higlass 2.2.1 → 2.2.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. package/app/missing-types.d.ts +6 -0
  2. package/app/scripts/HiGlassComponent.jsx +1 -1
  3. package/app/scripts/TiledPixiTrack.js +4 -4
  4. package/app/scripts/TiledPlot.jsx +1 -1
  5. package/app/scripts/hglib.jsx +20 -0
  6. package/app/scripts/utils/tile-to-canvas.js +1 -1
  7. package/dist/app/scripts/TiledPixiTrack.d.ts +5 -7
  8. package/dist/app/scripts/data-fetchers/DataFetcher.d.ts +0 -1
  9. package/dist/app/scripts/hglib.d.ts +2 -0
  10. package/dist/app/scripts/utils/tile-to-canvas.d.ts +2 -2
  11. package/dist/esm.html +1 -0
  12. package/dist/hglib.js +37408 -36581
  13. package/dist/hglib.min.js +95 -111
  14. package/dist/higlass.mjs +37599 -36772
  15. package/dist/package.json +7 -16
  16. package/dist/shadow-dom.html +242 -0
  17. package/package.json +7 -16
package/dist/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "higlass",
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- "version": "2.2.1",
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+ "version": "2.2.3",
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  "description": "HiGlass Hi-C / genomic / large data viewer",
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  "author": "Peter Kerpedjiev <pkerpedjiev@gmail.com>",
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  "main": "dist/hglib.js",
@@ -15,16 +15,8 @@
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  },
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  "./dist/*": "./dist/*"
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  },
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- "files": [
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- "app",
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- "dist"
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- ],
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- "keywords": [
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- "hi-c",
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- "genomics",
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- "matrix",
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- "tracks"
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- ],
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+ "files": ["app", "dist"],
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+ "keywords": ["hi-c", "genomics", "matrix", "tracks"],
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  "scripts": {
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  "start": "vite",
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  "build": "tsc -p tsconfig.emit.json && node ./scripts/build.mjs",
@@ -112,7 +104,7 @@
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  "@types/prop-types": "^15.7.3",
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  "@types/react": "^17.0.2",
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  "@types/react-dom": "^17.0.2",
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- "@vitejs/plugin-react": "^4.2.0",
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+ "@vitejs/plugin-react": "^5.1.4",
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  "@vitest/browser": "^3.0.5",
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  "@wojtekmaj/enzyme-adapter-react-17": "^0.6.7",
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  "ajv-cli": "^5.0.0",
@@ -125,10 +117,9 @@
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  "react": "^17.0.2",
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  "react-dom": "^17.0.2",
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  "sass": "^1.89.2",
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- "typescript": "^5.7.3",
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- "vite": "^5.0.3",
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- "vite-plugin-babel": "^1.1.3",
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- "vite-plugin-css-injected-by-js": "^3.3.0",
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+ "typescript": "^5.9.3",
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+ "vite": "^7.3.1",
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+ "vite-plugin-babel": "^1.5.1",
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  "vitest": "^3.0.5"
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  }
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  }
package/dist/shadow-dom.html ADDED
@@ -0,0 +1,242 @@
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta charset="utf-8">
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+ <meta name="viewport" content="width=device-width,initial-scale=1">
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+ <title>HiGlass — Shadow DOM</title>
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+ <script type="importmap">
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+ {
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+ "imports": {
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+ "react": "https://esm.sh/react@17",
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+ "react-dom": "https://esm.sh/react-dom@17",
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+ "pixi.js": "https://esm.sh/pixi.js@6"
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+ }
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+ }
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+ </script>
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+ <style type="text/css">
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+ #demo {
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+ position: absolute;
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+ left: 1rem;
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+ top: 1rem;
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+ bottom: 1rem;
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+ right: 1rem;
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+ overflow: hidden;
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+ }
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+ </style>
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+ </head>
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+
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+ <body>
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+ <div id="demo"></div>
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+ </body>
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+
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+ <script type="module">
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+ import { viewer, CSS } from "./higlass.mjs";
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+
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+ // Set up shadow root on #demo
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+ const demo = document.getElementById('demo');
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+ const shadow = demo.attachShadow({ mode: 'open' });
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+
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+ const style = document.createElement('style');
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+ style.textContent = CSS;
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+ shadow.appendChild(style);
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+
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+ const container = document.createElement('div');
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+ container.style.cssText = 'width:800px;height:600px';
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+ shadow.appendChild(container);
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+
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+ const viewConfig = {
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+ zoomFixed: false,
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+ views: [
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+ {
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+ layout: { w: 12, h: 7, x: 0, y: 0 },
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+ uid: 'aa',
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+ initialYDomain: [2534823997.9776945, 2547598956.834603],
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+ initialXDomain: [2521015726.4619913, 2558682921.8435397],
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+ tracks: {
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+ left: [],
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+ top: [
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+ {
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+ uid: 'genes',
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+ tilesetUid: 'OHJakQICQD6gTD7skx4EWA',
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-gene-annotations',
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+ height: 48,
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+ options: {
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+ labelColor: 'black',
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+ plusStrandColor: 'black',
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+ labelPosition: 'hidden',
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+ minusStrandColor: 'black',
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+ fontSize: 11,
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ geneAnnotationHeight: 10,
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+ geneLabelPosition: 'outside',
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+ geneStrandSpacing: 4
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+ },
