volcano-plot-script

# Volcano Plot Script Generator A skill for generating publication-ready volcano plots from differential gene expression analysis results. ## Overview Volcano plots visualize the relationship between statistical significance (p-values) and magnitude of change (fold changes) in gene expression data. This skill generates customizable R or Python scripts for creating high-quality figures suitable for publications. ## Use Cases - Visualize RNA-seq DEG analysis results - Identify significantly upregulated and downregulated genes - Highlight genes of interest (markers, pathways) - Generate publication-quality figures for manuscripts - Compare multiple experimental conditions ## Input Requirements Required input data format: - Gene identifier (gene symbol or ENSEMBL ID) - Log2 fold change values - Adjusted or raw p-values - Optional: gene annotations, pathways ## Output - Publication-ready volcano plot (PNG/PDF/SVG) - Customizable R or Python script - Optional: labeled significant gene lists ## Usage ```python # Example: Run the volcano plot generator python scripts/main.py --input deg_results.csv --output volcano_plot.png ``` ## Parameters | Parameter | Description | Default | |-----------|-------------|---------| | `--input` | Path to DEG results CSV/TSV | required | | `--output` | Output plot file path | volcano_plot.png | | `--log2fc-col` | Column name for log2 fold change | log2FoldChange | | `--pvalue-col` | Column name for p-value | padj | | `--gene-col` | Column name for gene IDs | gene | | `--log2fc-thresh` | Log2 FC threshold for significance | 1.0 | | `--pvalue-thresh` | P-value threshold | 0.05 | | `--label-genes` | File with genes to label | None | | `--top-n` | Label top N significant genes | 10 | | `--color-up` | Color for upregulated genes | #E74C3C | | `--color-down` | Color for downregulated genes | #3498DB | | `--color-ns` | Color for non-significant genes | #95A5A6 | ## Technical Difficulty **Medium** - Requires understanding of: - DEG analysis concepts (fold change, p-values, FDR) - Data visualization principles - Matplotlib/ggplot2 plotting libraries ## Dependencies ### Python - pandas - matplotlib - seaborn - numpy ### R - ggplot2 - dplyr - ggrepel (for label positioning) ## References - [Example datasets and templates](references/) - Best practices for volcano plot visualization - Color schemes for accessibility ## Author Auto-generated skill for bioinformatics visualization. ## 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 plots | Medium | | Instruction Tampering | Standard prompt guidelines | Low | | Data Exposure | Output files saved to workspace | Low | ## Security Checklist - [ ] No hardcoded credentials or API keys - [ ] 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 (pandas, matplotlib, seaborn, numpy) ## Prerequisites ```bash # Python dependencies pip install -r requirements.txt # R dependencies (if using R) install.packages(c("ggplot2", "dplyr", "ggrepel")) ``` ## Evaluation Criteria ### Success Metrics - [ ] Successfully generates executable Python/R script - [ ] Output plot is publication-ready quality - [ ] Correctly identifies significant genes based on thresholds - [ ] Handles missing or malformed data gracefully - [ ] Color scheme is accessible (colorblind-friendly) ### Test Cases 1. **Basic DEG Visualization**: Input standard DESeq2 results → Valid volcano plot 2. **Custom Thresholds**: Adjust log2FC and p-value thresholds → Correct gene classification 3. **Gene Labeling**: Specify genes to label → Labels appear correctly 4. **Large Dataset**: Input 20,000+ genes → Performance remains acceptable 5. **Malformed Data**: Input with missing values → Graceful error handling ## Lifecycle Status - **Current Stage**: Draft - **Next Review Date**: 2026-03-06 - **Known Issues**: None - **Planned Improvements**: - Add interactive plot option (Plotly) - Support for multiple comparison groups - Integration with pathway enrichment tools