https://github.com/moold/paf2dotplot
Draw a dot plot from a paf alignment
https://github.com/moold/paf2dotplot
Last synced: 12 months ago
JSON representation
Draw a dot plot from a paf alignment
- Host: GitHub
- URL: https://github.com/moold/paf2dotplot
- Owner: moold
- License: gpl-3.0
- Created: 2021-10-29T09:44:12.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-12-20T07:07:24.000Z (over 1 year ago)
- Last Synced: 2025-04-06T10:42:51.792Z (about 1 year ago)
- Language: R
- Size: 695 KB
- Stars: 26
- Watchers: 3
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-genome-visualization - paf2dotplot - genome-visualization/paf2dotplot.png) (Comparative)
README
# Paf2dotplot
Draw a dot plot from a paf alignment (usually generated by [minimap2](https://github.com/lh3/minimap2)). Paf2dotplot is adapted from [dotPlotly](https://github.com/tpoorten/dotPlotly/), but it has some extra features and parameters, for details, just have a try!
## Dependencies
The script requires two R packages: `optparse`, `ggplot2`
## Installation
```sh
# download
git clone https://github.com/moold/paf2dotplot.git
# install R packages
R --slave -e 'install.packages(c("optparse", "ggplot2"))'
```
## Usage
```sh
# do asm-to-ref mapping
minimap2 -cx asm10 asm1.fa asm2.fa > aln.paf
# draw
./paf2dotplot.r -f -b aln.paf
```
This will generate a result file `aln.paf.pdf` in the current directory. You can use [ImageMagick](https://github.com/ImageMagick/ImageMagick) command to do some format conversion or modification.
Here are two example images generated by Paf2dotplot:
 
## Parameters
Use `./paf2dotplot.r -h` to see options.