MorphoStat

MorphoStat is a modern, interactive R Shiny application for statistical morphological analysis using geometric morphometrics. It provides a comprehensive suite of tools for analyzing landmark-based morphometric data with publication-ready visualizations.

Features

Data Input

• Multiple file formats: Morphologika (.txt), TPS (.tps), NTS (.nts), FCSV (3D Slicer)
• Project save/load: Save and restore complete analysis sessions (.rds)
• Auto-detection: Automatically detects 2D/3D landmark configurations

Analysis Pipeline

• Generalized Procrustes Analysis (GPA): Removes size, position, and rotation effects
• Principal Component Analysis (PCA): Identifies major axes of shape variation
• PERMANOVA: Tests for significant shape differences between groups
• PERMDISP: Tests for homogeneity of group dispersions
• Allometry Analysis: Evaluates shape-size relationships
• Pairwise Comparisons: Multiple group comparisons with distance metrics

Visualizations

• PCA Plots: 2D colored, black & white, and 3D scatter plots
• Shape Deformations: Mean, min, and max PC shape visualization
• Procrustes Superimposition: View all specimens or individual samples
• Wireframe Diagrams: Multiple anatomical views (dorsal, sagittal, coronal)
• Statistical Plots: Centroid size boxplots, allometry regression, eigenvalue scree plots
• Outlier Detection: Identify potential outliers based on Procrustes distance

Customization

• Custom group colors: Assign specific colors to groups
• Group renaming: Rename groups for publication
• Data spread visualization: Confidence ellipses, convex hulls, density contours
• Diagram transformations: Flip and rotate shape visualizations
• Export options: PNG and SVG formats with customizable dimensions

Installation

Prerequisites

Make sure you have R (>= 4.0.0) installed. You'll also need the following R packages:

install.packages(c(
  "shiny",
  "shinydashboard", 
  "bslib",
  "shinyjs",
  "ggplot2",
  "DT",
  "colourpicker",
  "scatterplot3d",
  "rgl"
))

# Bioconductor/specialized packages
install.packages("geomorph")
install.packages("RRPP")
install.packages("Morpho")
install.packages("vegan")
install.packages("rstatix")

Running the App

1. Clone this repository:

git clone https://github.com/yourusername/morphostat.git
cd morphostat

2. Open R or RStudio and run:

shiny::runApp("App.R")

Or run directly:

shiny::runApp("path/to/morphostat")

Usage

Quick Start

1. Select input type: Choose your data format (Morphologika, TPS, NTS, or FCSV)
2. Upload data: Use the file input to upload your landmark data
3. Configure wireframe (optional): Define landmark connections
4. Run analysis: Click "Run Analysis" to perform GPA, PCA, and statistical tests
5. Explore results: Navigate through tabs to view plots and statistics
6. Export: Download results, plots, or save the entire project

Input File Formats

Morphologika Format (.txt)

[individuals]
10
[landmarks]
48
[dimensions]
3
[names]
Specimen_01
...
[labels]
Group_A
...
[rawpoints]
12.345 23.456 5.678
...

TPS Format (.tps)

LM=48
12.345 23.456
13.456 24.567
...
ID=Specimen_01

Wireframe Links

Define landmark connections as comma-separated pairs:

1,2, 2,3, 3,4, 4,5, 5,1

Screenshots

Coming soon

Statistical Methods

Method	Purpose	Package
GPA	Procrustes superimposition	geomorph
PCA	Shape variation analysis	geomorph
PERMANOVA	Group difference testing	vegan, RRPP
PERMDISP	Dispersion homogeneity	vegan
Allometry	Size-shape relationship	RRPP

Citation

If you use MorphoStat in your research, please cite:

Adasooriya, D. (2026). MorphoStat: An Interactive R Shiny Application for 
Statistical Morphological Analysis. Version 1.0.0.

Also cite the underlying R packages:

• Adams DC, Collyer ML, Kaliontzopoulou A. 2024. Geomorph: Software for geometric morphometric analyses. R package version 4.0.8.
• Oksanen J, et al. 2022. vegan: Community Ecology Package. R package version 2.6-4.

Author

Dinuka Adasooriya
Yonsei University College of Dentistry

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

Acknowledgments

• The R Shiny team for the excellent framework
• The geomorph package authors for their comprehensive morphometrics tools
• The vegan package authors for multivariate analysis tools