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Olson"},"license":"MIT","homepage":"https://github.com/warelab/tbrowse#readme","keywords":["react-component","phylogenetics","tree","msa","bioinformatics"],"repository":{"url":"git+https://github.com/warelab/tbrowse.git","type":"git"},"description":"Embeddable React component for visualizing phylogenetic trees and pluggable data zones.","maintainers":[{"name":"ajo2995","email":"olson@cshl.edu"}],"readme":"# tbrowse\n\nEmbeddable React component for visualizing phylogenetic trees with pluggable data zones.\n\n`<TBrowse>` renders a tree alongside a row-aligned set of zones (Tree, Labels, MSA, custom plug-ins). Tree topology, taxonomy, MSA, gene metadata, and per-node annotations are independent host inputs — TBrowse does no fetching of its own. View state (selection, collapse, prune, swap, zone widths, MSA viewport, search) is a single serializable object that round-trips through URL state via the controlled `viewState` / `onViewStateChange` props.\n\n## Status\n\n`2.0.0` is a complete rewrite of the original component on a fresh React 18 / TypeScript / Zustand stack. The 1.x line on npm (`tbrowse@1.0.x`) is the previous nwb / React 16 / Redux-Toolkit implementation, preserved at commit `b017a74` for archival reference. The 2.0 API is **not backwards-compatible** with 1.x.\n\nThe rewrite is functionally complete: chassis, four built-in zones (Tree / Labels / MSA / Neighborhood), Ensembl REST and Gramene adapters, animated transitions, branch-length compression, gene-family coloring, protein-domain annotations, splice-junction marks, and a `nodeOfInterest` pivot. See [CHANGELOG.md](./CHANGELOG.md) for the migration summary.\n\n## Quick start\n\n```tsx\nimport { TBrowse, treeZone, labelsZone, msaZone, type Tree, type MSA, type Taxonomy } from 'tbrowse';\n\nconst tree: Tree = { rootId: 'n0', nodes: { /* ... */ } };\nconst taxonomy: Taxonomy = { /* taxId → { scientificName, commonName, ... } */ };\nconst msa: MSA = { alphabet: 'protein', length: 60, sequences: { /* geneId → string */ } };\n\n<div style={{ width: 900, height: 600 }}>\n  <TBrowse\n    tree={tree}\n    taxonomy={taxonomy}\n    msa={msa}\n    zones={[treeZone, labelsZone, msaZone]}\n  />\n</div>\n```\n\n## Live Ensembl example\n\nThe bundled Vite playground (`npm run dev`) has a \"Load Ensembl tree\" button that fetches a real gene tree (BRCA2 — `ENSG00000139618`) from `rest.ensembl.org`, runs it through `fromEnsemblGeneTree`, and renders it pivoted to put human BRCA2 at the top. Demonstrates the entire stack against live data.\n\n```ts\nimport { fromEnsemblGeneTree, computePivotState, TBrowse } from 'tbrowse';\n\nconst json = await fetch(\n  'https://rest.ensembl.org/genetree/member/id/homo_sapiens/ENSG00000139618?aligned=1&sequence=protein',\n  { headers: { Accept: 'application/json' } },\n).then((r) => r.json());\n\nconst { tree, taxonomy, msa, geneMetadata } = fromEnsemblGeneTree(json);\n```\n\n## Development\n\n```sh\nnpm install\nnpm run dev         # Vite dev server (examples/playground)\nnpm run typecheck   # tsc --noEmit\nnpm test            # vitest\nnpm run build       # library build to dist/\n```\n\n## Host inputs\n\n```ts\ninterface TBrowseProps {\n  tree: Tree;                          // required\n  taxonomy?: Taxonomy;\n  msa?: MSA;\n  geneMetadata?: GeneMetadata;\n  nodeAnnotations?: NodeAnnotation[];\n  labelProviders?: LabelProvider[];\n\n  zones: ZoneDefinition[];             // built-ins + plugins\n  nodeOfInterest?: string;             // pivot the tree to this gene/node at mount\n\n  // Controlled / uncontrolled view state\n  viewState?: ViewState;\n  initialViewState?: Partial<ViewState>;\n  onViewStateChange?: (next: ViewState) => void;\n\n  theme?: 'light' | 'dark';\n  className?: string;\n}\n```\n\n`Tree.nodes` is flat: `{ id, parentId, distance, isLeaf, taxonomyId?, geneId?, eventType?, bootstrap? }`. `MSA.sequences` is keyed by gene id. The Ensembl adapter (`fromEnsemblGeneTree`) walks the nested REST response into this normalized shape.