facs-gating-viz-style

# FACS Gating Viz Style Beautify flow cytometry gating plots for publication. ## Parameters | Parameter | Type | Default | Required | Description | |-----------|------|---------|----------|-------------| | `--data`, `-d` | string | - | Yes | FCS file path | | `--style`, `-s` | string | contour | No | Plot style (contour, density, dot) | ## Usage ```bash python scripts/main.py --data fcs_file.fcs --style contour ``` ## Features - Contour plots - Density visualization - Publication-ready styling ## Risk Assessment | Risk Indicator | Assessment | Level | |----------------|------------|-------| | Code Execution | Python/R scripts executed locally | Medium | | Network Access | No external API calls | Low | | File System Access | Read input files, write output files | Medium | | Instruction Tampering | Standard prompt guidelines | Low | | Data Exposure | Output files saved to workspace | Low | ## Security Checklist - [ ] No hardcoded credentials or API keys - [ ] No unauthorized file system access (../) - [ ] Output does not expose sensitive information - [ ] Prompt injection protections in place - [ ] Input file paths validated (no ../ traversal) - [ ] Output directory restricted to workspace - [ ] Script execution in sandboxed environment - [ ] Error messages sanitized (no stack traces exposed) - [ ] Dependencies audited ## Prerequisites No additional Python packages required. ## Evaluation Criteria ### Success Metrics - [ ] Successfully executes main functionality - [ ] Output meets quality standards - [ ] Handles edge cases gracefully - [ ] Performance is acceptable ### Test Cases 1. **Basic Functionality**: Standard input → Expected output 2. **Edge Case**: Invalid input → Graceful error handling 3. **Performance**: Large dataset → Acceptable processing time ## Lifecycle Status - **Current Stage**: Draft - **Next Review Date**: 2026-03-06 - **Known Issues**: None - **Planned Improvements**: - Performance optimization - Additional feature support