cellcellcommunicationplots

Generate publication-ready network, heatmap, and circos plots from CellCellCommunication cccfile data.

22|4|Updated May 18, 2021

Search Tags:#visualization #ligand-receptor #cell-cell communication #heatmap #network-plot #circos #subset-filter

Ready to run

npx skills add https://github.com/pwwang/immunopipe --skill cellcellcommunicationplots

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cellcellcommunicationplots
Source: https://github.com/pwwang/immunopipe/tree/main/skills/cellcellcommunicationplots
Command: npx skills add https://github.com/pwwang/immunopipe --skill cellcellcommunicationplots

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Visualize and interpret cell-cell communication inference results by turning ligand-receptor interaction data into publication-ready visuals.

Core Features & Use Cases

Multiple plot types (network, heatmap, circos, dot, box, violin, ridge) to cover global and detailed views.
Subset and compare pathways or cell-type pairs using subset expressions.
Output formats and presentation-ready aesthetics suitable for reports and manuscripts.

Quick Start

Provide the CCC file output from CellCellCommunication and request a plot type to generate publication-ready visuals.

Frequently Asked Questions about cellcellcommunicationplots

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I visualize cell-cell communication inference results for a manuscript?▼

To visualize cell-cell communication results, provide the CCC file from your inference process and select a plot type. The tool outputs publication-ready network, heatmap, or circos graphics tailored for reports and manuscripts.

What plot types are available for ligand-receptor interaction data?▼

Available plot types for ligand-receptor interaction data include network, heatmap, circos, dot, box, violin, and ridge plots. These options allow both global overviews and detailed views of cell-cell communication.

Can I subset specific pathways or cell-type pairs when plotting CCC data?▼

Yes, you can subset specific pathways or cell-type pairs using subset expressions. This allows you to filter and compare targeted ligand-receptor interactions across cell types in your visualizations.

How do I customize the resolution and format of cell-cell communication network plots?▼

You can customize cell-cell communication network plots through configuration options for output formats and resolutions. The tool exposes settings to adjust presentation aesthetics for publication-ready visuals.

What is the difference between aggregation and interaction methods in CCC visualization?▼

The aggregation and interaction methods represent different ways to process and display ligand-receptor interaction data. The configuration exposes these methods to tailor how communication scores are calculated and visualized across cell types.

Does this tool require a specific input file format for cell-cell communication plots?▼

Yes, it requires a CCC file generated from the CellCellCommunication process. This specific input file contains the ligand-receptor interaction data required to generate the publication-ready visuals.