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translator-graph-view

A React TypeScript component library for interactive knowledge graph visualization, designed for use with the NIH's Biomedical Data Translator. Built on ReactFlow (via @xyflow/react) and ELKjs.

Renders Biolink Model knowledge graphs with automatic layout, type-based color coding and icons, interactive selection, and hover geometry for tooltip positioning.

Features

  • Interactive graph visualization — pan, zoom, box-select, and click interactions powered by ReactFlow
  • Five automatic layout algorithms — hierarchical (top-down and left-right), force-directed, grid, and radial, all computed off-thread via an ELK web worker
  • Biolink type awareness — nodes are color-coded by their Biolink type and display dedicated SVG icons for 13 common entity types (Drug, Gene, Disease, Protein, ChemicalEntity, SmallMolecule, AnatomicalEntity, BiologicalEntity, PhenotypicFeature, PathologicalProcess, PhysiologicalProcess, Polypeptide, and a default fallback)
  • Controlled and uncontrolled selection — click or box-drag to select; optionally drive selection from outside via selectedIds
  • Controlled and uncontrolled hover — built-in hover styles plus bidirectional controlled hover for syncing graph highlights with external UI (sidebars, lists, detail panels)
  • Hover geometry with anchor points — callbacks receive bounding rects and pre-computed anchor positions in viewport coordinates, re-measured on pan/zoom via requestAnimationFrame, ideal for tooltip positioning
  • Multi-edge rendering — parallel edges between the same node pair automatically spread into distinct quadratic bezier curves with configurable spacing
  • Inferred edge styling — edges marked inferred: true render with a dashed stroke
  • Predicate labels — edge labels extracted from Biolink predicates with optional show/hide
  • Edge path styles — bezier, straight, step, and smoothstep path options
  • MiniMap and zoom controls — zoomable/pannable minimap with neutral node dots
  • Draggable graph annotations — parent-controlled text notes with editable content, clickable links, hover delete controls, configurable styling, and savable graph-space positions
  • Node chrome — optional client-rendered hover controls at the node corners, with onNodeRemove / onNodeMenu callbacks
  • Optional connection handles — hide and disable node connection handles via showHandles
  • Smart text formatting — gene/protein names uppercased, other names title-cased, Roman numerals detected and preserved
  • Full TypeScript type definitions — complete generics for nodes, edges, selections, geometry, and all props
  • Dual module output — ESM and CommonJS builds with a separate CSS stylesheet

How It Works

Architecture

The library exports a single primary component (GraphView) that wraps ReactFlow in a ReactFlowProvider, a settings context, and a node-chrome context. Internally it:

  1. Transforms input data — converts the Biolink-model GraphData (a record-based format with nodes and edges keyed by ID) into ReactFlow's flat node/edge arrays. During transformation, each node is assigned a deterministic color via a hash of its primary Biolink type, a display label (first name), a simplified type string, and an SVG icon. Edges sharing the same node pair are indexed so the renderer can offset them.

  2. Computes layout via web worker — the useGraphLayout hook instantiates an ELK instance pointing at a user-provided worker URL. It builds an ELK graph descriptor with the chosen layout algorithm's options, sends it to the worker, and applies the returned positions to the ReactFlow nodes. Layout is recomputed whenever the data or layout type changes, with stale-cancellation to avoid race conditions.

  3. Syncs layout to ReactFlow state — the useLayoutSync hook pushes layouted nodes/edges into ReactFlow's controlled state and triggers fitView with a short delay so the viewport frames the graph.

  4. Handles selection — the useSelection hook translates ReactFlow's OnSelectionChangeParams back into domain-level GraphNode[] and GraphEdge[] objects. The optional useControlledSelection hook allows the parent to drive selection from the outside by toggling selected flags on the flow nodes/edges.

  5. Handles hover with geometry — the useHoverGeometry hook tracks which node or edge the pointer is over, queries the DOM for its bounding rect (scoped to the current GraphView instance to avoid cross-graph collisions), computes a named anchor point, and invokes the caller's onNodeHover/onEdgeHover with the geometry. On viewport pan/zoom, geometry is re-measured via requestAnimationFrame so tooltip positions stay accurate.

