A specialized tool for generating high-quality R or Python volcano plots from differential gene expression analysis data.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install volcano-plot-script
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install volcano-plot-script using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is Volcano Plot Script Generator?
The Volcano Plot Script Generator is a powerful addition to Openclaw Skills designed for bioinformaticians and data scientists. It automates the creation of publication-ready figures that visualize the relationship between statistical significance (p-values) and the magnitude of change (fold change) in genomic datasets. By synthesizing raw Differential Gene Expression (DEG) results into polished visualizations, this skill allows researchers to quickly identify biological trends and highlight significant gene markers.
This skill provides a bridge between raw data and scientific communication by generating fully customizable scripts in either R or Python. It is built to support the rigorous standards of academic publishing, ensuring that users can produce high-resolution, reproducible figures directly from their analysis pipelines while maintaining full control over aesthetic and statistical parameters.
Volcano Plot Script Generator Use Cases
- Visualizing RNA-seq DEG analysis results to identify overall biological trends and data distribution.
- Identifying significantly upregulated and downregulated genes using custom p-value and fold-change thresholds.
- Highlighting specific genes of interest, such as biomarkers or pathway members, for inclusion in manuscripts.
- Generating high-resolution PNG, PDF, or SVG figures suitable for peer-reviewed academic publications.
- Comparing multiple experimental conditions across large-scale genomic studies for comparative transcriptomics.
How Volcano Plot Script Generator Works
- The user provides a CSV or TSV file containing differential gene expression analysis results, including gene identifiers, log2 fold change, and p-values.
- The skill analyzes the input structure and applies user-defined parameters such as significance thresholds (e.g., p < 0.05) and column mapping.
- Based on the configuration, the skill generates or executes a custom R script using ggplot2 or a Python script using Matplotlib and Seaborn.
- The script classifies every gene as upregulated, downregulated, or non-significant based on the provided thresholds.
- A final high-quality volcano plot is rendered, featuring labeled genes and customized color schemes, and saved to the local workspace for immediate use.
Volcano Plot Script Generator Setup
To use this feature within Openclaw Skills, ensure your environment has the necessary plotting libraries installed.
# For Python-based visualization
pip install pandas matplotlib seaborn numpy
# For R-based visualization (run within an R environment)
install.packages(c("ggplot2", "dplyr", "ggrepel"))
Once dependencies are met, you can trigger the script generator by passing your DEG results file to the CLI utility.
Volcano Plot Script Generator Data Schema & Taxonomy
The skill expects a structured table as input and produces visual and script-based outputs as detailed below:
| Component | Format | Description |
|---|---|---|
| Input Data | CSV/TSV | Tables containing gene IDs, fold change, and p-values. |
| Script Output | .R / .py | Executable code for reproducibility and manual edits. |
| Plot Output | PNG/PDF/SVG | Publication-quality image files. |
Key Metadata Fields:
gene: Unique identifier (Gene Symbol or ENSEMBL ID).log2FoldChange: The log2 transformed ratio of expression between conditions.padj/pvalue: The statistical significance value used for the Y-axis.
Volcano Plot Script Generator Advanced Features
- Support for colorblind-friendly and custom color palettes for upregulated, downregulated, and non-significant genes.
- Automated intelligent labeling of the Top N most significant genes using ggrepel to prevent overlapping text.
- Flexible column mapping to ensure compatibility with outputs from various DEG tools such as DESeq2, EdgeR, or Limma.
- Standalone script generation allowing for complete reproducibility and manual post-processing in local IDEs.
- Seamless integration into multi-agent bioinformatics research workflows powered by Openclaw Skills.
SKILL.md
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