Merge pull request #2534 from GMOD/add-arc-plugin

New display type for drawing arcs

packages/core/util/jexl.ts

@@ -42,6 +42,7 @@ export default function (/* config?: any*/): JexlNonBuildable {
   j.addFunction('floor', Math.floor)
   j.addFunction('round', Math.round)
   j.addFunction('abs', Math.abs)
+  j.addFunction('log10', Math.log10)
   j.addFunction('parseInt', Number.parseInt)
   j.addFunction('parseFloat', Number.parseFloat)
 

plugins/arc/package.json

@@ -0,0 +1,53 @@
+{
+  "name": "@jbrowse/plugin-arc",
+  "version": "1.5.1",
+  "description": "JBrowse 2 arc adapters, tracks, etc.",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "plugins/arc"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "srcMain": "src/index.ts",
+  "main": "src/index.ts",
+  "distModule": "dist/plugin-arc.esm.js",
+  "module": "",
+  "files": [
+    "dist",
+    "src"
+  ],
+  "scripts": {
+    "start": "tsdx watch --verbose --noClean",
+    "build": "tsdx build",
+    "test": "cd ../..; jest plugins/arc",
+    "prepublishOnly": "yarn test",
+    "prepack": "yarn build; yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js"
+  },
+  "dependencies": {
+    "react-svg-tooltip": "^0.0.11"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^1.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
+    "@jbrowse/plugin-wiggle": "^1.0.0",
+    "@material-ui/core": "^4.12.2",
+    "mobx": "^5.10.1",
+    "mobx-react": "^6.0.0",
+    "mobx-state-tree": "3.14.1",
+    "prop-types": "^15.0.0",
+    "react": ">=16.8.0",
+    "rxjs": "^6.0.0"
+  },
+  "private": true
+}

plugins/arc/src/ArcRenderer/ArcRenderer.tsx

@@ -0,0 +1,3 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
+
+export default class extends FeatureRendererType {}

plugins/arc/src/ArcRenderer/ArcRendering.test.tsx

@@ -0,0 +1,45 @@
+import SimpleFeature from '@jbrowse/core/util/simpleFeature'
+import React from 'react'
+import { render } from '@testing-library/react'
+import Rendering from './ArcRendering'
+
+test('no features', () => {
+  const { container } = render(
+    <Rendering
+      width={500}
+      height={500}
+      regions={[{ refName: 'zonk', start: 0, end: 300 }]}
+      blockKey={1}
+      config={{}}
+      bpPerPx={3}
+      displayModel={{}}
+      features={new Map()}
+    />,
+  )
+
+  expect(container.firstChild).toMatchSnapshot()
+})
+
+test('one feature', () => {
+  const { container } = render(
+    <Rendering
+      width={500}
+      height={500}
+      regions={[{ refName: 'zonk', start: 0, end: 1000 }]}
+      blockKey={1}
+      features={
+        new Map([
+          [
+            'one',
+            new SimpleFeature({ uniqueId: 'one', score: 10, start: 1, end: 3 }),
+          ],
+        ])
+      }
+      config={{ type: 'DummyRenderer' }}
+      bpPerPx={3}
+      displayModel={{}}
+    />,
+  )
+
+  expect(container.firstChild).toMatchSnapshot()
+})

plugins/arc/src/ArcRenderer/ArcRendering.tsx

@@ -0,0 +1,131 @@
+import React from 'react'
+import { readConfObject } from '@jbrowse/core/configuration'
+import { bpSpanPx, measureText } from '@jbrowse/core/util'
+import { observer } from 'mobx-react'
+import { Tooltip } from 'react-svg-tooltip'
+
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function ArcRendering(props: any) {
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  const onClick = (event: any, id: any) => {
+    const { onFeatureClick: handler } = props
+    if (!handler) {
+      return undefined
+    }
+    return handler(event, id)
+  }
+
+  const {
+    features,
+    config,
+    regions,
+    blockKey,
+    bpPerPx,
+    displayModel: { selectedFeatureId },
+  } = props
+  const [region] = regions
+  const arcsRendered = []
+
+  for (const feature of features.values()) {
+    const [left, right] = bpSpanPx(
+      feature.get('start'),
+      feature.get('end'),
+      region,
+      bpPerPx,
+    )
+
+    const featureId = feature.id()
+    const id = blockKey + '-' + featureId
+    let stroke = readConfObject(config, 'color', { feature })
+    let textStroke = 'black'
+    if (
+      selectedFeatureId &&
+      String(selectedFeatureId) === String(feature.id())
+    ) {
+      stroke = textStroke = 'red'
+    }
+    const label = readConfObject(config, 'label', { feature })
+    const caption = readConfObject(config, 'caption', { feature })
+    const strokeWidth = readConfObject(config, 'thickness', { feature }) || 1
+    const height = readConfObject(config, 'height', { feature }) || 100
+    const ref = React.createRef<SVGPathElement>()
+    const tooltipWidth = 20 + measureText(caption?.toString())
+
+    const t = 0.5
+    // formula: https://en.wikipedia.org/wiki/B%C3%A9zier_curve#Cubic_B%C3%A9zier_curves
+    const textYCoord =
+      (1 - t) * (1 - t) * (1 - t) * 0 +
+      3 * ((1 - t) * (1 - t)) * (t * height) +
+      3 * (1 - t) * (t * t) * height +
+      t * t * t * 0
+
+    arcsRendered.push(
+      <g key={id} onClick={e => onClick(e, featureId)}>
+        <path
+          id={id}
+          d={`M ${left} 0 C ${left} ${height}, ${right} ${height}, ${right} 0`}
+          stroke={stroke}
+          strokeWidth={strokeWidth}
+          fill="transparent"
+          onClick={e => onClick(e, featureId)}
+          ref={ref}
+          pointerEvents="stroke"
+        />
+        <Tooltip triggerRef={ref}>
+          <rect
+            x={12}
+            y={0}
+            width={tooltipWidth}
+            height={20}
+            rx={5}
+            ry={5}
+            fill="black"
+            fillOpacity="50%"
+          />
+          <text
+            x={22}
+            y={14}
+            fontSize={10}
+            fill="white"
+            textLength={tooltipWidth - 20}
+          >
+            {caption}
+          </text>
+        </Tooltip>
+        <text
+          x={left + (right - left) / 2}
+          y={textYCoord + 3}
+          style={{ stroke: 'white', strokeWidth: '0.6em' }}
+        >
+          {label}
+        </text>
+        <text
+          x={left + (right - left) / 2}
+          y={textYCoord + 3}
+          style={{ stroke: textStroke }}
+        >
+          {label}
+        </text>
+      </g>,
+    )
+  }
+
+  const width = (region.end - region.start) / bpPerPx
+  const height = 500
+
+  return (
+    <svg
+      className="ArcRendering"
+      width={width}
+      height={height}
+      style={{
+        outline: 'none',
+        position: 'relative',
+      }}
+    >
+      {arcsRendered}
+    </svg>
+  )
+}
+
+export default observer(ArcRendering)