  6. Renders custom node and edge components — GraphNode displays the type icon, a formatted label, top/bottom handles (optionally hidden), and client-provided hover chrome. GraphEdge supports four path algorithms plus a multi-edge quadratic bezier mode, dashed stroke for inferred edges, and a floating label rendered via ReactFlow's EdgeLabelRenderer.

Layout Algorithms

All layout is performed by ELK in a web worker (~1.5 MB engine kept out of the main bundle):

Layout ELK Algorithm Description
hierarchical layered (DOWN) Layered top-to-bottom with 80px node spacing and 100px inter-layer spacing
hierarchicalLR layered (RIGHT) Layered left-to-right
force force (Eades model) Force-directed with 400 iterations
grid box Aspect-ratio-aware box packing
radial stress Stress-minimization producing radial/circular layouts

Data Flow

GraphData (Biolink model)
  │
  ├─ transformNodesToFlow() → FlowNode[] (with color, label, icon, type)
  ├─ transformEdgesToFlow() → FlowEdge[] (with pair indexing, labels)
  │
  └─ useGraphLayout() → ELK worker → positioned FlowNode[]
       │
       └─ useLayoutSync() → ReactFlow state → rendered graph

Installation

npm install translator-graph-view elkjs

React 18+ (or 19+) and elkjs 0.9+ are required as peer dependencies.

Usage

import { GraphView } from 'translator-graph-view';
import 'translator-graph-view/styles.css';

const data = {
  nodes: {
    'n1': { id: 'n1', names: ['Aspirin'], types: ['biolink:Drug'] },
    'n2': { id: 'n2', names: ['Headache'], types: ['biolink:Disease'] },
  },
  edges: {
    'e1': { id: 'e1', subject: 'n1', object: 'n2', predicate: 'biolink:treats' },
  },
};

const elkWorkerUrl = new URL('elkjs/lib/elk-worker.min.js', import.meta.url).href;

function App() {
  return (
    <div style={{ width: '100%', height: '600px' }}>
      <GraphView
        data={data}
        layout="hierarchical"
        elkWorkerUrl={elkWorkerUrl}
        onNodeClick={(node) => console.log('Clicked:', node)}
        onSelectionChange={(selection) => console.log('Selected:', selection)}
      />
    </div>
  );
}

The GraphView container must have a defined width and height.

API

<GraphView />

Prop Type Default Description
data GraphData required Graph nodes and edges
elkWorkerUrl string required URL to the ELKjs web worker script (see below)
layout LayoutType 'hierarchical' Layout algorithm
onSelectionChange (selection: Selection) => void - Fires when selection changes
onSelectionDelete (selection: DeleteSelection) => void - Fires on Delete/Backspace with a selection; the view never removes anything itself (see below)
onNodeClick (node: GraphNode) => void - Fires when a node is clicked
onEdgeClick (edge: GraphEdge) => void - Fires when an edge is clicked
onNodeHover (node: GraphNode | null, geometry: HoverGeometry | null) => void - Fires when a node is hovered or unhovered
onEdgeHover (edge: GraphEdge | null, geometry: HoverGeometry | null) => void - Fires when an edge is hovered or unhovered
onAnnotationHover (annotationId: string | null) => void - Fires when an annotation is hovered or unhovered
hoveredNodeId string | null - Controlled hover: focuses the given node and dims the rest
hoveredEdgeId string | null - Controlled hover: focuses the given edge + endpoints and dims the rest
hoveredAnnotationId string | null - Controlled hover: shows annotation hovered state (no dimming)
nodeHoverAnchor HoverAnchorPosition 'topCenter' Anchor point returned in HoverGeometry for node hovers
edgeHoverAnchor HoverAnchorPosition 'midpoint' Anchor point returned in HoverGeometry for edge hovers
clearHoverOnViewportChange boolean false Clear the hover when the viewport pans/zooms instead of re-measuring it every frame
selectedIds string[] - Controlled selection by node/edge ID
edgeType EdgeType 'straight' Edge path style: 'bezier', 'straight', 'step', or 'smoothstep'
showEdgeLabels boolean true Show predicate labels on edges
showMiniMap boolean true Show the zoomable/pannable minimap
showHandles boolean true Show connection handles on hover and allow connections
nodeChrome GraphNodeChrome - Client-rendered chrome at the top-left and bottom-right of each graph node
getNodeIcon GraphNodeIconRenderer - Client icon lookup; null/undefined uses the library default, false hides the icon
getNodeColor GraphNodeColorRenderer - Client background-color lookup; null/undefined keeps the default node background
onNodeRemove (nodeId: string) => void - Fires from node chrome onRemove
onNodeMenu (nodeId: string, position: { x: number; y: number }) => void - Fires from node chrome onMenu with a viewport position
multiEdgeSpacing number 60 Pixel spacing between parallel edges sharing the same node pair
annotations GraphAnnotation[] - Controlled annotation overlays (positions in graph coordinates)
onAnnotationsChange (annotations: GraphAnnotation[]) => void - Fires when an annotation is dragged, edited, or deleted
annotationStyles GraphAnnotationStyles - Client-configurable annotation appearance (background, delete button, icons, link rendering)
hoverStyles GraphHoverStyles - Client-configurable hover / dim appearance (opacity, classNames)
className string - Additional CSS class for the container

