Installation

Requirements

pycmplot requires Python 3.9 or later. The following packages are installed automatically as dependencies:

Package	Purpose
pandas, numpy	Data loading and numerical operations
scipy	Beta-distribution confidence bands for QQ plots
matplotlib	Plotting backend
pycirclize	Circular (Circos-style) track rendering
natsort	Natural-order chromosome sorting (chr1 < chr2 < … < chrX)
adjustText	Automatic label collision avoidance
pyliftover	hg19 → hg38 coordinate conversion
Pillow	Image format utilities

From PyPI (recommended)

pip install pycmplot

From GitHub (development version)

git clone https://github.com/esohkevin/pycmplot.git
cd pycmplot
pip install -e .

If your system Python is externally managed (common on Ubuntu 22.04+):

pip install -e . --break-system-packages

Using a virtual environment

If you cannot or prefer not to install into the system Python, use a virtual environment:

python -m venv ~/envs/pycmplot
source ~/envs/pycmplot/bin/activate

pip install --upgrade pip setuptools wheel
pip install pycmplot

Verify the installation

pycmplot -h

A successful installation prints the full help message with all command-line options.