Spearman Correlation Heatmap Generator

Interactive python script which generates a heatmap of Spearman correlation coefficients with significant p-values annotated, from any Excel sheet.

📦 Usage

```bash python spearman_heatmap.py "data.xlsx" "Sheet1" --title "Correlation Heatmap" --output "heatmap.png"

Spearman Correlation Heatmap Tool

This script generates a Spearman correlation matrix and a corresponding heatmap from data in an Excel file. It annotates significant correlations and can export results as CSV.

Requirements

• Python 3.x
• Required Python packages:
  • pandas
  • numpy
  • matplotlib
  • seaborn
  • scipy
  • openpyxl (for reading .xlsx files)

Install them (if not already installed) with: bash pip install pandas numpy matplotlib seaborn scipy openpyxl

How to Use

1. Prepare your Excel file

   • Ensure your data is in a single sheet.
   • The sheet should contain only numeric columns you wish to analyze.

2. Run the script from the command line: bash python spearman_heatmap.py <EXCEL_FILE_PATH> <SHEET_NAME> [--title TITLE] [--output OUTPUT_FILE] [--export_csv]

Arguments

• <EXCEL_FILE_PATH>: Path to your Excel file (e.g., data.xlsx)
• <SHEET_NAME>: Name of the sheet to analyze (e.g., Sheet1)
• --title TITLE: (Optional) Custom title for the heatmap.
• --output OUTPUT_FILE: (Optional) Output filename for the heatmap image (default: spearman_correlation_heatmap.png)
• --export_csv: (Optional) If provided, exports the correlation and p-value matrices as CSV files.

Example

bash python spearman_heatmap.py data.xlsx Sheet1 --title "My Correlation Heatmap" --output my_heatmap.png --export_csv

This will: - Read data.xlsx from the sheet named Sheet1 - Create a heatmap image saved as my_heatmap.png with the custom title - Export correlation_matrix.csv and pvalue_matrix.csv for further analysis

Output

• A heatmap image file with annotated Spearman correlation coefficients (and significance indicated by *)
• Optionally, two CSV files with the raw correlation and p-value matrices.

Tip:
If you see errors about missing columns or empty data, check your Excel sheet to ensure it contains numeric data and no missing values in the columns you wish to analyze.

📄 Citation If you use this tool in your research, please cite:

Rajpurohit, K., & Vibash Kalyaan, V. L. (2025). Spearman Correlation Heatmap Generator (Version 1.0.1) [Computer software]. https://doi.org/10.5281/zenodo.15797835

BibTeX:

bibtex Copy Edit @software{rajpurohit2025heatmap, author = {Kailash Rajpurohit}, title = {{Spearman Correlation Heatmap Generator}}, version = {v1.0.1}, year = 2025, publisher = {Zenodo}, doi = {10.5281/zenodo.15797835}, url = {https://doi.org/10.5281/zenodo.15797835} } 🔍 License This project is licensed under the MIT License.