elkWorkerUrl

Layout computation is offloaded to a web worker, keeping the ~1.5 MB ELK engine out of your main bundle. You must provide a URL pointing to the ELK worker script. In Vite-based apps:

const elkWorkerUrl = new URL('elkjs/lib/elk-worker.min.js', import.meta.url).href;

For webpack or other bundlers, serve node_modules/elkjs/lib/elk-worker.min.js as a static asset and pass its URL.

Annotations

Annotations are draggable text notes rendered on top of the graph. They are parent-controlled: the host application creates, persists, and restores them via the annotations prop. Positions are in graph coordinates, so they stay anchored as the user pans and zooms.

import { useState } from 'react';
import { GraphView, type GraphAnnotation } from 'translator-graph-view';

function App() {
  const [annotations, setAnnotations] = useState<GraphAnnotation[]>([]);

  const addAnnotation = () =>
    setAnnotations((prev) => [
      ...prev,
      { id: crypto.randomUUID(), text: '', position: { x: 100, y: 100 } },
    ]);

  return (
    <>
      <button type="button" onClick={addAnnotation}>Add annotation</button>
      <GraphView
        data={data}
        elkWorkerUrl={elkWorkerUrl}
        annotations={annotations}
        onAnnotationsChange={setAnnotations}
        annotationStyles={{
          backgroundColor: '#FFF9C4',
          deleteButton: { backgroundColor: '#fff' },
        }}
      />
    </>
  );
}

Each annotation shows as a text note with a pale yellow background by default. On hover, a delete button appears in the top-left corner (white circle with an X icon by default). Override colors, CSS classes, and the delete icon via annotationStyles.

Annotations have two faces. At rest a note renders as static text with its links clickable; clicking the note (anywhere but a link) swaps in a textarea with the caret where you clicked, and blurring commits. Escape leaves edit mode and discards the draft. Read-only annotations never enter edit mode, but their links still work.

Links in annotation text

Annotation text is plain text; the display view turns three forms into anchors:

Typed Renders as
https://example.com/x the URL, linked (trailing sentence punctuation stays outside the link)
www.example.com the text, linked to https://www.example.com
curator@example.org the address, linked to mailto:
[the paper](https://example.com/p) the paper, linked

Links open in a new tab with rel="noopener noreferrer". Only http, https, and mailto targets are linked — anything else (javascript:, data:, and so on) renders as the literal text the user typed. Nothing is ever parsed as HTML: anchors are built from a token stream, so markup in annotation text stays inert text.

Set annotationStyles.linkify: false to render annotation text verbatim, and annotationStyles.linkClassName to style the generated anchors.

onAnnotationsChange fires when:

  • the user finishes dragging an annotation (onNodeDragStop)
  • the user edits text and blurs the textarea
  • the user clicks the delete button

Persist the returned array (localStorage, API, etc.) and pass it back through annotations on reload.

