bio-pathway-enrichment-visualization
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.
npx skills add BioTender-max/awesome-bio-agent-skills --skill enrichment-visualization --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Enrichment Visualization **"Create publication-quality plots from my enrichment analysis"** → Generate dotplots, gene-concept networks, enrichment maps, GSEA running score plots, and ridgeplots from clusterProfiler results. - R: `dotplot()`, `cnetplot()`, `emapplot()`, `gseaplot2()` (enrichplot) ## Scope This skill covers **enrichplot package functions** designed for clusterProfiler results: - `dotplot()`, `barplot()` - Summary views - `cnetplot()`, `emapplot()`, `treeplot()` - Network/hierarchical views - `gseaplot2()`, `ridgeplot()` - GSEA-specific - `goplot()`, `heatplot()`, `upsetplot()` - Specialized views **For custom ggplot2 dotplots and statistical annotation**, see `data-visualization/distribution-plots` and `data-visualization/ggplot2-fundamentals`. ## Setup **Goal:** Load required packages fo
- Version Compatibility
- Scope
- Setup
- Dot Plot
- Bar Plot
- Gene-Concept Network (cnetplot)
- Enrichment Map (emapplot)
- pairwisetermsim() Method Selection
- Tree Plot
- Upset Plot
- GSEA-Specific Plots
- Running Score Plot (gseaplot2)
- Ridge Plot
- GO-Specific Plot (goplot)
What does the bio-pathway-enrichment-visualization skill do?
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill enrichment-visualization --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.