@weng-lab/genomebrowser 1.3.0 → 1.4.0

package/LICENSE

@@ -1,7 +1,7 @@
-Copyright 2025 Weng Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Copyright 2025 Weng Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

package/README.md

@@ -1,211 +1,211 @@
-# Genome Browser
-
-A powerful, interactive React-based genome browser for visualizing genomic data. Built with TypeScript, Vite, and modern web technologies.
-
-## Features
-
-- 🧬 **Multiple Track Types**: BigWig, BigBed, BulkBed, Transcript, Motif, and Importance tracks
-- 🎛️ **Interactive Controls**: Smooth pan and zoom with crisp SVG graphics, drag-and-drop track reordering
-- 🔧 **Customizable**: Configurable colors, heights, display modes, and styling
-- 📊 **Efficient Data Loading**: GraphQL-based API with intelligent batching
-- 🖱️ **Rich Interactions**: Click and hover on genomic features with tooltips and real-time updates
-- 📱 **Responsive**: Works across different screen sizes with consistently sharp graphics
-- ⚡ **Performance**: Optimized rendering with React and Zustand state management
-- 🎨 **SVG-Based**: Uses Scalable Vector Graphics (SVG) for crisp, resolution-independent rendering that scales beautifully
-- 🔍 **Publication Ready**: Export high-quality SVG images suitable for papers and presentations
-
-## Installation
-
-```bash
-npm install @weng-lab/genomebrowser
-```
-
-```bash
-yarn add @weng-lab/genomebrowser
-```
-
-```bash
-pnpm add @weng-lab/genomebrowser
-```
-
-## Quick Start
-
-```tsx
-import React from "react";
-import { Browser, Track, InitialBrowserState, createBrowserStore, createTrackStore, BrowserStoreInstance } from "@weng-lab/genomebrowser";
-
-function GenomeBrowserExample() {
-  // Define your tracks
-  const initialTracks: Track[] = [...];
-
-  // Configure initial browser state
-  const initialState: InitialBrowserState = {
-    domain: {
-      chromosome: "chr12",
-      start: 53360037,
-      end: 53400206,
-    },
-    marginWidth: 150,
-    trackWidth: 1350,
-    multiplier: 3, // a multiplier to fetch more data for smooth panning
-  };
-
-  // Create stores to hold browser data
-  const browserStore = createBrowserStore(initialState)
-  const trackStore = createTrackStore(initialTracks)
-
-  return (
-    <div style={{ width: "90%", margin: "0 auto" }}>
-      <h1>My Genome Browser</h1>
-      <DomainDisplay browserStore={browserStore} />
-      <Browser browserStore={browserStore} trackStore={trackStore} />
-    </div>
-  );
-}
-
-// Use the stores to access information
-function DomainDisplay({browserStore} : {browserStore: BrowserStoreInstance}) {
-  // Zustand-like selectors for getting fields and functions
-  const domain = browserStore((state) => state.domain)
-  return (
-    <h1>{domain.chromosome}:{domain.start}-{domain.end}</h1>
-  )
-}
-
-```
-
-## Browser Configuration
-
-### State Example
-
-```tsx
-const initialState: InitialBrowserState = {
-  domain: {
-    chromosome: "chr1",
-    start: 1000000,
-    end: 2000000,
-  },
-  marginWidth: 150, // Width of the track margins
-  trackWidth: 1350, // Width of the viewable track area
-  multiplier: 3, // Data fetching multiplier for smooth panning
-  highlights: [
-    // Optional: initial highlights
-    {
-      id: "highlight1",
-      color: "#ffaabb",
-      domain: { chromosome: "chr1", start: 1500000, end: 1600000 },
-    },
-  ],
-};
-```
-
-## Track Examples
-
-### BigWig Tracks
-
-Display continuous signal data (e.g., ChIP-seq, RNA-seq signals).
-
-```tsx
-{
-  id: "signal",
-  title: "Signal Data",
-  trackType: TrackType.BigWig,
-  displayMode: DisplayMode.Full, // Multiple display modes supported
-  height: 100,
-  color: "#3498db",
-  url: "https://example.com/signal.bw",
-}
-```
-
-### BigBed Tracks
-
-Display discrete genomic regions (e.g., peaks, annotations).
-
-```tsx
-{
-  id: "peaks",
-  title: "Peak Calls",
-  trackType: TrackType.BigBed,
-  displayMode: DisplayMode.Dense,
-  height: 20,
-  color: "#e74c3c",
-  url: "https://example.com/peaks.bigBed",
-  onClick: (rect) => console.log("Clicked:", rect), // Mouse interactivitiy
-  onHover: (rect) => console.log("Hovered:", rect),
-  tooltip: (rect) => <text>{rect.name}</text>, // Custom svg tooltips
-}
-```
-
-### BulkBed Tracks
-
-Display multiple BigBed datasets in a single track.
-
-```tsx
-{
-  id: "bulk-data",
-  title: "Multiple Datasets",
-  trackType: TrackType.BulkBed,
-  displayMode: DisplayMode.Full,
-  height: 40,
-  gap: 2, // Gap between datasets
-  color: "#9b59b6",
-  datasets: [
-    { name: "Dataset 1", url: "https://example.com/data1.bigBed" },
-    { name: "Dataset 2", url: "https://example.com/data2.bigBed" },
-  ],
-}
-```
-
-### Transcript Tracks
-
-Display gene annotations and transcripts.
-
-```tsx
-{
-  id: "genes",
-  title: "Gene Annotations",
-  trackType: TrackType.Transcript,
-  displayMode: DisplayMode.Squish,
-  height: 50,
-  color: "#2ecc71",
-  assembly: "GRCh38", // "mm10" also supported
-  version: 47, // GENCODE version
-}
-```
-
-Explore our comprehensive [Storybook]() documentation for detailed information about additional track types and their configuration options.
-
-## Development
-
-```bash
-# Install dependencies
-npm install
-
-# Start development server
-npm run dev
-
-# Run Storybook for component development
-npm run storybook
-
-# Build for production
-npm run build
-
-# Run linting
-npm run lint
-```
-
-## Contributing
-
-1. Fork the repository
-2. Create a feature branch
-3. Make your changes
-4. Add tests if applicable
-5. Submit a pull request