plugins/arc/src/ArcRenderer/__snapshots__/ArcRendering.test.tsx.snap

@@ -0,0 +1,40 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`no features 1`] = `
+<svg
+  class="ArcRendering"
+  height="500"
+  style="outline: none; position: relative;"
+  width="100"
+/>
+`;
+
+exports[`one feature 1`] = `
+<svg
+  class="ArcRendering"
+  height="500"
+  style="outline: none; position: relative;"
+  width="333.3333333333333"
+>
+  <g>
+    <path
+      d="M 0.3 0 C 0.3 100, 1 100, 1 0"
+      fill="transparent"
+      id="1-one"
+      pointer-events="stroke"
+      stroke-width="1"
+    />
+    <g />
+    <text
+      style="stroke: white; stroke-width: 0.6em;"
+      x="0.6499999999999999"
+      y="78"
+    />
+    <text
+      style="stroke: black;"
+      x="0.6499999999999999"
+      y="78"
+    />
+  </g>
+</svg>
+`;

plugins/arc/src/ArcRenderer/configSchema.tsx

@@ -0,0 +1,36 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default ConfigurationSchema(
+  'ArcRenderer',
+  {
+    color: {
+      type: 'color',
+      description: 'the color of the arcs',
+      defaultValue: 'darkblue',
+    },
+    thickness: {
+      type: 'number',
+      description: 'the thickness of the arcs',
+      defaultValue: `jexl:logThickness(feature,'score')`,
+    },
+    label: {
+      type: 'string',
+      description: 'the label to appear at the apex of the arcs',
+      defaultValue: `jexl:get(feature,'score')`,
+      contextVariable: ['feature'],
+    },
+    height: {
+      type: 'number',
+      description: 'the height of the arcs',
+      defaultValue: `jexl:log10(get(feature,'end')-get(feature,'start'))*50`,
+    },
+    caption: {
+      type: 'string',
+      description:
+        'the caption to appear when hovering over any point on the arcs',
+      defaultValue: `jexl:get(feature,'name')`,
+      contextVariable: ['feature'],
+    },
+  },
+  { explicitlyTyped: true },
+)

plugins/arc/src/ArcRenderer/index.tsx

@@ -0,0 +1,3 @@
+export { default as ReactComponent } from './ArcRendering'
+export { default as configSchema } from './configSchema'
+export { default } from './ArcRenderer'

plugins/arc/src/LinearArcDisplay/configSchema.tsx

@@ -0,0 +1,24 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { types } from 'mobx-state-tree'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export function configSchemaFactory(pluginManager: PluginManager) {
+  const LGVPlugin = pluginManager.getPlugin(
+    'LinearGenomeViewPlugin',
+  ) as import('@jbrowse/plugin-linear-genome-view').default
+  // @ts-ignore
+  const { baseLinearDisplayConfigSchema } = LGVPlugin.exports
+  return ConfigurationSchema(
+    'LinearArcDisplay',
+    {
+      renderer: types.optional(
+        pluginManager.pluggableConfigSchemaType('renderer'),
+        { type: 'ArcRenderer' },
+      ),
+    },
+    {
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
+    },
+  )
+}

plugins/arc/src/LinearArcDisplay/index.tsx

@@ -0,0 +1,2 @@
+export { configSchemaFactory } from './configSchema'
+export { stateModelFactory } from './model'