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

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

Basic Functionality: Standard input → Expected output
Edge Case: Invalid input → Graceful error handling
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