Node chrome

Pass nodeChrome to render hover controls at the top-left and bottom-right corners of each graph node. Chrome is hidden until the node is hovered or contains focus (keyboard users can tab to chrome buttons). Memoize the nodeChrome object (or hoist slot renderers) so GraphView does not rebuild it every render.

onRemove and onMenu are only present when you pass onNodeRemove / onNodeMenu. Pointer-triggered menus use clientX / clientY; keyboard activation (or calling onMenu() with no event) falls back to the node's bounding-rect center.

const nodeChrome = {
  topLeft: ({ onRemove }) =>
    onRemove ? <button type="button" onClick={onRemove}>Remove</button> : null,
  bottomRight: ({ onMenu }) =>
    onMenu ? <button type="button" onClick={onMenu}>Menu</button> : null,
};

<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  showHandles={false}
  nodeChrome={nodeChrome}
  onNodeRemove={(nodeId) => console.log('remove', nodeId)}
  onNodeMenu={(nodeId, position) => console.log('menu', nodeId, position)}
/>

Node icons

Pass getNodeIcon to replace the built-in type icon on each graph node. The first argument is the simplified primary type (for example "Drug"), not a Biolink CURIE. Full types are on node.types.

  • Return null or undefined to keep the library icon for that node.
  • Return false to hide the icon.
  • Icons are wrapped in a 24×24 slot that sizes both svg and img.

The library keeps the callback identity stable, so an inline getNodeIcon does not re-render edges or annotations. Hoist or wrap in useCallback if you also want to avoid extra work inside the renderer itself. Compose with getNodeTypeIcon when you only want to override some types.

import { GraphView, getNodeTypeIcon } from 'translator-graph-view';

<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  getNodeIcon={(type, node) => {
    if (node.id === 'special') return <img alt="" src="/special.svg" />;
    if (type === 'Drug') return <MyDrugIcon />;
    return getNodeTypeIcon(type);
  }}
/>

Node spacing

Layouts space nodes by their bounding boxes, so the boxes handed to ELK track what the stylesheet actually paints: NODE_HEIGHT is the real 32px node height, and each node's width comes from estimateNodeWidth, clamped to the stylesheet's own 60–200px bounds. A box larger than the painted node would reappear as gap the configured spacing never asked for.

layoutConfigs therefore expresses spacing as the gap you actually see. Adjust those values to trade density against breathing room; note that the radial (stress) algorithm positions mainly by elk.stress.desiredEdgeLength and largely ignores elk.spacing.nodeNode.

Node colors

Pass getNodeColor to set a node's background from its type. Like getNodeIcon, the first argument is the simplified primary type (for example "Drug"), not a Biolink CURIE; full types are on node.types.

  • Return { background, hoverBackground } to color the node.
  • Omit hoverBackground to reuse background on hover.
  • Return null or undefined to leave that node on the default background.

With no renderer supplied, every node keeps the default #DCDCE6 background, so adding the prop is opt-in per node. Colors are applied as the --tgv-node-bg and --tgv-node-bg-hover custom properties, and the hover background also applies when a node is hovered externally via hoveredNodeId.

const typeColors: Record<string, { background: string; hoverBackground: string }> = {
  Drug: { background: '#DCE9FF', hoverBackground: '#C4DAFF' },
  Disease: { background: '#FFE0E0', hoverBackground: '#FFC9C9' },
};

<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  getNodeColor={(type) => typeColors[type] ?? null}
/>

The library keeps the callback identity stable, so an inline getNodeColor does not re-render edges or annotations.

Interaction Model

The graph supports the following built-in interactions:

Action Behavior
Left-click node/edge Select it
Shift+Click Add to selection
Drag from empty area Box selection (partial overlap)
Delete / Backspace Report the selection through onSelectionDelete
Middle/right-button drag Pan the viewport
Scroll Zoom in/out (0.15x to 3x)
MiniMap drag Pan the viewport
MiniMap scroll Zoom

Deleting a selection

Pressing Delete or Backspace with elements selected calls onSelectionDelete and nothing else — the view never drops the elements from its own state. Its nodes and edges mirror the data prop, so an internal delete would leave the two out of step until the next data change put the element back. Remove the reported ids from data to make the deletion stick, which also leaves undo entirely in the client's hands. Delete keys are only armed when onSelectionDelete is provided.

<GraphView
  data={data}
  elkWorkerUrl="/elk-worker.min.js"
  onSelectionDelete={({ nodes, edges }) => removeFromMyStore(nodes, edges)}
/>

edges includes every edge incident to a deleted node, not only the edges the user selected. That differs from node-chrome onNodeRemove, which reports a single node id and does not include incident edges — wire both if your UI exposes chrome remove and keyboard delete, and expand edges yourself for the chrome path if you need parity.

