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 (limited maintenance); ProteinPaint via API
• Web: cBioPortal, ProteinPaint, MutationMapper

The Single Most Important Modern Insight -- Hotspot Recurrence Drives the Plot