npm - jbrowse-plugin-gwas - Versions diffs - 1.0.3 → 1.0.4 - Mend

jbrowse-plugin-gwas 1.0.3 → 1.0.4

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Files changed (22) hide show

package/CHANGELOG.md +4 -0
package/README.md +12 -67
package/dist/LinearManhattanDisplay/configSchemaFactory.d.ts +2 -0
package/dist/LinearManhattanDisplay/index.d.ts +2 -1
package/dist/LinearManhattanRenderer/index.d.ts +1 -1
package/dist/jbrowse-plugin-gwas.cjs.development.js +26 -25
package/dist/jbrowse-plugin-gwas.cjs.development.js.map +1 -1
package/dist/jbrowse-plugin-gwas.cjs.production.min.js +1 -1
package/dist/jbrowse-plugin-gwas.cjs.production.min.js.map +1 -1
package/dist/jbrowse-plugin-gwas.esm.js +22 -21
package/dist/jbrowse-plugin-gwas.esm.js.map +1 -1
package/dist/jbrowse-plugin-gwas.umd.development.js +28 -29
package/dist/jbrowse-plugin-gwas.umd.development.js.map +1 -1
package/dist/jbrowse-plugin-gwas.umd.production.min.js +1 -1
package/dist/jbrowse-plugin-gwas.umd.production.min.js.map +1 -1
package/package.json +1 -1
package/src/LinearManhattanDisplay/configSchemaFactory.ts +64 -0
package/src/LinearManhattanDisplay/index.ts +4 -66
package/src/LinearManhattanRenderer/LinearManhattanRenderer.ts +1 -2
package/src/LinearManhattanRenderer/index.ts +14 -0
package/src/index.ts +8 -15
package/src/LinearManhattanRenderer/index.js +0 -19

package/CHANGELOG.md CHANGED Viewed

@@ -1,3 +1,7 @@
+# v1.0.4
+Make the code always try to render (never produce the force load)
 # v1.0.3
 - Fix for v1.1.0 of jbrowse-web requires passing pluginManager to renderer constructor

package/README.md CHANGED Viewed

@@ -1,89 +1,34 @@
-# `jbrowse-plugin-gwas` (work in progress)
+# jbrowse-plugin-gwas
 Plugin for displaying GWAS results such as manhattan plot renderings
-## Install
-### For use in [JBrowse Web](https://jbrowse.org/jb2/docs/quickstart_web)
-No installation required
-### For use in [`@jbrowse/react-linear-view`](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view)
-```
-yarn add jbrowse-plugin-gwas
-```
-## Usage
-### In [JBrowse Web](https://jbrowse.org/jb2/docs/quickstart_web)
-#### Development
-```
-git clone https://github.com/cmdcolin/jbrowse-plugin-gwas.git
-cd jbrowse-plugin-gwas
-yarn
-yarn start
-```
-Then open JBrowse Web to (assuming it is running on port 3000):
-http://localhost:3000/?config=http://localhost:9000/config.json
-#### Demo
+## Screenshot
-https://s3.amazonaws.com/jbrowse.org/code/jb2/master/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gwas%2Fdist%2Fconfig.json&session=share-iehjT6AoHd&password=lZS7v
+![](img/1.png)
+![](img/2.png)
-#### Production
+## Usage in jbrowse-web
-Add to the "plugins" of your JBrowse Web config:
+Add to the "plugins" of your JBrowse Web config. The unpkg CDN should be stable, or you can download the js file to your server
 ```json
 {
   "plugins": [
     {
-      "name": "gwas",
+      "name": "GWAS",
       "url": "https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js"
     }
   ]
 }
 ```
-### In [`@jbrowse/react-linear-view`](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view)
+This plugin is currently quite basic, and there is no mouseover interactivity or drawn labels on features
-```tsx
-import React from "react";
-import "fontsource-roboto";
-import {
-  createViewState,
-  createJBrowseTheme,
-  JBrowseLinearGenomeView,
-  ThemeProvider,
-} from "@jbrowse/react-linear-view";
-import GWAS from "jbrowse-plugin-gwas";
+#### Demo
-const theme = createJBrowseTheme();
+https://jbrowse.org/code/jb2/main/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gwas%2Fdist%2Fconfig.json&session=share-iehjT6AoHd&password=lZS7v
-function View() {
-  const state = createViewState({
-    assembly: {
-      /* assembly */
-    },
-    tracks: [
-      /* tracks */
-    ],
-    plugins: [GWAS],
-  });
-  return (
-    <ThemeProvider theme={theme}>
-      <JBrowseLinearGenomeView viewState={state} />
-    </ThemeProvider>
-  );
-}
-```
-## Screenshot
+### For use in jbrowse/react-linear-genome-view
-![](img/1.png)
-![](img/2.png)
+See [DEVELOPMENT](DEVELOPMENT.md)

package/dist/LinearManhattanDisplay/configSchemaFactory.d.ts ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import PluginManager from "@jbrowse/core/PluginManager";
2	+ export declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;