Keystrokes typed inside an input, textarea, or contenteditable — annotation text editing included — never trigger it.

Hover

The component supports both uncontrolled hover (internal styling only) and controlled hover (you drive the highlight state from outside). Use controlled hover to synchronize highlights between the graph and an external UI like a sidebar or detail panel.

When a controlled hover id is set, the graph applies neighborhood focus:

  • Node: the hovered node, its incident edges, and neighbor nodes stay full opacity; everything else is dimmed.
  • Edge: that edge and its two endpoints stay full opacity; everything else is dimmed.
  • Annotation: the annotation shows its hovered style; the rest of the graph is not dimmed.

Uncontrolled — nodes and edges show hover styles on mouseover with no props needed.

Outbound events — use onNodeHover / onEdgeHover / onAnnotationHover to react to hover changes:

const [hoveredNode, setHoveredNode] = useState<GraphNode | null>(null);

<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  onNodeHover={(node) => setHoveredNode(node)}
/>

{hoveredNode && <div>Hovering: {hoveredNode.names[0]}</div>}

Controlled (bidirectional) — pass hoveredNodeId / hoveredEdgeId / hoveredAnnotationId to drive highlights from external UI (e.g. a sidebar list), and use the outbound hover callbacks to update that state when the user hovers inside the graph:

const [hoveredNodeId, setHoveredNodeId] = useState<string | null>(null);

// Sidebar list item triggers graph highlight
<li
  onMouseEnter={() => setHoveredNodeId(node.id)}
  onMouseLeave={() => setHoveredNodeId(null)}
>
  {node.names[0]}
</li>

// Graph triggers sidebar highlight
<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  hoveredNodeId={hoveredNodeId}
  onNodeHover={(node) => setHoveredNodeId(node?.id ?? null)}
/>

Hover styles

Override dimming / hovered appearance via hoverStyles (sensible defaults apply when omitted):

<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  hoverStyles={{
    dimmedOpacity: 0.25,
    dimmedNodeClassName: 'my-dimmed-node',
    hoveredAnnotationClassName: 'my-hovered-annotation',
  }}
/>
Field Default Description
dimmedOpacity 0.3 Opacity for dimmed elements (--tgv-dimmed-opacity)
dimmedNodeClassName - Extra class on dimmed nodes
dimmedEdgeClassName - Extra class on dimmed edges
dimmedAnnotationClassName - Extra class on dimmed annotations
hoveredNodeClassName - Extra class on hovered nodes
hoveredEdgeClassName - Extra class on hovered edges
hoveredAnnotationClassName - Extra class on hovered annotations

Hover geometry

The onNodeHover and onEdgeHover callbacks receive a second HoverGeometry argument containing the hovered element's bounding rect and a pre-computed anchor point in viewport coordinates — useful for positioning tooltips without querying the DOM yourself.

import type { GraphNodeType, HoverGeometry } from 'translator-graph-view';

<GraphView
  data={data}
  elkWorkerUrl={elkWorkerUrl}
  nodeHoverAnchor="topCenter"
  onNodeHover={(node, geometry) => {
    if (node && geometry) {
      showTooltip({ x: geometry.anchor.x, y: geometry.anchor.y });
    } else {
      hideTooltip();
    }
  }}
/>

HoverAnchorPosition can be one of: 'topLeft', 'topCenter', 'topRight', 'centerLeft', 'center', 'centerRight', 'bottomLeft', 'bottomCenter', 'bottomRight', or 'midpoint' (edges only — computes the true midpoint of the SVG path's visible segment).

When the hover callback fires with null (mouse leaves), geometry is also null. If DOM measurement fails (e.g. SSR), geometry is null.

While the pointer stays over the same node or edge, geometry is re-measured on pan and zoom (throttled with requestAnimationFrame) so anchors stay aligned with the viewport.

Clearing hover while the viewport moves

Re-measuring calls your hover callback once per frame for as long as the gesture lasts. If your consumer stores the geometry in state, that is a re-render per frame, and any hover-driven dimming stays on — forcing the compositor to blend every dimmed element on every frame of the pan. On large graphs this makes a pan that starts over a node noticeably heavier than one that starts over empty space.

