <code>data</code> to use. Takes one
of the following inputs:<dl>
 <dt>TRUE/FALSE:</dt>
<dd>All columns will used.</dd>

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

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

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


</dl></dd>


<dt>other_cols</dt>
<dd>Preserve in the output non-target columns present in the
input data. The "taxon_id" column will always be preserved. 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_other_cols: Parse the other_cols option

Description

Usage

Arguments

See Also