bio-data-visualization-lollipop-protein-maps
Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurrence count, and variant classification with maftools, g3-lollipop, trackViewer, and ProteinPaint. Use when visualizing recurrent mutation hotspots on a single gene's protein, marking domain boundaries from UniProt/Pfam, comparing missense vs truncating distributions, or contrasting two cohorts on the same lollipop.
npx skills add BioTender-max/awesome-bio-agent-skills --skill lollipop-protein-maps --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: maftools 2.18+, trackViewer 1.38+, g3-lollipop (JavaScript via R `g3viz` 1.2+), Bio.PDB 1.83+ (for domain coordinates). ProteinPaint is a hosted service. Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` - Python: `pip show <package>` then `help(module.function)` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Lollipop / Needle Protein Maps **"Plot mutations on a gene's protein"** -> Render a horizontal protein backbone with colored domain rectangles (from UniProt/Pfam/InterPro), then stack vertical lines ("stems") at mutated amino-acid positions, capped with circles ("lollipops") whose size reflects mutation count and whose color encodes variant class. The biological story is hotspot identification — a tall stack of recurrences at a single residue (e.g., KRAS G12, PIK3CA E545/H1047) is the visual signature of a driver mutation. - R: `maftools::lollipopPlot`, `trackViewer::lolliplot`, `g3viz::g3Lollipop` - Python: `pyLollipop` (limi
- Version Compatibility
- The Single Most Important Modern Insight -- Hotspot Recurrence Drives the Plot
- Decision Tree by Question
- maftools::lollipopPlot
- trackViewer::lolliplot -- Fine Control over Track Layout
- g3viz / g3-lollipop -- Interactive HTML
- Domain Annotation Sources
- Per-Method Failure Modes
- Mutations not labeled with AA position
- Isoform mismatch
- Domain map outdated
- Recurrence at low-coverage region overinterpreted
- Counts encoded only as size; no actual numbers shown
- Domain colors random; no functional grouping
What does the bio-data-visualization-lollipop-protein-maps skill do?
Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurrence count, and variant classification with maftools, g3-lollipop, trackViewer, and ProteinPaint. Use when visualizing recurrent mutation hotspots on a single gene's protein, marking domain boundaries from UniProt/Pfam, comparing missense vs truncating distributions, or contrasting two cohorts on the same lollipop.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill lollipop-protein-maps --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.