package/dist/LinearManhattanDisplay/index.d.ts CHANGED Viewed

@@ -1,9 +1,10 @@
 import PluginManager from "@jbrowse/core/PluginManager";
-export declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export { configSchemaFactory } from "./configSchemaFactory";
 export declare function stateModelFactory(pluginManager: PluginManager, configSchema: any): import("mobx-state-tree").IModelType<import("mobx-state-tree").ModelProperties & {
     type: import("mobx-state-tree").ISimpleType<"LinearManhattanDisplay">;
 }, {
     readonly rendererTypeName: string;
     readonly needsScalebar: boolean;
+    readonly regionTooLarge: boolean;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export declare type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;

package/dist/LinearManhattanRenderer/index.d.ts CHANGED Viewed

@@ -1,2 +1,2 @@
-export function configSchemaFactory(pluginManager: any): any;
 export { default } from "./LinearManhattanRenderer";
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;

package/dist/jbrowse-plugin-gwas.cjs.development.js CHANGED Viewed

@@ -5,7 +5,10 @@ Object.defineProperty(exports, '__esModule', { value: true });
 function _interopDefault (ex) { return (ex && (typeof ex === 'object') && 'default' in ex) ? ex['default'] : ex; }
 var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
+var DisplayType = _interopDefault(require('@jbrowse/core/pluggableElementTypes/DisplayType'));
 var configuration = require('@jbrowse/core/configuration');
+var util = require('@jbrowse/core/util');
+var mobxStateTree = require('mobx-state-tree');
 function _classCallCheck(instance, Constructor) {
   if (!(instance instanceof Constructor)) {
@@ -275,7 +278,6 @@ function rendererFactory(pluginManager) {
   var _WigglePlugin$exports = WigglePlugin.exports,
       getScale = _WigglePlugin$exports.utils.getScale,
       WiggleBaseRenderer = _WigglePlugin$exports.WiggleBaseRenderer;
-  var featureSpanPx = pluginManager.lib["@jbrowse/core/util"].featureSpanPx;
   return /*#__PURE__*/function (_WiggleBaseRenderer) {
     _inherits(ManhattanPlotRenderer, _WiggleBaseRenderer);
@@ -323,7 +325,7 @@ function rendererFactory(pluginManager) {
           for (_iterator.s(); !(_step = _iterator.n()).done;) {
             var feature = _step.value;
-            var _featureSpanPx = featureSpanPx(feature, region, bpPerPx),
+            var _featureSpanPx = util.featureSpanPx(feature, region, bpPerPx),
                 _featureSpanPx2 = _slicedToArray(_featureSpanPx, 1),
                 leftPx = _featureSpanPx2[0];
@@ -356,30 +358,25 @@ function rendererFactory(pluginManager) {
   }(WiggleBaseRenderer);
 }
-function configSchemaFactory(pluginManager) {
-  var ConfigurationSchema = pluginManager.lib["@jbrowse/core/configuration"].ConfigurationSchema;
-  return ConfigurationSchema("LinearManhattanRenderer", {
-    color: {
-      type: "color",
-      description: "the color of the marks",
-      defaultValue: "darkblue"
-    }
-  }, {
-    explicitlyTyped: true
-  });
-}
+var configSchema = /*#__PURE__*/configuration.ConfigurationSchema("LinearManhattanRenderer", {
+  color: {
+    type: "color",
+    description: "the color of the marks",
+    defaultValue: "darkblue"
+  }
+}, {
+  explicitlyTyped: true
+});
-function configSchemaFactory$1(pluginManager) {
-  var types = pluginManager.lib["mobx-state-tree"].types;
-  var ConfigurationSchema = pluginManager.lib["@jbrowse/core/configuration"].ConfigurationSchema;
+function configSchemaFactory(pluginManager) {
   var LGVPlugin = pluginManager.getPlugin("LinearGenomeViewPlugin"); //@ts-ignore
   var baseLinearDisplayConfigSchema = LGVPlugin.exports.baseLinearDisplayConfigSchema;
-  return ConfigurationSchema("LinearManhattanDisplay", {
+  return configuration.ConfigurationSchema("LinearManhattanDisplay", {
     autoscale: {
       type: "stringEnum",
       defaultValue: "local",
-      model: types.enumeration("Autoscale type", ["global", "local", "globalsd", "localsd", "zscore"]),
+      model: mobxStateTree.types.enumeration("Autoscale type", ["global", "local", "globalsd", "localsd", "zscore"]),
       description: "global/local using their min/max values or w/ standard deviations (globalsd/localsd)"
     },
     minScore: {
@@ -399,7 +396,7 @@ function configSchemaFactory$1(pluginManager) {
     },
     scaleType: {
       type: "stringEnum",
-      model: types.enumeration("Scale type", ["linear", "log"]),
+      model: mobxStateTree.types.enumeration("Scale type", ["linear", "log"]),
       description: "The type of scale to use",
       defaultValue: "linear"
     },
@@ -410,7 +407,7 @@ function configSchemaFactory$1(pluginManager) {
     },
     defaultRendering: {
       type: "stringEnum",
-      model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
+      model: mobxStateTree.types.enumeration("Rendering", ["density", "xyplot", "line"]),
       defaultValue: "xyplot"
     }
   }, {
@@ -418,6 +415,7 @@ function configSchemaFactory$1(pluginManager) {
     explicitlyTyped: true
   });
 }
 function stateModelFactory(pluginManager, configSchema) {
   var types = pluginManager.lib["mobx-state-tree"].types;
   var WigglePlugin = pluginManager.getPlugin("WigglePlugin"); //@ts-ignore
@@ -433,6 +431,10 @@ function stateModelFactory(pluginManager, configSchema) {
       get needsScalebar() {
         return true;
+      },
+      get regionTooLarge() {
+        return false;
       }
     };
@@ -458,12 +460,11 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
     key: "install",
     value: function install(pluginManager) {
       var WigglePlugin = pluginManager.getPlugin("WigglePlugin");
-      var DisplayType = pluginManager.lib["@jbrowse/core/pluggableElementTypes/DisplayType"];
       var _WigglePlugin$exports = WigglePlugin.exports,
           LinearWiggleDisplayReactComponent = _WigglePlugin$exports.LinearWiggleDisplayReactComponent,
           XYPlotRendererReactComponent = _WigglePlugin$exports.XYPlotRendererReactComponent;
       pluginManager.addDisplayType(function () {
-        var configSchema = configSchemaFactory$1(pluginManager);
+        var configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
           name: "LinearManhattanDisplay",
           configSchema: configSchema,
@@ -476,11 +477,11 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
       pluginManager.addRendererType(function () {
         //@ts-ignore
         var ManhattanRenderer = new rendererFactory(pluginManager);
-        var configSchema = configSchemaFactory(pluginManager);
+        var configSchema$1 = configSchema;
         return new ManhattanRenderer({
           name: "LinearManhattanRenderer",
           ReactComponent: XYPlotRendererReactComponent,
-          configSchema: configSchema,
+          configSchema: configSchema$1,
           pluginManager: pluginManager
         });
       });

