ReactomeGSA-Viz

ReactomeGSA-Viz is a specialized Python tool designed to transform raw JSON results from the ReactomeGSA service into professional, interactive HTML reports.

This package simplifies the interpretation of Gene Set Analysis (GSA) by providing clear summaries for individual datasets and powerful comparative visualizations across multiple datasets.

Key Features

• Automated Summaries: Generates concise overview reports for every dataset analyzed.
• Comparative Analysis: Built-in logic to compare enrichment results across different experimental conditions or datasets.
• Interactive Bubble Plots: Visualizes pathway enrichment (p-values, fold changes, and pathway size) using interactive charts.
• Detailed Data Tables: Searchable and sortable tables for deep dives into specific pathway results.
• Self-Contained: All assets are embedded directly into a single HTML file for easy sharing.

Requirements

The package requires Python 3.6 or higher.

Installation

Install the package via pip:

pip install reactomegsa-viz

Usage

Integrate the report generator into your own pipelines:

import json
import gzip
from reactomegsa_viz import HtmlReportGenerator

# 1. Load your ReactomeGSA results
with gzip.open("tests/results.json.gz", "rt") as f:
    data = json.load(f)

# 2. Generate the interactive report
HtmlReportGenerator.create_report(
    json_dict=data, 
    out_html="test_package.html", 
    r_script_token="R_SCRIPT_TOKEN",
    reactome_url="https://gsa.reactome.org"
)