pheatmap-python

Python version of pheatmap that runs on a faithful port of R's native grid graphics system instead of matplotlib.

• 🎨 No matplotlib. Renders through grid_py's Cairo backend (PNG / PDF / SVG / PS / JPEG / TIFF / BMP).
• 📐 Grammar of Graphics. Built on grid_py + gtable_py — the same primitives ggplot2 stands on.
• 🧩 Abstract layout. Sizes stay as compound Unit expressions (1npc - rown_width - legend_width - …) and resolve at draw time.
• 🎯 R is the gold standard. Behaviour almost like the pheatmap.r and verified against R reference renders.

Install

pip install pheatmap-python

Or, for a local development checkout:

git clone https://github.com/Bio-Babel/pheatmap-python.git
cd pheatmap_py
pip install -e ".[dev]"

Quick start

import numpy as np, pandas as pd
from pheatmap import pheatmap

test = pd.DataFrame(
    np.random.default_rng(1).standard_normal((20, 10)),
    index=[f"Gene{i+1}" for i in range(20)],
    columns=[f"Test{i+1}" for i in range(10)],
)

pheatmap(test)

See tutorials/pheatmap_tutorial.ipynb for a full walk-through.

Docs

pip install -e ".[docs]"
mkdocs serve