-
-## License
-
-MIT License - see LICENSE file for details.
-
-## Support
-
-For questions and support, please open an issue on GitHub.
+# Genome Browser
+
+A powerful, interactive React-based genome browser for visualizing genomic data. Built with TypeScript, Vite, and modern web technologies.
+
+## Features
+
+- 🧬 **Multiple Track Types**: BigWig, BigBed, BulkBed, Transcript, Motif, and Importance tracks
+- 🎛️ **Interactive Controls**: Smooth pan and zoom with crisp SVG graphics, drag-and-drop track reordering
+- 🔧 **Customizable**: Configurable colors, heights, display modes, and styling
+- 📊 **Efficient Data Loading**: GraphQL-based API with intelligent batching
+- 🖱️ **Rich Interactions**: Click and hover on genomic features with tooltips and real-time updates
+- 📱 **Responsive**: Works across different screen sizes with consistently sharp graphics
+- ⚡ **Performance**: Optimized rendering with React and Zustand state management
+- 🎨 **SVG-Based**: Uses Scalable Vector Graphics (SVG) for crisp, resolution-independent rendering that scales beautifully
+- 🔍 **Publication Ready**: Export high-quality SVG images suitable for papers and presentations
+
+## Installation
+
+```bash
+npm install @weng-lab/genomebrowser
+```
+
+```bash
+yarn add @weng-lab/genomebrowser
+```
+
+```bash
+pnpm add @weng-lab/genomebrowser
+```
+
+## Quick Start
+
+```tsx
+import React from "react";
+import { Browser, Track, InitialBrowserState, createBrowserStore, createTrackStore, BrowserStoreInstance } from "@weng-lab/genomebrowser";
+
+function GenomeBrowserExample() {
+  // Define your tracks
+  const initialTracks: Track[] = [...];
+
+  // Configure initial browser state
+  const initialState: InitialBrowserState = {
+    domain: {
+      chromosome: "chr12",
+      start: 53360037,
+      end: 53400206,
+    },
+    marginWidth: 150,
+    trackWidth: 1350,
+    multiplier: 3, // a multiplier to fetch more data for smooth panning
+  };
+
+  // Create stores to hold browser data
+  const browserStore = createBrowserStore(initialState)
+  const trackStore = createTrackStore(initialTracks)
+
+  return (
+    <div style={{ width: "90%", margin: "0 auto" }}>
+      <h1>My Genome Browser</h1>
+      <DomainDisplay browserStore={browserStore} />
+      <Browser browserStore={browserStore} trackStore={trackStore} />
+    </div>
+  );
+}
+
+// Use the stores to access information
+function DomainDisplay({browserStore} : {browserStore: BrowserStoreInstance}) {
+  // Zustand-like selectors for getting fields and functions
+  const domain = browserStore((state) => state.domain)
+  return (
+    <h1>{domain.chromosome}:{domain.start}-{domain.end}</h1>
+  )
+}
+
+```
+
+## Browser Configuration
+
+### State Example
+
+```tsx
+const initialState: InitialBrowserState = {
+  domain: {
+    chromosome: "chr1",
+    start: 1000000,
+    end: 2000000,
+  },
+  marginWidth: 150, // Width of the track margins
+  trackWidth: 1350, // Width of the viewable track area
+  multiplier: 3, // Data fetching multiplier for smooth panning
+  highlights: [
+    // Optional: initial highlights
+    {
+      id: "highlight1",
+      color: "#ffaabb",
+      domain: { chromosome: "chr1", start: 1500000, end: 1600000 },
+    },
+  ],
+};
+```
+
+## Track Examples
+
+### BigWig Tracks
+
+Display continuous signal data (e.g., ChIP-seq, RNA-seq signals).
+
+```tsx
+{
+  id: "signal",
+  title: "Signal Data",
+  trackType: TrackType.BigWig,
+  displayMode: DisplayMode.Full, // Multiple display modes supported
+  height: 100,
+  color: "#3498db",
+  url: "https://example.com/signal.bw",
+}
+```
+
+### BigBed Tracks
+
+Display discrete genomic regions (e.g., peaks, annotations).
+
+```tsx
+{
+  id: "peaks",
+  title: "Peak Calls",
+  trackType: TrackType.BigBed,
+  displayMode: DisplayMode.Dense,
+  height: 20,
+  color: "#e74c3c",
+  url: "https://example.com/peaks.bigBed",
+  onClick: (rect) => console.log("Clicked:", rect), // Mouse interactivitiy
+  onHover: (rect) => console.log("Hovered:", rect),
+  tooltip: (rect) => <text>{rect.name}</text>, // Custom svg tooltips
+}
+```
+
+### BulkBed Tracks
+
+Display multiple BigBed datasets in a single track.
+
+```tsx
+{
+  id: "bulk-data",
+  title: "Multiple Datasets",
+  trackType: TrackType.BulkBed,
+  displayMode: DisplayMode.Full,
+  height: 40,
+  gap: 2, // Gap between datasets
+  color: "#9b59b6",
+  datasets: [
+    { name: "Dataset 1", url: "https://example.com/data1.bigBed" },
+    { name: "Dataset 2", url: "https://example.com/data2.bigBed" },
+  ],
+}
+```
+
+### Transcript Tracks
+
+Display gene annotations and transcripts.
+
+```tsx
+{
+  id: "genes",
+  title: "Gene Annotations",
+  trackType: TrackType.Transcript,
+  displayMode: DisplayMode.Squish,
+  height: 50,
+  color: "#2ecc71",
+  assembly: "GRCh38", // "mm10" also supported
+  version: 47, // GENCODE version
+}
+```
+
+Explore our comprehensive [Storybook]() documentation for detailed information about additional track types and their configuration options.
+
+## Development
+
+```bash
+# Install dependencies
+npm install
+
+# Start development server
+npm run dev
+
+# Run Storybook for component development
+npm run storybook
+
+# Build for production
+npm run build
+
+# Run linting
+npm run lint
+```
+
+## Contributing
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Add tests if applicable
+5. Submit a pull request
+
+## License
+
+MIT License - see LICENSE file for details.
+
+## Support
+
+For questions and support, please open an issue on GitHub.

