"""
Colorblind-Friendly Color Palettes for Scientific Visualization
This module provides carefully curated color palettes optimized for
scientific publications and accessibility.
Usage:
from color_palettes import OKABE_ITO, apply_palette
import matplotlib.pyplot as plt
apply_palette('okabe_ito')
plt.plot([1, 2, 3], [1, 4, 9])
"""
# Okabe-Ito Palette (2008)
# The most widely recommended colorblind-friendly palette
OKABE_ITO = {
'orange': '#E69F00',
'sky_blue': '#56B4E9',
'bluish_green': '#009E73',
'yellow': '#F0E442',
'blue': '#0072B2',
'vermillion': '#D55E00',
'reddish_purple': '#CC79A7',
'black': '#000000'
}
OKABE_ITO_LIST = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
'#0072B2', '#D55E00', '#CC79A7', '#000000']
# Wong Palette (Nature Methods)
WONG = ['#000000', '#E69F00', '#56B4E9', '#009E73',
'#F0E442', '#0072B2', '#D55E00', '#CC79A7']
# Paul Tol Palettes (https://personal.sron.nl/~pault/)
TOL_BRIGHT = ['#4477AA', '#EE6677', '#228833', '#CCBB44',
'#66CCEE', '#AA3377', '#BBBBBB']
TOL_MUTED = ['#332288', '#88CCEE', '#44AA99', '#117733',
'#999933', '#DDCC77', '#CC6677', '#882255', '#AA4499']
TOL_LIGHT = ['#77AADD', '#EE8866', '#EEDD88', '#FFAABB',
'#99DDFF', '#44BB99', '#BBCC33', '#AAAA00', '#DDDDDD']
TOL_HIGH_CONTRAST = ['#004488', '#DDAA33', '#BB5566']
# Sequential colormaps (for continuous data)
SEQUENTIAL_COLORMAPS = [
'viridis', # Default, perceptually uniform
'plasma', # Perceptually uniform
'inferno', # Perceptually uniform
'magma', # Perceptually uniform
'cividis', # Optimized for colorblind viewers
'YlOrRd', # Yellow-Orange-Red
'YlGnBu', # Yellow-Green-Blue
'Blues', # Single hue
'Greens', # Single hue
'Purples', # Single hue
]
# Diverging colormaps (for data with meaningful center)
DIVERGING_COLORMAPS_SAFE = [
'RdYlBu', # Red-Yellow-Blue (reversed is common)
'RdBu', # Red-Blue
'PuOr', # Purple-Orange (excellent for colorblind)
'BrBG', # Brown-Blue-Green (good for colorblind)
'PRGn', # Purple-Green (use with caution)
'PiYG', # Pink-Yellow-Green (use with caution)
]
# Diverging colormaps to AVOID (red-green combinations)
DIVERGING_COLORMAPS_AVOID = [
'RdGn', # Red-Green (problematic!)
'RdYlGn', # Red-Yellow-Green (problematic!)
]
# Fluorophore colors (traditional - use with caution)
FLUOROPHORES_TRADITIONAL = {
'DAPI': '#0000FF', # Blue
'GFP': '#00FF00', # Green (problematic for colorblind)
'RFP': '#FF0000', # Red
'Cy5': '#FF00FF', # Magenta
'YFP': '#FFFF00', # Yellow
}
# Fluorophore colors (colorblind-friendly alternatives)
FLUOROPHORES_ACCESSIBLE = {
'Channel1': '#0072B2', # Blue
'Channel2': '#E69F00', # Orange (instead of green)
'Channel3': '#D55E00', # Vermillion (instead of red)
'Channel4': '#CC79A7', # Magenta
'Channel5': '#F0E442', # Yellow
}
# Genomics/Bioinformatics
DNA_BASES = {
'A': '#00CC00', # Green
'C': '#0000CC', # Blue
'G': '#FFB300', # Orange
'T': '#CC0000', # Red
}
DNA_BASES_ACCESSIBLE = {
'A': '#009E73', # Bluish Green
'C': '#0072B2', # Blue
'G': '#E69F00', # Orange
'T': '#D55E00', # Vermillion
}
def apply_palette(palette_name='okabe_ito'):
"""
Apply a color palette to matplotlib's default color cycle.
Parameters
----------
palette_name : str
Name of the palette to apply. Options:
'okabe_ito', 'wong', 'tol_bright', 'tol_muted',
'tol_light', 'tol_high_contrast'
Returns
-------
list
List of colors in the palette
Examples
--------
>>> apply_palette('okabe_ito')
>>> plt.plot([1, 2, 3], [1, 4, 9]) # Uses Okabe-Ito colors
"""
try:
import matplotlib.pyplot as plt
except ImportError:
print("matplotlib not installed")
return None
palettes = {
'okabe_ito': OKABE_ITO_LIST,
'wong': WONG,
'tol_bright': TOL_BRIGHT,
'tol_muted': TOL_MUTED,
'tol_light': TOL_LIGHT,
'tol_high_contrast': TOL_HIGH_CONTRAST,
}
if palette_name not in palettes:
available = ', '.join(palettes.keys())
raise ValueError(f"Palette '{palette_name}' not found. Available: {available}")
colors = palettes[palette_name]
plt.rcParams['axes.prop_cycle'] = plt.cycler(color=colors)
return colors
def get_palette(palette_name='okabe_ito'):
"""
Get a color palette as a list.
Parameters
----------
palette_name : str
Name of the palette
Returns
-------
list
List of color hex codes
"""
palettes = {
'okabe_ito': OKABE_ITO_LIST,
'wong': WONG,
'tol_bright': TOL_BRIGHT,
'tol_muted': TOL_MUTED,
'tol_light': TOL_LIGHT,
'tol_high_contrast': TOL_HIGH_CONTRAST,
}
if palette_name not in palettes:
available = ', '.join(palettes.keys())
raise ValueError(f"Palette '{palette_name}' not found. Available: {available}")
return palettes[palette_name]
if __name__ == "__main__":
print("Available colorblind-friendly palettes:")
print(f" - Okabe-Ito: {len(OKABE_ITO_LIST)} colors")
print(f" - Wong: {len(WONG)} colors")
print(f" - Tol Bright: {len(TOL_BRIGHT)} colors")
print(f" - Tol Muted: {len(TOL_MUTED)} colors")
print(f" - Tol Light: {len(TOL_LIGHT)} colors")
print(f" - Tol High Contrast: {len(TOL_HIGH_CONTRAST)} colors")
print("\nOkabe-Ito palette (most recommended):")
for name, color in OKABE_ITO.items():
print(f" {name:15s}: {color}")