Reproducible Color Characterization of Digital Images for Biological Studies

Provides a standardized and reproducible framework for characterizing and classifying discrete color classes from digital images of biological organisms. The package automatically determines the presence or absence of 10 human-visible color categories (black, blue, brown, green, grey, orange, purple, red, white, yellow) using a biologically-inspired Color Look-Up Table (CLUT) that partitions HSV color space. Supports both fully automated and semi-automated (interactive) workflows with complete provenance tracking for reproducibility. Pre-processes images using the 'recolorize' package (Weller et al. 2024 ) for spatial-color binning, and integrates with 'pavo' (Maia et al. 2019 ) for color pattern geometry statistics. Designed for high-throughput analysis and seamless integration with downstream evolutionary analyses.

charisma

charisma provides a standardized, reproducible framework for characterizing discrete color classes in digital images of biological organisms.

Overview

charisma automatically classifies colors in images into 10 human-visible categories using a biologically-inspired Color Look-Up Table (CLUT):

Black · Blue · Brown · Green · Grey · Orange · Purple · Red · White · Yellow

Key Features

✨ Fully Reproducible: Complete provenance tracking of all operations

🎨 10 Color Classes: Biologically-relevant discrete color categories

🔧 Flexible Workflows: From fully automated to completely manual

📊 Evolutionary Integration: Seamless compatibility with geiger, phytools, pavo

⚡ High-Throughput: Designed for analyzing large image datasets

🔍 Validated CLUT: Non-overlapping HSV color space partitions

Installation

System Dependencies

charisma depends on spatial R packages that require system-level libraries. Install these first:

macOS (via Homebrew):

brew install udunits gdal proj geos

Ubuntu/Debian:

sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev

Fedora/RedHat:

sudo dnf install udunits2-devel gdal-devel geos-devel proj-devel

Development Version (GitHub)

# install.packages("remotes")
remotes::install_github("shawntz/charisma")

Stable Version (CRAN)

install.packages("charisma")  # Coming soon!

Quick Start

library(charisma)

# Load example image
img <- system.file(
  "extdata", 
  "Tangara_fastuosa_LACM60421.png",
  package = "charisma"
)

# Basic analysis
result <- charisma(img, threshold = 0.05)

# Visualize
plot(result)

# Interactive mode with manual curation
result_interactive <- charisma(
  img,
  interactive = TRUE,
  threshold = 0.0
)

# Save outputs
result_saved <- charisma(
  img,
  threshold = 0.05,
  logdir = file.path(tempdir(), "charisma_outputs")
)

How It Works

The charisma pipeline consists of three stages:

1. Image Preprocessing

Uses recolorize to perform spatial-color binning, removing noisy pixels and creating a smoothed representation of dominant colors.

2. Color Classification

Converts RGB cluster centers to HSV and matches against the CLUT using color2label():

color2label(c(255, 0, 0))    # "red"
color2label(c(0, 0, 255))    # "blue"
color2label(c(255, 255, 0))  # "yellow"

3. Optional Manual Curation

In interactive mode:

• Merge color clusters (e.g., c(2,3))
• Replace pixels between clusters
• Full operation history maintained for reproducibility

The charisma object contains:

• Color classifications: Discrete labels for each cluster
• Proportions: Pixel counts and proportions per color
• Operation history: Complete log of merges and replacements
• Pavo statistics: Color pattern geometry metrics (optional)

Example Workflows

Advanced Features

Re-analyze Saved Objects

# Load previous analysis
obj <- system.file("extdata", "Tangara_fastuosa.RDS", package = "charisma")
obj <- readRDS(obj)

# Apply different threshold
result2 <- charisma2(
  obj, 
  new.threshold = 0.10
)

# Revert to specific state
result3 <- charisma2(
  obj, 
  which.state = "merge", 
  state.index = 2
)

Custom Color Look-Up Tables

# Create custom CLUT
my_clut <- charisma::clut  # Start with default
# ... modify HSV ranges ...

# Validate completeness
validate(clut = my_clut)

# Use in analysis
result <- charisma(img, clut = my_clut)

Evolutionary Analyses

# Batch process images
results <- lapply(image_paths, function(img) {
  charisma(img, threshold = 0.05)
})

# Extract color presence/absence
color_matrix <- do.call(rbind, lapply(results, summarize))

# Phylogenetic analyses with geiger
library(geiger)

fit_er <- fitDiscrete(
  phylogeny, 
  color_matrix[, "blue"], 
  model = "ER"
)

fit_ard <- fitDiscrete(
  phylogeny, 
  color_matrix[, "blue"], 
  model = "ARD"
)

Citation

If you use charisma in your research, please cite:

Schwartz, S.T., Tsai, W.L.E., Karan, E.A., Juhn, M.S., Shultz, A.J., McCormack, J.E., Smith, T.B., and Alfaro, M.E. (2025). charisma: An R package to perform reproducible color characterization of digital images for biological studies. (In Review).

Getting Help

📖 Documentation

🐛 Report Issues

📧 Email: [email protected]

Acknowledgments

charisma integrates with:

• recolorize (Weller et al. 2024) - Image preprocessing
• pavo (Maia et al. 2019) - Color pattern geometry

License

MIT © 2025 Shawn T. Schwartz