emale_ava

One row per alignment block. Alignments were computed with minimap2.

datasets

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

emale_ava function

A data frame with 125 rows and 23 columns<dl>
<dt>file_id</dt>
<dd>name of the file the data was read from</dd><dt>seq_id</dt>
<dd>identifier of the sequence the feature appears on</dd><dt>length</dt>
<dd>length of the sequence</dd><dt>start</dt>
<dd>start of the feature on the sequence</dd><dt>end</dt>
<dd>end of the feature on the sequence</dd><dt>strand</dt>
<dd>orientation of the feature relative to the sequence (+ or -)</dd><dt>seq_id2</dt>
<dd>identifier of the sequence the feature appears on</dd><dt>length2</dt>
<dd>length of the sequence</dd><dt>start2</dt>
<dd>start of the feature on the sequence</dd><dt>end2</dt>
<dd>end of the feature on the sequence</dd><dt>map_match, map_length, map_quality, NM, ms, AS, nn, tp, cm, s1, de, rl, cg</dt>
<dd>see <a href="https://github.com/lh3/miniasm/blob/master/PAF.md">https://github.com/lh3/miniasm/blob/master/PAF.md</a> for additional columns</dd>
</dl>

Format

All-versus-all whole genome alignments of 6 EMALE genomes — emale_ava

A data frame with 125 rows and 23 columns<dl>
<dt>file_id</dt>
<dd>name of the file the data was read from</dd>

<dt>seq_id</dt>
<dd>identifier of the sequence the feature appears on</dd>

<dt>length</dt>
<dd>length of the sequence</dd>

<dt>start</dt>
<dd>start of the feature on the sequence</dd>

<dt>end</dt>
<dd>end of the feature on the sequence</dd>

<dt>strand</dt>
<dd>orientation of the feature relative to the sequence (+ or -)</dd>

<dt>seq_id2</dt>
<dd>identifier of the sequence the feature appears on</dd>

<dt>length2</dt>
<dd>length of the sequence</dd>

<dt>start2</dt>
<dd>start of the feature on the sequence</dd>

<dt>end2</dt>
<dd>end of the feature on the sequence</dd>

<dt>map_match, map_length, map_quality, NM, ms, AS, nn, tp, cm, s1, de, rl, cg</dt>
<dd>see <a href='https://github.com/lh3/miniasm/blob/master/PAF.md'>https://github.com/lh3/miniasm/blob/master/PAF.md</a> for additional columns</dd>


</dl>

emale_ava: All-versus-all whole genome alignments of 6 EMALE genomes

Description

Usage

Arguments

Format