Set clearHoverOnViewportChange to drop the hover instead. The callback fires once with null on the first frame of the gesture, tooltips and dimming clear, and nothing further fires until the pointer enters another element:

<GraphView
  data={data}
  elkWorkerUrl="/elk-worker.min.js"
  clearHoverOnViewportChange
  onNodeHover={(node, geometry) => setHover(node ? { node, geometry } : null)}
/>

Keep the default (false) if your tooltips are meant to track their element while the user pans.

DOM queries are scoped to this GraphView instance, so multiple graphs on one page do not pick each other's elements. Element ids are escaped for attribute selectors (CSS.escape when available).

Multi-edge rendering

When multiple edges connect the same pair of nodes (in either direction), they automatically spread into distinct quadratic bezier curves offset perpendicular to the straight-line path between the nodes. The label for each edge is positioned at the bezier's midpoint (t=0.5). Control the spacing with multiEdgeSpacing (default 60px).

Inferred edges

Edges with inferred: true in the data render with a dashed stroke to visually distinguish them from direct evidence edges.

Layout types

  • 'hierarchical' — Layered top-to-bottom (default)
  • 'hierarchicalLR' — Layered left-to-right
  • 'force' — Force-directed (Eades model, 400 iterations)
  • 'grid' — Aspect-ratio-aware box packing
  • 'radial' — Stress-minimization (radial/circular)

Node rendering

Each node displays:

  • An SVG icon based on its primary Biolink type (13 dedicated icons plus a default)
  • A formatted label — gene/protein names are uppercased; other names are title-cased with Roman numeral detection
  • A colored left border derived deterministically from the type via a hash into an 18-color palette
  • Selection and hover visual states (border/shadow changes)

Data format

interface GraphData {
  nodes: Record<string, GraphNode>;
  edges: Record<string, GraphEdge>;
  results?: Result[];
  paths?: Record<string, Path>;
  publications?: Record<string, Publication>;
  trials?: Record<string, Trial>;
}

interface GraphNode {
  id: string;
  names: string[];
  types: string[];           // e.g. ['biolink:Drug']
  curies?: string[];
}

interface GraphEdge {
  id: string;
  subject: string;           // source node ID
  object: string;            // target node ID
  predicate: string;         // e.g. 'biolink:treats'
  predicate_url?: string;
  knowledge_level?: string;
  inferred?: boolean;        // renders with dashed stroke when true
  provenance?: Provenance[];
  publications?: { inferred?: Publication[] };
  trials?: Trial[];
  support?: unknown[];
  aras?: string[];
  description?: string;
}

interface Result {
  id: string;
  drug_name?: string;
  subject: string;
  object: string;
  paths?: string[];
}

interface Path {
  id: string;
  edges: string[];
}

interface Publication {
  id: string;
  title?: string;
  authors?: string[];
  year?: number;
  journal?: string;
  pmid?: string;
  doi?: string;
}

interface Trial {
  id: string;
  title?: string;
  status?: string;
  phase?: string;
  nctid?: string;
}

interface Provenance {
  source?: string;
  url?: string;
  evidence_type?: string;
}

interface GraphAnnotation {
  id: string;
  text: string;
  position: { x: number; y: number };
}

interface GraphAnnotationStyles {
  backgroundColor?: string;
  className?: string;
  deleteButton?: {
    backgroundColor?: string;
    className?: string;
    icon?: React.ReactNode;
  };
  linkify?: boolean;        // default true
  linkClassName?: string;
}

interface GraphNodeChromeContext {
  node: GraphNode;
  selected: boolean;
  onRemove?: () => void;
  onMenu?: (event?: React.MouseEvent) => void;
}

interface GraphNodeChrome {
  topLeft?: (ctx: GraphNodeChromeContext) => React.ReactNode;
  bottomRight?: (ctx: GraphNodeChromeContext) => React.ReactNode;
}

type GraphNodeIconRenderer = (
  type: string,
  node: GraphNode,
) => React.ReactNode | null | undefined;

Exported Hooks

  • useGraphLayout({ nodes, edges, layout, elkWorkerUrl }) — Computes ELK layout positions for ReactFlow nodes/edges via a web worker. Returns { nodes, edges, isLayouting }.
  • useSelection({ data, onSelectionChange }) — Manages node/edge selection state, translating ReactFlow selection events back into domain-level objects.
  • useGraphSettings() — Access the GraphSettings context (multiEdgeSpacing, annotationStyles, hoverStyles).
  • useNodeChrome() — Access the node-chrome context (nodeChrome, onNodeRemove, onNodeMenu, getNodeIcon) when rendering GraphNode outside GraphView.