\n\n## ViewState\n\nThe single serializable object that captures everything URL-shareable.\n\n```ts\ninterface ViewState {\n  selectedNodeId: NodeId | null;\n  collapsedNodeIds: NodeId[];          // internal nodes shown as triangles\n  prunedNodeIds: NodeId[];             // subtrees hidden + replaced with stub glyphs\n  swappedNodeIds: NodeId[];            // internal nodes whose children render in reversed order\n  zones: { id: string; width: number; visible: boolean }[];\n  zoneStates: Record<string, unknown>; // per-zone state slot (built-ins use well-known keys)\n  search: { field: string; query: string } | null;\n}\n```\n\nAll chassis interactions (resize, reorder, collapse via tooltip, prune via tooltip, swap, MSA pan/zoom, label-field picker, show/hide) write to this object via `onViewStateChange`. Persist it to a URL fragment for shareable views.\n\n## Built-in zones\n\n| Zone | Id | Default width |\n|---|---|---|\n| `treeZone` | `tree` | 280px |\n| `labelsZone` | `labels` | 220px |\n| `msaZone` | `msa` | 360px |\n\nThe Tree zone supports collapse/expand, prune/regrow, swap children, click-tooltip with contextual actions, internal-node event glyphs (speciation circle / duplication square), proportional-height collapsed-subtree triangles, and animated transitions. Labels supports a configurable field picker (gene id, gene name, gene description, scientific name, common name) plus optional async `LabelProvider` plug-ins. MSA renders a canvas alignment with a coverage minimap (drag-to-pan), wheel-driven pan + ctrl/shift-zoom, and four built-in color schemes (Plain, Clustal, Hydrophobicity, Nucleotide).\n\nCustom zones implement `ZoneDefinition`:\n\n```ts\ninterface ZoneDefinition<S = unknown> {\n  id: string;\n  displayName: string;\n  Header: ComponentType<ZoneRenderProps<S>>;\n  Body: ComponentType<ZoneRenderProps<S>>;\n  defaultWidth: number;\n  minWidth: number;\n  defaultZoneState: S;\n  isAvailable: (data: HostData) => boolean;\n}\n```\n\nBoth `Header` and `Body` receive the same `ZoneRenderProps`: `visibleRows` (already collapsed/pruned/swapped), virtualization `rowRange`, hover/select callbacks, the host's data, and per-zone state plumbing.\n\n## Helpers\n\n| Export | What |\n|---|---|\n| `computeVisibleRows` | Pure derivation: `(tree, collapsed, pruned, swapped) → VisibleRow[]`. |\n| `computeTreeLayout` | Pure phylogram layout against a column width. |\n| `computePivotState` | Resolve a gene id / node id and return collapse + swap sets that pivot the tree. |\n| `fromEnsemblGeneTree` | Convert Ensembl REST gene-tree JSON to TBrowse inputs. |\n| `createStubZone` | Build a placeholder zone for development. |\n\n## Bundle\n\nESM + CJS, types via `vite-plugin-dts`. Peer-deps on `react` / `react-dom` only; runtime dep on `zustand`. Current bundle ~14 kB gzipped (CJS).\n\n## Project layout\n\n```\nsrc/\n  TBrowse.tsx, types.ts, store.tsx, treeIndex.ts\n  visibleRows.ts        chassis row derivation\n  pivot.ts              nodeOfInterest helper\n  layout/               grid + virtualization + animation\n  zones/\n    tree/               SVG branches, glyphs, triangles, tooltip\n    labels/             field picker, label-provider cache\n    msa/                canvas paint, minimap, color schemes\n  adapters/\n    ensembl.ts          Ensembl REST → TBrowse inputs\n  *.test.ts             vitest unit tests\nexamples/playground/    Vite dev app (kitchen-sink demo)\n```\n\n## License\n\nMIT.\n","readmeFilename":"README.md"}