Hierarchical Clustering and Circular Dendrogram for Genotype Traits

Overview

This R script performs hierarchical clustering on genotype trait data and visualizes the results using circular dendrograms. It is designed for plant breeders and researchers who want to explore patterns of variation, identify clusters of genotypes, and summarize trait values within clusters.

The workflow includes:

• Standardization of data for clustering.
• Calculation of distance matrices and hierarchical clustering using Ward's method.
• Visualization of clusters with circular dendrograms.
• Calculation of Within-Cluster Sum of Squares (WCSS) to evaluate cluster compactness.
• Calculation of R² values to assess clustering quality.
• Assignment of genotypes to clusters and summarization of cluster means for all traits.
• Exporting clustered data and summaries to CSV files.

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Features

• Handles multiple genotype traits simultaneously.
• Generates circular dendrograms colored by cluster.
• Provides cluster assignments for each genotype.
• Calculates WCSS for elbow method to determine optimal cluster number.
• Calculates R² values for clustering quality assessment.
• Summarizes cluster means for all traits.
• Exports results to CSV for further analysis.

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Input Requirements

• A CSV file with columns including:
  • Treatment or genotype identifiers
  • Numeric columns for traits
• Data can include adjusted means from previous analyses.

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Output

The script produces:

• Circular dendrogram visualizations with clusters colored.
• Cluster assignments for each genotype.
• Cluster means for each trait.
• WCSS values for cluster evaluation (elbow method).
• R² values for assessing clustering quality.
• Exported CSV files for clustered data and cluster summaries.

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Example Plot

The hierarchical clustering and circular dendrogram output is saved as HCA.JPG in the repository. See more

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Author

Ehtisham Khokhar
New Mexico State University
Email: ehtishamshakeel@gmail.com