def_names

def_types

Intended to be used in <code><a href="https://readr.tidyverse.org/reference/read_delim.html">readr::read_tsv()</a></code>-like functions that accept a
<code>col_names</code> and a <code>col_types</code> argument.

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

def_names function

<dl><dt>format</dt>
<dd>specify a format known to gggenomes, such as <code>gff3</code>, <code>gbk</code>, ...</dd></dl>

Arguments

<ul>
<li><code>def_names()</code>: default column names for defined formats</li>
<li><code>def_types()</code>: default column types for defined formats</li>
</ul>

Functions

<pre><code>
 gff3 ccciicccc seq_id,source,type,start,end,score,strand,phase,attributes
 paf ciiicciiiiid seq_id,length,start,end,strand,seq_id2,length2,start2,end2,map_match,map_length,map_quality
 blast ccdiiiiiiidd seq_id,seq_id2,pident,length,mismatch,gapopen,start,end,start2,end2,evalue,bitscore
 bed ciicdc seq_id,start,end,name,score,strand
 fai ci--- seq_id,seq_desc,length
 seq_len cci seq_id,seq_desc,length
 vcf cicccdccc seq_id,start,feat_id,ref,alt,qual,filter,info,format
</code></pre>

Defined formats, column types and names

Intended to be used in <code><a href='https://readr.tidyverse.org/reference/read_delim.html'>readr::read_tsv()</a></code>-like functions that accept a
<code>col_names</code> and a <code>col_types</code> argument.

Default column names and types for defined formats — def_names

<dl>

<dt>format</dt>
<dd>specify a format known to gggenomes, such as <code>gff3</code>, <code>gbk</code>, ...</dd>

</dl>

<pre><code>
 gff3 ccciicccc seq_id,source,type,start,end,score,strand,phase,attributes
 paf ciiicciiiiid seq_id,length,start,end,strand,seq_id2,length2,start2,end2,map_match,map_length,map_quality
 blast ccdiiiiiiidd seq_id,seq_id2,pident,length,mismatch,gapopen,start,end,start2,end2,evalue,bitscore
 bed ciicdc seq_id,start,end,name,score,strand
 fai ci--- seq_id,seq_desc,length
 seq_len cci seq_id,seq_desc,length
 vcf cicccdccc seq_id,start,feat_id,ref,alt,qual,filter,info,format
</code></pre>

def_names: Default column names and types for defined formats

Description

Usage

Value

Arguments

Functions

Defined formats, column types and names

Examples