PyBuenColors

A pythonic port of the BuenColors R package for convenient scientific color palettes and matplotlib styles.

Color palettes are a direct port from the R package, with many based on the wesanderson R package.

Installation

pip install buencolors

Quick Start

Using the Pretty Plot Style

The easiest way to improve your matplotlib plots is to use the included pretty-plot style:

import matplotlib.pyplot as plt
import numpy as np

# Apply the pretty-plot style
plt.style.use('pretty-plot')

# Create a beautiful plot
x = np.linspace(0, 10, 100)
plt.plot(x, np.sin(x), label='sin(x)')
plt.plot(x, np.cos(x), label='cos(x)')
plt.xlabel('x')
plt.ylabel('y')
plt.legend()
plt.show()

Before (default):

After (pretty-plot):

Using Color Palettes

BuenColors automatically registers all palettes as matplotlib colormaps:

import buencolors as bc
import matplotlib.pyplot as plt
import numpy as np

# List available palettes
bc.list_palettes()

# Palettes are available directly as colormaps
plt.style.use('pretty-plot')
data = np.random.randn(100, 100)
plt.imshow(data, cmap='Zissou')
plt.colorbar()
plt.show()

# Or use get_palette() to extract individual colors
colors = bc.get_palette('Zissou')
for i, color in enumerate(colors):
    plt.plot([0, 1], [i, i], color=color, linewidth=10)
plt.show()

Features

Helper Functions

BuenColors provides several utility functions to make your plots publication-ready:

Eject Legend

Move legends outside the plot area to avoid obscuring data:

import matplotlib as plt
import buencolors as bc

# Your plot code here
plt.plot(x, y1, label='Dataset 1')
plt.plot(x, y2, label='Dataset 2')

# Eject the legend to the right
bc.eject_legend()

Rotate X-Tick Labels

Automatically rotate discrete x-tick labels for better readability:

bc.rotate_discrete_xticks()

Grab Legend

Extract a legend to a separate figure for independent saving or publication:

# Create a plot with legend
plt.plot(x, y1, label='Dataset 1')
plt.plot(x, y2, label='Dataset 2')
plt.legend()

# Extract legend to separate figure (removes from original by default)
legend_fig = bc.grab_legend()
legend_fig.savefig('legend.pdf', bbox_inches='tight')
plt.savefig('plot.pdf')  # Plot saved without legend

# Or keep legend on original plot
legend_fig = bc.grab_legend(remove=False)
legend_fig.savefig('legend_copy.pdf', bbox_inches='tight')
plt.show()  # Original plot still has legend

Color by Density

Color scatter plot points by their density:

x = np.random.randn(1000)
y = np.random.randn(1000)
density = bc.get_density(x, y)

plt.scatter(x, y, c=density, cmap='viridis', s=5)
plt.colorbar(label='Density')

Shuffle Plot Order

Randomize the order of plot elements to avoid overplotting bias:

x_shuffled, y_shuffled, colors_shuffled = bc.shuffle(x, y, colors)
plt.scatter(x_shuffled, y_shuffled, c=colors_shuffled)

Number to Color

Map numerical values to colors from a palette:

values = [1, 2, 3, 4, 5]
colors = bc.number_to_color(values, palette='Zissou')

Single-Cell Analysis

BuenColors provides specialized functions for single-cell analysis visualization, designed to work seamlessly with Scanpy and AnnData objects.

Installation for Single-Cell Features

To use the single-cell features, install with scanpy and anndata:

pip install buencolors scanpy anndata

Clean UMAP Visualization

The clean_umap() function creates publication-ready UMAP plots with minimal decorations:

import scanpy as sc
import buencolors as bc
import matplotlib.pyplot as plt

# Load example dataset
adata = sc.datasets.pbmc3k_processed()

# Create a clean UMAP colored by cell type
with plt.style.context('pretty-plot'):
    bc.clean_umap(adata, color='louvain', palette='lawhoops')

Features of clean_umap():

• Minimal decorations: No borders, ticks, or frame
• Custom L-shaped axis indicators: Small arrows showing UMAP dimensions
• Auto-ejected legend: Automatically positioned to the right to avoid obscuring data
• Shuffled cells: Randomizes plotting order to avoid non-random ordering artifacts
• scVelo-style outlines: Concentric black/white rings around points

scVelo-Style Outlines

Add concentric outline rings to UMAP points via the outline_style parameter:

# Outline every cell
bc.clean_umap(adata, color='louvain', outline_style=True)

# Highlight one group — all other cells are dimmed
bc.clean_umap(adata, color='louvain', outline_style='CD4 T cells')

# Highlight multiple groups
bc.clean_umap(adata, color='louvain', outline_style=['NK cells', 'CD8 T cells'])

# Adjust ring widths: (black_bg_fraction, white_gap_fraction)
bc.clean_umap(adata, color='louvain', outline_style=True, outline_width=(0.5, 0.1))

outline_style accepts:

Examples

For detailed examples and interactive notebooks, see the documentation or the docs/examples directory.

Available Palettes

License

This project is licensed under the MIT License.

Credits

• Original BuenColors R package
• Wes Anderson palettes inspired by wesanderson