@weng-lab/genomebrowser 0.0.2 → 0.0.4

package/README.md

@@ -1,50 +1,125 @@
-# React + TypeScript + Vite
-
-This template provides a minimal setup to get React working in Vite with HMR and some ESLint rules.
-
-Currently, two official plugins are available:
-
-- [@vitejs/plugin-react](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react/README.md) uses [Babel](https://babeljs.io/) for Fast Refresh
-- [@vitejs/plugin-react-swc](https://github.com/vitejs/vite-plugin-react-swc) uses [SWC](https://swc.rs/) for Fast Refresh
-
-## Expanding the ESLint configuration
-
-If you are developing a production application, we recommend updating the configuration to enable type aware lint rules:
-
-- Configure the top-level `parserOptions` property like this:
-
-```js
-export default tseslint.config({
-  languageOptions: {
-    // other options...
-    parserOptions: {
-      project: ['./tsconfig.node.json', './tsconfig.app.json'],
-      tsconfigRootDir: import.meta.dirname,
-    },
-  },
-})
-```
-
-- Replace `tseslint.configs.recommended` to `tseslint.configs.recommendedTypeChecked` or `tseslint.configs.strictTypeChecked`
-- Optionally add `...tseslint.configs.stylisticTypeChecked`
-- Install [eslint-plugin-react](https://github.com/jsx-eslint/eslint-plugin-react) and update the config:
-
-```js
-// eslint.config.js
-import react from 'eslint-plugin-react'
-
-export default tseslint.config({
-  // Set the react version
-  settings: { react: { version: '18.3' } },
-  plugins: {
-    // Add the react plugin
-    react,
-  },
-  rules: {
-    // other rules...
-    // Enable its recommended rules
-    ...react.configs.recommended.rules,
-    ...react.configs['jsx-runtime'].rules,
-  },
-})
-```
+# Genome Browser Component Library
+
+## Installation
+`yarn add @weng-lab/genomebrowser`
+
+`npm install @weng-lab/genomebrowser`
+
+## Usage
+
+The library revolves around creating tracks and adding them to the browser. To do this, first you import the Genome Browser component, creating the browser state and dispatch function, and adding your tracks to the state. Then you pass the state and dispatch function to the GenomeBrowser component as props.
+
+### Walkthrough
+First, import the Genome Browser component:
+```tsx
+import { GenomeBrowser } from '@weng-lab/genomebrowser';
+```
+Then you create the browser state and dispatch function with the `useBrowserState` hook:
+
+```tsx
+import { useBrowserState } from '@weng-lab/genomebrowser';
+const [browserState, browserDispatch] = useBrowserState({
+  domain: { chromosome: "chr11", start: 5220000, end: 5420000 },
+  preRenderedWidth: 1350,
+  width: 1500,
+  zoomLevel: 148,
+  delta: 0,
+  tracks: []
+});
+```
+
+There are a few ways to add tracks to the browser.
+1. You can add a track by dispatching the `ADD_TRACK` action:
+```tsx
+import { BigWigTrackProps } from '@weng-lab/genomebrowser';
+const myBigWig: BigWigTrackProps = { ... }
+browserDispatch({ type: BrowserActionType.ADD_TRACK, track: myBigWig });
+```
+2. You can add a track by passing a track component as a child to the GenomeBrowser component:
+```tsx
+import { BigBedTrack } from '@weng-lab/genomebrowser';
+<GenomeBrowser browserState={browserState} browserDispatch={browserDispatch}>
+    <BigBedTrack ... />
+</GenomeBrowser>
+```
+3. You can also add a track by appending it to the 'tracks' array in the browser state:
+```tsx
+import { BigWigTrackProps, BrowserState } from '@weng-lab/genomebrowser';
+const myBigWig: BigWigTrackProps = { ... }
+const myState: BrowserState = {
+    domain: { chromosome: "chr11", start: 5220000, end: 5420000 },
+    ... // initialize the rest of the state
+    tracks: [myBigWig] // add the track to the state
+}
+```
+
+## Full Example
+
+```tsx
+// in trackExamples.ts
+export const bigWigExample: BigWigTrackProps = {
+    ...DefaultBigWig,
+    id: "1",
+    title: "bigwig",
+    height: 100,
+    url: "https://downloads.wenglab.org/DNAse_All_ENCODE_MAR20_2024_merged.bw",
+    color: "blue"
+}
+export const bigBedExample: BigBedTrackProps = {
+    ...DefaultBigBed,
+    id: "2",
+    title: "bigbed",
+    height: 75,
+    rowHeight: 12,
+    color: "red",
+    url: "https://downloads.wenglab.org/GRCh38-cCREs.DCC.bigBed"
+}
+export const transcriptExample: TranscriptTrackProps = {
+    ...DefaultTranscript,
+    id: "3",
+    title: "transcript",
+    rowHeight: 12,
+    assembly: "GRCh38",
+    queryType: "gene",
+    version: TranscriptHumanVersion.V47,
+    height: 100,
+    color: "green"
+}
+```
+
+```tsx
+// in main.tsx
+import { useEffect } from 'react'
+import {
+    GenomeBrowser, BrowserState, BrowserActionType, useBrowserState,
+    BigBedTrack
+} from '../lib'
+import { bigWigExample, bigBedExample, transcriptExample } from './trackExamples'
+
+const defaultState: BrowserState = {
+    domain: { chromosome: "chr11", start: 5220000, end: 5420000 },
+    preRenderedWidth: 1350,
+    width: 1500,
+    zoomLevel: 148,
+    delta: 0,
+    tracks: [bigWigExample] // adds a BigWig track to the state
+}
+
+function Main() {
+    const [browserState, browserDispatch] = useBrowserState(defaultState)
+
+    useEffect(() => {
+        // add a Transcript track to the state
+        browserDispatch({ type: BrowserActionType.ADD_TRACK, track: transcriptExample })
+    }, [])
+
+    return (
+        <GenomeBrowser browserState={browserState} browserDispatch={browserDispatch}>
+            <BigBedTrack {...bigBedExample} /> // add a BigBed track to the browser
+        </GenomeBrowser>
+    )
+}
+```
+
+The browser will look something like this:
+![Browser Example](image.png)