package/dist/api/queryExecutor.d.ts

@@ -7,7 +7,6 @@ export interface QueryExecutors {
     fetchImportance: LazyQueryExecFunction<unknown, OperationVariables>;
     fetchBulkBed: LazyQueryExecFunction<unknown, OperationVariables>;
     fetchMethylC: LazyQueryExecFunction<unknown, OperationVariables>;
-    fetchLD: LazyQueryExecFunction<unknown, OperationVariables>;
 }
 /**
  * Execute all queries concurrently based on built requests

package/dist/api/requestBuilder.d.ts

@@ -1,13 +1,12 @@
 import { Domain } from '../utils/types';
 import { Track } from '../store/trackStore';
-import { BigRequest, TranscriptRequest, MotifRequest, LDRequest } from './apiTypes';
+import { BigRequest, TranscriptRequest, MotifRequest } from './apiTypes';
 export interface AllRequests {
     bigRequests: BigRequest[];
     transcriptRequest?: TranscriptRequest;
     motifRequest?: MotifRequest;
     importanceRequests: BigRequest[];
     bulkBedRequests: BigRequest[];
-    ldRequest?: LDRequest;
     methylCRequest?: BigRequest[];
 }
 /**
@@ -34,7 +33,6 @@ export declare function buildImportanceRequests(tracks: Track[], currentDomain:
 /**
  * Build LD request for given tracks (first LD track found)
  */
-export declare function buildLDRequest(tracks: Track[], _: Domain): LDRequest | undefined;
 export declare function buildMethylCRequest(tracks: Track[], domain: Domain, preRenderedWidth: number): BigRequest[] | undefined;
 /**
  * Build all requests for all track types in one coordinated call

package/dist/components/tracks/ldtrack/types.d.ts

@@ -1,7 +1,6 @@
 import { Config, TrackDimensions, TrackType } from '../types';
 export interface LDTrackConfig extends Config<any> {
     trackType: TrackType.LDTrack;
-    study: string[];
     show?: string[];
 }
 export type LDProps = {