NORMA: The Network Makeup Artist

A web tool for interactive network annotation visualization and topological analysis.

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📖 Table of Contents

1. Overview
2. Key Features
3. Installation
4. Usage
5. Input Formats
6. Examples & Demo Data
7. Contact & Support
8. Publications
9. License

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📝 Overview

NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:

• Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
• Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
• Detect communities automatically when no annotations are provided
• Refine layouts for optimal group separation with common graph algorithms
• Highlight and export publication-quality figures interactively
• Compare network topology metrics across different datasets

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🚀 Key Features

• Multi-network support: Load and visualize several networks side by side.

• Annotation overlays:

  • Pie-chart nodes for multi-category annotations
  • Convex-hulls for set-overlap style visualization

• Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.

• Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.

• Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.

• Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.

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🛠 Installation

1. Install R (≥4.0)

2. Install RStudio (optional, but recommended)

3. Clone this repo

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

4. Install required packages

   # From your R console:
   install.packages(c(
     "shiny", "igraph", "visNetwork", "plotly",
     "data.table", "DT", "RColorBrewer"
   ))

5. Run the app

   # In RStudio or R console:
   shiny::runApp("path/to/NORMA")

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💻 Usage

• Online demo: Launch NORMA in your browser

• Local: Once the app is running, use the sidebar to upload:

  • Network file (edge list or adjacency)
  • Annotation file (tab-delimited with node → category)

• Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.

• Explore Layout, Annotation, and Analysis tabs for customization.

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📂 Input Formats

• Network:

  • Edge list: source<TAB>target
  • Adjacency matrix: CSV or TSV

• Annotations:

  • Plain table:

    node_id<TAB>category1,category2,...
    

• See the Help → Input File tab in the app for detailed examples.

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📊 Examples & Demo Data

Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:

• Human protein–protein interaction subnetworks
• GO term enrichment outputs for test datasets
• Synthetic networks demonstrating overlapping modules

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📬 Contact & Support

For questions, issues, or feature requests, please email:

George A. Pavlopoulos pavlopoulos@fleming.gr

Or open an issue on GitHub: https://github.com/yourusername/NORMA/issues

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📚 Publications

• NORMA: The Network Makeup Artist Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A. Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24. doi: 10.1016/j.gpb.2021.02.005 PMID: 34171457

• The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A. Bioinformatics Advances. 2022 May 13;2(1):vbac036. doi: 10.1093/bioadv/vbac036 PMID: 36699373

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📄 License

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