cenplot 0.1.6

Centromere plotting library.

CenPlot

A Python library for producing centromere figures.

CDR plot. HOR plot.

Combined plot. Identity plots.

Getting Started

Install the package from pypi.

pip install cenplot

CLI

Generating a split HOR tracks using the cenplot draw command and an input layout.

# examples/example_cli.sh
cenplot draw \
-t examples/tracks_hor.toml \
-c "chm13_chr10:38568472-42561808" \
-p 4 \
-d plots \
-o "plot/merged_image.png"

Python API

The same HOR track can be created with a few lines of code.

# examples/example_api.py
from cenplot import plot_tracks, read_tracks

chrom = "chm13_chr10:38568472-42561808"
track_list, settings = read_tracks("examples/tracks_hor.toml", chrom=chrom)
fig, axes, _ = plot_tracks(track_list.tracks, settings)

Development

Requires Python >= 3.12 and Git LFS to pull test files.

Create a venv, build cenplot, and install it. Also, generate the docs.

which python3.12 pip
git lfs install && git lfs pull
make dev && make build && make install
pdoc ./cenplot -o docs/

The generated venv will have the cenplot script.

# source venv/bin/activate
venv/bin/cenplot -h

To run tests.

make test

Documentation

Read the documentation here.

Cite

Gao S, Oshima KK, Chuang SC, Loftus M, Montanari A, Gordon DS, Human Genome Structural Variation Consortium, Human Pangenome Reference Consortium, Hsieh P, Konkel MK, Ventura M, Logsdon GA. A global view of human centromere variation and evolution. bioRxiv. 2025. p. 2025.12.09.693231. doi:10.64898/2025.12.09.693231