Volcano Plot Script

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expressi...

Security Scan

The skill is internally consistent with its stated purpose (generating volcano-plot code/figures), requests no credentials or extra privileges, and contains only a local Python script and documentation — minor documentation and robustness issues exist but nothing that indicates covert or unrelated behavior.

Purpose & Capability

Name/description match the included artifacts: SKILL.md documents a volcano-plot generator and the package includes a Python entrypoint (scripts/main.py) plus example data and references. No unrelated credentials, binaries, or cloud APIs are requested.

Instruction Scope

Runtime instructions ask the agent to validate inputs and run the packaged Python script only. The SKILL.md does not instruct reading unrelated system files or contacting external endpoints. Notes: the README claims additional packaged assets (e.g., assets/example_volcano.R) that are not present in the manifest — this is a documentation inconsistency but not a direct security issue. There are small code robustness issues (e.g., selection of p-value column when computing top-N genes can fail if no matching column is found), which could cause crashes but not exfiltration.

Install Mechanism

No install spec is provided (instruction-only with bundled script), so nothing will be downloaded or installed automatically. dependencies are typical Python plotting/data libs (requirements.txt) and are proportionate to the task.

Credentials

The skill requires no environment variables, no credentials, and no config paths. All data access is via user-supplied input file paths. This is proportionate to the stated purpose.

Persistence & Privilege

always:false and no mechanisms to alter other skills or system-wide settings. The skill is user-invocable and can be invoked autonomously per platform defaults, which is expected for skills; it does not request persistent privileges.

Assessment

This skill appears to do what it says: it contains a local Python script to produce volcano plots and asks for only user-provided input files. Before running: 1) inspect scripts/main.py locally (the repo snippet shows no network calls or obfuscated code), 2) run python -m py_compile scripts/main.py and test on a non-sensitive sample, 3) use a virtualenv to install the requirements, 4) be aware of small bugs (the script's top-N gene selection can error if no p-value-like column is detected) and a documentation mismatch (SKILL.md references an assets/ item that isn't in the manifest). If you need higher assurance, ask the author for the missing asset list or a full code review; otherwise this is safe to run on non-sensitive DEG files.

Volcano Plot Script Generator

A skill for generating publication-ready volcano plots from differential gene expression analysis results.

When to Use

• Use this skill when the task is to Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.
• Use this skill for data analysis tasks that require explicit assumptions, bounded scope, and a reproducible output format.
• Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Key Features

• Scope-focused workflow aligned to: Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.
• Packaged executable path(s): scripts/main.py.
• Reference material available in references/ for task-specific guidance.
• Reusable packaged asset(s), including assets/example_volcano.R.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Data Analytics/volcano-plot-script"
python -m py_compile scripts/main.py
python scripts/main.py --help

Example run plan:

1. Confirm the user input, output path, and any required config values.
2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
3. Run python scripts/main.py with the validated inputs.
4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related details.

• Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
• Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
• Primary implementation surface: scripts/main.py.
• Reference guidance: references/ contains supporting rules, prompts, or checklists.
• Packaged assets: reusable files are available under assets/.
• Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
• Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py --input "Audit validation sample with explicit symptoms, history, assessment, and next-step plan."

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

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

# 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

Python

• pandas
• matplotlib
• seaborn
• numpy

R

• ggplot2
• dplyr
• ggrepel (for label positioning)

References

• Example datasets and templates
• 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

# 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

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of volcano-plot-script and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

volcano-plot-script only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.