Paf2dotplot

Draw a dot plot from a paf alignment (usually generated by minimap2). Paf2dotplot is adapted from 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

# download
git clone https://github.com/moold/paf2dotplot.git
# install R packages
R --slave -e 'install.packages(c("optparse", "ggplot2", "RColorBrewer"))'

Usage

# 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 command to do some format conversion or modification. Here are two example images generated by Paf2dotplot:

Parameters

Use ./paf2dotplot.r -h to see options.

Update Notes

• Version 1.0.1 (2025.09.18):

  • Fixed generate_colors() when n < 3 (ensures correct length), #5 (Thanks to @dukecomeback).

• Version 1.0.0 (2025.08.19):

  • Added -e, --ref-bed: support reference BED file (vertical dotted lines).
  • Added -E, --query-bed: support query BED file (horizontal dotted lines).
  • Added -v, --version: show script version and exit.