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+ },
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+ {
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+ uid: 'line1',
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+ tilesetUid: 'PjIJKXGbSNCalUZO21e_HQ',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: '#4a35fc',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ }
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+ },
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+ {
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+ uid: 'line2',
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+ tilesetUid: 'PdAaSdibTLK34hCw7ubqKA',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: '#d104fa',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ },
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+ },
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+ {
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+ uid: 'line3',
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+ tilesetUid: 'e0DYtZBSTqiMLHoaimsSpg',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: '#ff0000',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ },
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+ },
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+ {
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+ uid: 'line4',
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+ tilesetUid: 'cE0nGyd0Q_yVYSyBUe89Ww',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: 'orange',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ },
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+ },
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+ {
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+ uid: 'chroms',
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+ height: 18,
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+ chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv',
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+ type: 'horizontal-chromosome-labels',
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+ options: {
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+ color: '#777777',
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+ stroke: '#FFFFFF',
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+ fontSize: 11,
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+ fontIsLeftAligned: true,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000'
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+ },
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+ }
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+ ],
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+ right: [],
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+ center: [
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+ {
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+ uid: 'center',
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+ type: 'combined',
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+ contents: [
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+ {
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+ server: 'http://higlass.io/api/v1',
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+ tilesetUid: 'dVBREuC2SvO01uXYMUh2aQ',
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+ type: 'heatmap',
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+ uid: 'Yqetzqw6Qfy-hREAJhAXEA',
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+ options: {
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+ backgroundColor: '#eeeeee',
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+ labelPosition: 'topLeft',
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+ labelTextOpacity: 0.4,
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+ colorRange: [
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+ 'white',
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+ 'rgba(245,166,35,1.0)',
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+ 'rgba(208,2,27,1.0)',
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+ 'black'
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+ ],
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+ maxZoom: null,
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+ colorbarPosition: 'topRight',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ heatmapValueScaling: 'log',
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: true,
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+ scaleStartPercent: '0.00000',
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+ scaleEndPercent: '1.00000',
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+ showMousePositionGlobally: true,
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+ },
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+ }
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+ ],
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+ }
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+ ],
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+ bottom: [],
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+ whole: [],
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+ gallery: []
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+ },
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+ chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv',
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+ genomePositionSearchBox: {
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+ visible: true,
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+ chromInfoServer: 'http://higlass.io/api/v1',
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+ chromInfoId: 'hg19',
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+ autocompleteServer: 'http://higlass.io/api/v1',
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+ autocompleteId: 'OHJakQICQD6gTD7skx4EWA'
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+ }
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+ }
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+ ],
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+ editable: true,
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+ viewEditable: true,
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+ tracksEditable: true,
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+ exportViewUrl: '/api/v1/viewconfs',
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+ trackSourceServers: ['http://higlass.io/api/v1'],
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+ };
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+
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+ const hgApi = window.hgApi = await viewer(
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+ container,
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+ viewConfig,
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+ { bounded: true },
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+ );
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+ </script>
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+ </html>
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "higlass",
3
- "version": "2.2.1",
3
+ "version": "2.2.3",
4
4
  "description": "HiGlass Hi-C / genomic / large data viewer",
5
5
  "author": "Peter Kerpedjiev <pkerpedjiev@gmail.com>",
6
6
  "main": "dist/hglib.js",
@@ -15,16 +15,8 @@
15
15
  },
16
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  "./dist/*": "./dist/*"
17
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  },
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- "files": [
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- "app",
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- "dist"
21
- ],
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- "keywords": [
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- "hi-c",
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- "genomics",
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- "matrix",
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- "tracks"
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- ],
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+ "files": ["app", "dist"],
19
+ "keywords": ["hi-c", "genomics", "matrix", "tracks"],
28
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  "scripts": {
29
21
  "start": "vite",
30
22
  "build": "tsc -p tsconfig.emit.json && node ./scripts/build.mjs",
@@ -112,7 +104,7 @@
112
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  "@types/prop-types": "^15.7.3",
113
105
  "@types/react": "^17.0.2",
114
106
  "@types/react-dom": "^17.0.2",
115
- "@vitejs/plugin-react": "^4.2.0",
107
+ "@vitejs/plugin-react": "^5.1.4",
116
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  "@vitest/browser": "^3.0.5",
117
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  "@wojtekmaj/enzyme-adapter-react-17": "^0.6.7",
118
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  "ajv-cli": "^5.0.0",
@@ -125,10 +117,9 @@
125
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  "react": "^17.0.2",
126
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  "react-dom": "^17.0.2",
127
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  "sass": "^1.89.2",
128
- "typescript": "^5.7.3",
129
- "vite": "^5.0.3",
130
- "vite-plugin-babel": "^1.1.3",
131
- "vite-plugin-css-injected-by-js": "^3.3.0",
120
+ "typescript": "^5.9.3",
121
+ "vite": "^7.3.1",
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+ "vite-plugin-babel": "^1.5.1",
132
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  "vitest": "^3.0.5"
133
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  }
134
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  }