facs-gating-viz-style

What This Skill Does

The facs-gating-viz-style skill is a specialized utility designed for researchers and scientists working in the field of flow cytometry. It automates the transformation of raw Flow Cytometry Standard (FCS) data into publication-quality visualizations. By processing raw gating data, the skill applies aesthetic enhancements such as contour mapping, density smoothing, or dot-plot refinements, ensuring that complex biological data is presented clearly and professionally for manuscripts or presentations. This removes the manual burden of tweaking plotting parameters in traditional software.

Installation

To integrate this skill into your environment, utilize the OpenClaw CLI tool. Open your terminal and execute the following command: clawhub install openclaw/skills/skills/aipoch-ai/facs-gating-viz-style Ensure that you have the appropriate permissions to write to your workspace directory, as the skill generates image output files based on your input FCS files.

Use Cases

This skill is ideal for laboratory environments where high-throughput gating is required. It is particularly useful for generating standardized figures for comparative analysis across different patient cohorts. Researchers can use it to maintain visual consistency across all figures in a document, ensuring that style choices like contour levels remain uniform, thereby increasing the reproducibility and credibility of the findings.

Example Prompts

1. "OpenClaw, please beautify the gating plot for my sample file_001.fcs using the contour style for the upcoming conference poster."
2. "Generate a publication-ready density plot based on my flow data located at ./data/experiment_alpha.fcs."
3. "Can you process the cytometry file sample_002.fcs and apply the default visualization style so I can review the gate boundaries?"

Tips & Limitations

• Input Validation: Always ensure your FCS file is not corrupted before running the skill. The tool performs internal validation, but pre-checking files saves processing time.
• Performance: While designed for efficiency, very large FCS files (exceeding several gigabytes) may experience longer processing times. It is recommended to use subsetted files if you are working with extremely high-parameter datasets.
• Security: As this skill executes local scripts, always verify the source of your FCS files. The skill adheres to sandbox protocols, but users should be mindful of the files they process within the local environment. It currently does not support interactive real-time gating adjustments; it is intended for the visualization of pre-defined gate structures.