read_context

Powers <code>read_seqs()</code>, <code>read_feats()</code>, <code>read_links()</code>

An extension of 'ggplot2' for creating complex genomic
maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style
geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It
implements a layout concept inspired by 'ggraph' and introduces tracks to bring
tidiness to the mess that is genomics data.

Thomas Hackl

gggenomes

A Grammar of Graphics for Comparative Genomics

Markus J. Ankenbrand

Bart van Adrichem

Kristina Haslinger

read_context function

<dl><dt>files</dt>
<dd>files to reads. Should all be of same format. In many cases,
compressed files (<code>.gz</code>, <code>.bz2</code>, <code>.xz</code>, or <code>.zip</code>) are supported.
Similarly, automatic download of remote files starting with <code>http(s)://</code> or
<code>ftp(s)://</code> works in most cases.</dd>
<dt>context</dt>
<dd>the context ("seqs", "feats", "links") in which a given format
should be read.</dd>
<dt>.id</dt>
<dd>the column with the name of the file a record was read from.
Defaults to "file_id". Set to "bin_id" if every file represents a different
bin.</dd>
<dt>format</dt>
<dd>specify a format known to gggenomes, such as <code>gff3</code>, <code>gbk</code>, ...
to overwrite automatic determination based on the file extension (see
<code>def_formats()</code> for full list).</dd>
<dt>parser</dt>
<dd>specify the name of an R function to overwrite automatic
determination based on format, e.g. <code>parser="read_tsv"</code>.</dd>
<dt>...</dt>
<dd>additional arguments passed on to the format-specific read
function called down the line.</dd></dl>

Arguments

<ul>
<li><code>read_context()</code>: bla keywords internal</li>
</ul>

Functions

Read files in different contexts — read_context

<dl>

<dt>files</dt>
<dd>files to reads. Should all be of same format. In many cases,
compressed files (<code>.gz</code>, <code>.bz2</code>, <code>.xz</code>, or <code>.zip</code>) are supported.
Similarly, automatic download of remote files starting with <code>http(s)://</code> or
<code>ftp(s)://</code> works in most cases.</dd>


<dt>context</dt>
<dd>the context ("seqs", "feats", "links") in which a given format
should be read.</dd>


<dt>.id</dt>
<dd>the column with the name of the file a record was read from.
Defaults to "file_id". Set to "bin_id" if every file represents a different
bin.</dd>


<dt>format</dt>
<dd>specify a format known to gggenomes, such as <code>gff3</code>, <code>gbk</code>, ...
to overwrite automatic determination based on the file extension (see
<code>def_formats()</code> for full list).</dd>


<dt>parser</dt>
<dd>specify the name of an R function to overwrite automatic
determination based on format, e.g. <code>parser="read_tsv"</code>.</dd>


<dt>...</dt>
<dd>additional arguments passed on to the format-specific read
function called down the line.</dd>

</dl>

read_context: Read files in different contexts

Description

Usage

Value

Arguments

Functions