make_dada2_tax_table

Attempts to save the taxonomy information assocaited with an abundance matrix in a taxmap object
in the dada2 taxonomy matrix format. If the taxmap object was created using
<code>parse_dada2</code>, then it should be able to replicate the format exactly with the
default settings.

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

make_dada2_tax_table function

<dl><dt>obj</dt>
<dd>A taxmap object</dd>
<dt>asv_table</dt>
<dd>The name of the abundance matrix in the taxmap object to use.</dd>
<dt>asv_id</dt>
<dd>The name of the column in <code>asv_table</code> with unique ASV ids or sequences.</dd></dl>

Arguments

Make a imitation of the dada2 taxonomy matrix — make_dada2_tax_table

<dl>

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


<dt>asv_table</dt>
<dd>The name of the abundance matrix in the taxmap object to use.</dd>


<dt>asv_id</dt>
<dd>The name of the column in <code>asv_table</code> with unique ASV ids or sequences.</dd>

</dl>

make_dada2_tax_table: Make a imitation of the dada2 taxonomy matrix

Description

Usage

Value

Arguments

See Also