Exported Utilities

Function Description
transformNodesToFlow(data) Convert GraphData to ReactFlow node array with colors, labels, and types
transformEdgesToFlow(data, edgeType?, showLabels?) Convert GraphData to ReactFlow edge array with pair indexing
transformAnnotationsToFlow(annotations) Convert GraphAnnotation[] to ReactFlow annotation nodes
extractAnnotationsFromFlow(nodes) Extract GraphAnnotation[] from a ReactFlow node array
isAnnotationNode(node) Type guard for annotation flow nodes
getColorForType(type) Get a deterministic color for a Biolink type string (18-color palette)
getNodeTypeIcon(type) Return the library SVG icon for a simplified (or biolink:) type
simplifyTypeName(type) Extract a readable name from a prefixed type URI ("biolink:Drug" → "Drug")
getPrimaryType(types) Return the first type from a types array
formatPredicate(predicate) Format a predicate for display ("biolink:treats" → "treats")
getNodesById(data, ids) Look up nodes by ID array
getEdgesById(data, ids) Look up edges by ID array
NODE_WIDTH / NODE_HEIGHT Fallback node dimensions used by the layout engine (120×32)
NODE_MIN_WIDTH / NODE_MAX_WIDTH Width bounds the node stylesheet enforces (60 / 200)
getNodeDisplayLabel(label, type) The label text as rendered (all caps for Gene/Protein, otherwise title case)
estimateNodeWidth(label, type) Estimated rendered node width, used as the node's layout box

Exported Types

All TypeScript types are exported for consumer use:

GraphData, GraphNodeType, GraphEdgeType, GraphViewProps, LayoutType, EdgeType, Selection, DeleteSelection, Result, Path, Publication, Trial, Provenance, GraphNodeData, GraphEdgeData, FlowNode, FlowGraphNode, FlowAnnotationNode, FlowEdge, HoverAnchorPosition, HoverGeometry, GraphAnnotation, GraphAnnotationStyles, GraphHoverStyles, GraphNodeChrome, GraphNodeChromeContext, GraphNodeColors, GraphNodeColorRenderer

Development

npm install
npm run dev          # Start Vite dev server with example app
npm run build        # Build the library (ESM + CJS + types + CSS)
npm run typecheck    # Type-check without emitting
npm run lint         # Run ESLint
npm run test         # Run unit tests (Vitest)
npm run test:watch   # Run tests in watch mode
npm run test:e2e     # Run Playwright end-to-end tests
npm run test:e2e:ui  # Run Playwright tests with UI

Example App

The example/ directory contains a full demo application that showcases all library features:

  • Dataset switching (small, medium, large graphs)
  • All five layout algorithms
  • Selection panel with node/edge lists
  • Bidirectional controlled hover between sidebar and graph
  • Tooltip positioning using hover geometry anchors
  • Node chrome (hover remove/menu controls) and optional connection handles
  • Graph statistics display

Project Structure

src/
├── components/
│   ├── GraphView/      # Main component, layout sync, controlled selection/hover hooks
│   ├── nodes/          # Custom ReactFlow node component with icons and formatting
│   └── edges/          # Custom ReactFlow edge component with multi-edge and path types
├── hooks/              # useGraphLayout, useSelection, useGraphSettings
├── layouts/            # ELK layout configurations for each algorithm
├── utils/              # Data transforms, color generation, hover geometry measurement
├── assets/icons/       # SVG icons for Biolink entity types
└── types/              # TypeScript type definitions
example/                # Demo application
e2e/                    # Playwright end-to-end tests

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MIT

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A React TypeScript component for interactive knowledge graph visualization, designed for use with the NIH's Biomedical Data Translator. Built on ReactFlow and ELKjs.

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