@weng-lab/genomebrowser 0.0.2 → 0.0.3

package/README.md

@@ -1,50 +1,125 @@
-# React + TypeScript + Vite
+# Genome Browser Component Library
 
-This template provides a minimal setup to get React working in Vite with HMR and some ESLint rules.
+## Installation
+`yarn add @weng-lab/genomebrowser`
 
-Currently, two official plugins are available:
+`npm install @weng-lab/genomebrowser`
 
-- [@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
+## Usage
 
-## Expanding the ESLint configuration
+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.
 
-If you are developing a production application, we recommend updating the configuration to enable type aware lint rules:
+### 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
+}
+```
 
-- Configure the top-level `parserOptions` property like this:
+## Full Example
 
-```js
-export default tseslint.config({
-  languageOptions: {
-    // other options...
-    parserOptions: {
-      project: ['./tsconfig.node.json', './tsconfig.app.json'],
-      tsconfigRootDir: import.meta.dirname,
-    },
-  },
-})
+```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"
+}
 ```
 
-- 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,
-  },
-})
+```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/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@weng-lab/genomebrowser",
   "private": false,
-  "version": "0.0.2",
+  "version": "0.0.3",
   "repository": {
     "type": "git",
     "url": "git+https://github.com/weng-lab/genomebrowser.git"