ColorMyCells

A Biological Approach to Cell Type Visualization

colormycells is a Python package that solves a common problem in single-cell analysis: creating colormaps where the perceptual distance between colors meaningfully represents the biological similarity between cell types.

The Problem: Color Selection in Single-Cell Visualization

Standard colormaps like tab10 or rainbow aren't great when applied to single-cell data:

• Biological meaning is lost: Default colormaps assign colors arbitrarily, with no relation to cell type similarity
• Perceptual imbalance: Some colors jump out while others blend together, drawing attention to cell types for no biological reason
• Limited palette: Most standard colormaps support 10-20 colors, but you may have hundreds of cell types

Standard Colormap	ColorMyCells

Installation

pip install colormycells

For 3D visualization support (optional):

pip install colormycells[full]

Dependencies

• numpy
• pandas
• matplotlib
• seaborn
• scikit-learn
• scipy
• colour-science

Optional Dependencies (for 3D visualization)

• pillow
• ipython

Usage

import scanpy as sc
from colormycells import get_colormap

# Load your data
adata = sc.read_h5ad("your_data.h5ad")

# Create a colormap based on cell type similarities
colors = get_colormap(adata, key="cell_type")

# Use the colormap for plotting
sc.pl.umap(adata, color="cell_type", palette=colors)

# Visualize the color space with 2D and 3D plots
colors = get_colormap(adata, key="cell_type", plot_colorspace=True)
# A 2D scatter plot will be displayed, and in Jupyter notebooks
# an interactive 3D rotating visualization will also be shown

# Create reproducible colormap with seed
colors1 = get_colormap(adata, key="cell_type", seed=123)
colors2 = get_colormap(adata, key="cell_type", seed=123)  # colors1 and colors2 will be identical

You can also pass a file path directly:

# Load directly from file
colors = get_colormap("your_data.h5ad", key="cell_type")

# Works with various file formats
colors = get_colormap("expression_matrix.csv", key="cell_type")

Parameters

• adata: AnnData object with observations/cells as rows and variables/genes as columns
• key: Key in adata.obs encoding cell type information (default: "cell_type")
• plot_colorspace: Whether to visualize the colorspace (default: False)
• include_unknown: Whether to include "Unknown" category in the colormap (default: False)
• unknown_color: Color to use for "Unknown" category if not included (default: 'w')
• deficiency: Type of color vision deficiency to simulate (options: None, "Deuteranomaly", "Protanomaly", "Tritanomaly", default: None)
• severity: Severity of color vision deficiency (0-100, default: 0)
• seed: Random seed for reproducible colormaps (default: 42, set to None for stochastic behavior)

Our Approach: Biology-Driven Color Assignment

colormycells takes a fundamentally different approach:

1. Biological similarity drives color selection: Similar cell types receive similar colors
2. Gene expression determines color: We use the average expression profile of each cell type (pseudobulk) to measure cell type similarity
3. Perceptually uniform color space: We map cell type relationships to the LUV color space, where perceptual distances are uniform
4. Intuitive visualization: The result is a colormap where visual intuition aligns with biological reality

The result is a colormap where:

• Similar cell types appear in similar colors
• Color distances reflect biological relationships
• Visualizations become more intuitive to interpret

Note

Color vision deficiency simulation is currently not fully implemented.

License

GPL-3.0 License

How to Cite

If you use ColorMyCells in your research, please cite:

Ari Benjamin. (2025). ColorMyCells: A Python package for biologically faithful colormaps for cell type visualization. (Version 0.1.0). Zenodo. https://doi.org/10.5281/zenodo.15595324

or the bibtex entry:

@software{colormycells2025,
  author       = {Benjamin, Ari},
  title        = {{ColorMyCells: A Python package for biologically
                  faithful colormaps for cell type visualization}},
  month        = jun,
  year         = 2025,
  publisher    = {Zenodo},
  version      = {0.1.0},
  doi          = {10.5281/zenodo.15595324},
  url          = {https://doi.org/10.5281/zenodo.15595324},
  note         = {Available at: https://github.com/ZadorLaboratory/colormycells}
}