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biopalette

Image-Inspired Color Palettes for Biomedical Visualization

📚 Documentation • 💬 Issues • 🎨 Tessera • 🧪 Palette Lab

Languages: English | 简体中文

Overview

biopalette is an R package providing image-inspired color palettes for biomedical visualization.

Every palette begins with a real image — a film still, a scientific figure, an artwork — and is translated into a reproducible color system. The source is always documented: where the colors came from, what they mean, and when to use them.

library(biopalette)

get_palette("babel", n = 5)
get_palette("three_body")
get_palette("walter_white", type = "diverging")

preview_palette("gene_red")
palette_gallery()

# Discrete and continuous ggplot2 scales
scale_color_biopalette("three_body")
scale_fill_biopalette_gradient("mitonuclear_blue")

Installation

# Development version
devtools::install_github("evanbio/biopalette")

Palettes

Each name links to its source page — source image, color table, and intended use.

Name	Type	Colors	Recommended use	Source
`gene_red`	Qualitative	2	Emphasized signal versus a dark or neutral counterpart	Better Call Saul — Gene Takavic’s red coat
`walter_white`	Diverging	5	Signed continuous values around a neutral center	Breaking Bad — desert to sky
`walter_white2`	Qualitative	5	Up to five unordered groups	Breaking Bad — muted earth tones
`walter_white3`	Diverging	5	Warm-register signed continuous values	Breaking Bad — warm counterpart
`babel`	Qualitative	21	Many categorical groups with labels or position support	Pan-cancer myeloid atlas (Cell, 2021) — 22 cell types, 21 voices
`bcell_atlas`	Qualitative	7	Four-to-seven categorical groups with direct labels or position support	Pan-cancer B-cell atlas (Cell, 2024) — graphical abstract
`bcell_atlas2`	Diverging	5	Signed change between warm and cool biological states	Pan-cancer B-cell atlas (Cell, 2024) — IgA to IgG shift
`bcell_clusters`	Qualitative	20	Many labeled categorical groups with position or faceting support	Pan-cancer B-cell atlas (Cell, 2024) — Figure 1B cluster legend
`three_body`	Qualitative	3	Three groups, lineages, or trajectories	Pan-cancer myeloid atlas (Cell, 2021) — three DC trajectories
`mitonuclear_blue`	Sequential	6	Cool low-to-high continuous values	Mito-nuclear communication in aging (TIBS, 2022) — young blue
`mitonuclear_orange`	Sequential	6	Warm low-to-high continuous values	Mito-nuclear communication in aging (TIBS, 2022) — aged orange
`heat_light`	Qualitative	2	Paired categories or experimental conditions	Bond ampholysis (Nature, 2024) — heat and light turn radicals into an ion pair
`tam_pastel`	Qualitative	6	Four-to-six categorical groups on light backgrounds	Pan-cancer myeloid atlas (Cell, 2021) — soft TAM states
`cancer_mosaic`	Qualitative	15	Ten-to-fifteen categories with labels or position support	Pan-cancer myeloid atlas (Cell, 2021) — cancer-type mosaic
`lactate_steps`	Qualitative	5	Five discrete workflow stages or study groups	Lactate metabolism and immunotherapy (JECCR, 2024) — five study stages

Name

Type

Colors

Recommended use

Source

gene_red

Qualitative

Emphasized signal versus a dark or neutral counterpart

Better Call Saul — Gene Takavic’s red coat

walter_white

Diverging

Signed continuous values around a neutral center

Breaking Bad — desert to sky

walter_white2

Qualitative

Up to five unordered groups

Breaking Bad — muted earth tones

walter_white3

Diverging

Warm-register signed continuous values

Breaking Bad — warm counterpart

babel

Qualitative

Many categorical groups with labels or position support

Pan-cancer myeloid atlas (Cell, 2021) — 22 cell types, 21 voices

bcell_atlas

Qualitative

Four-to-seven categorical groups with direct labels or position support

Pan-cancer B-cell atlas (Cell, 2024) — graphical abstract

bcell_atlas2

Diverging

Signed change between warm and cool biological states

Pan-cancer B-cell atlas (Cell, 2024) — IgA to IgG shift

bcell_clusters

Qualitative

Many labeled categorical groups with position or faceting support

Pan-cancer B-cell atlas (Cell, 2024) — Figure 1B cluster legend

three_body

Qualitative

Three groups, lineages, or trajectories

Pan-cancer myeloid atlas (Cell, 2021) — three DC trajectories

mitonuclear_blue

Sequential

Cool low-to-high continuous values

Mito-nuclear communication in aging (TIBS, 2022) — young blue

mitonuclear_orange

Sequential

Warm low-to-high continuous values

Mito-nuclear communication in aging (TIBS, 2022) — aged orange

heat_light

Qualitative

Paired categories or experimental conditions

Bond ampholysis (Nature, 2024) — heat and light turn radicals into an ion pair

tam_pastel

Qualitative

Four-to-six categorical groups on light backgrounds

Pan-cancer myeloid atlas (Cell, 2021) — soft TAM states

cancer_mosaic

Qualitative

Ten-to-fifteen categories with labels or position support

Pan-cancer myeloid atlas (Cell, 2021) — cancer-type mosaic

lactate_steps

Qualitative

Five discrete workflow stages or study groups

Lactate metabolism and immunotherapy (JECCR, 2024) — five study stages

From Palette to Figure

biopalette provides the R interface for retrieving and applying image-inspired palettes. Tessera documents their source images, example data, and reproducible R figure recipes. Palette Lab keeps the data and graphical structure fixed while comparing palette behavior across 17 graphical contexts. The overview and panels below are rendered from Palette Lab; Tessera links provide the corresponding figure recipes and data context.

The same palette can behave differently as points, lines, filled regions, heatmap cells, set overlaps, survival curves, or genome-wide signals. These examples show the kinds of figures available through the Tessera recipes and the corresponding palette comparisons in Palette Lab.

Function Reference

License

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.

_{Grouped scatter · babel}	_{Multi-line comparison · walter_white2}
_{Correlation heatmap · walter_white}	_{Eye color composition by hair color · lactate_steps}
_{Kaplan–Meier survival curve · heat_light}	_{Manhattan plot · cancer_mosaic}