package/dist/components/context/domainContext.d.ts

@@ -1,9 +1,8 @@
 import { Domain } from '../../utils/types';
-type stateContext<T> = [
-    T,
-    React.Dispatch<React.SetStateAction<T>>
-];
+export type DeltaContextType = {
+    delta: number;
+    setDelta: (delta: number) => void;
+};
 export declare const DomainContext: import('react').Context<Domain>;
 export declare const DomainDispatchContext: import('react').Context<any>;
-export declare const DeltaContext: import('react').Context<stateContext<number>>;
-export {};
+export declare const DeltaContext: import('react').Context<DeltaContextType>;

package/dist/components/context/providers.d.ts

@@ -1,6 +1,7 @@
 import { ReactNode } from 'react';
 import { BrowserState, BrowserAction } from './browserContext';
 import { TrackModalInfo } from '../../hooks/useModal';
+import { DeltaContextType } from './domainContext';
 export declare const ModalContext: import('react').Context<{
     openModal: TrackModalInfo | null;
     showModal: (trackId: string, mouseX: number, mouseY: number) => void;
@@ -10,7 +11,7 @@ interface ContextObjects {
     children: ReactNode;
     browserState: BrowserState;
     browserDispatch: React.Dispatch<BrowserAction>;
-    deltaContext: [number, React.Dispatch<React.SetStateAction<number>>];
+    deltaContext: DeltaContextType;
     modalState: {
         openModal: TrackModalInfo | null;
         showModal: (trackId: string, mouseX: number, mouseY: number) => void;

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

@@ -1,7 +1,5 @@
 import { default as React } from 'react';
 import { Domain } from '../../../utils/types';
-export declare const humanVersions: number[];
-export declare const mouseVersions: number[];
 export interface GenomicElement {
     coordinates: Domain;
 }

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

@@ -51,14 +51,14 @@ export type BigBedTrackProps = {
     props?: BigBedOptions;
 } & BaseTrack;
 export declare enum TranscriptHumanVersion {
-    V47 = 47,
-    V48 = 48,
-    V29 = 29
+    V29 = 29,
+    V40 = 40,
+    V47 = 47
 }
 export declare enum TranscriptMouseVersion {
-    V36 = 36,
+    V21 = 21,
     V25 = 25,
-    V21 = 21
+    V36 = 36
 }
 export declare function TranscriptTrack(_: TranscriptTrackProps): null;
 export type TranscriptTrackProps = {