package/dist/jbrowse-plugin-gwas.cjs.development.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"jbrowse-plugin-gwas.cjs.development.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.js","../src/LinearManhattanDisplay/index.ts","../src/index.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n const { featureSpanPx } = pluginManager.lib[\"@jbrowse/core/util\"];\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\n\nexport function configSchemaFactory(pluginManager) {\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n return ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n );\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport rendererFactory, {\n configSchemaFactory as linearManhattanRendererConfigSchemaFactory,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as linearManhattanDisplayConfigSchemaFactory,\n stateModelFactory as linearManhattanDisplayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const DisplayType =\n pluginManager.lib[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = linearManhattanDisplayConfigSchemaFactory(\n pluginManager,\n );\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: linearManhattanDisplayModelFactory(\n pluginManager,\n configSchema,\n ),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = linearManhattanRendererConfigSchemaFactory(\n pluginManager,\n );\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n 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1	+ {"version":3,"file":"jbrowse-plugin-gwas.cjs.development.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.ts","../src/LinearManhattanDisplay/configSchemaFactory.ts","../src/LinearManhattanDisplay/index.ts","../src/index.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\nimport { featureSpanPx } from \"@jbrowse/core/util\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport const configSchema = ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n);\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { types } from \"mobx-state-tree\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nexport { configSchemaFactory } from \"./configSchemaFactory\";\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n get regionTooLarge() {\n return 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n=0,o=function(){};return{s:o,n:function(){return n>=e.length?{done:!0}:{done:!1,value:e[n++]}},e:function(e){throw e},f:o}}throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}var a,i=!0,u=!1;return{s:function(){r=e[Symbol.iterator]()},n:function(){var e=r.next();return i=e.done,e},e:function(e){u=!0,a=e},f:function(){try{i||null==r.return||r.return()}finally{if(u)throw a}}}}(i.values());try{for(P.s();!(a=P.n()).done;){var j=a.value,S=g(o.featureSpanPx(j,d,u),1)[0],x=j.get("score");e.fillStyle=n.readConfObject(l,"color",[j]),e.beginPath(),e.arc(S,O(x),2,0,2*Math.PI),e.fill()}}catch(e){P.e(e)}finally{P.f()}p&&(e.lineWidth=1,e.strokeStyle="rgba(200,200,200,0.8)",y.forEach((function(t){e.beginPath(),e.moveTo(0,Math.round(O(t))),e.lineTo(v,Math.round(O(t))),e.stroke()})))}}]),a}(t.WiggleBaseRenderer)}var w=n.ConfigurationSchema("LinearManhattanRenderer",{color:{type:"color",description:"the color of the marks",defaultValue:"darkblue"}},{explicitlyTyped:!0});function O(e,t){var r=e.lib["mobx-state-tree"].types,n=e.getPlugin("WigglePlugin");return r.compose("LinearManhattanDisplay",(0,n.exports.linearWiggleDisplayModelFactory)(e,t),r.model({type:r.literal("LinearManhattanDisplay")}).views((function(){return{get rendererTypeName(){return"LinearManhattanRenderer"},get needsScalebar(){return!0},get regionTooLarge(){return!1}}})))}exports.default=function(e){p(u,t);var o=b(u);function u(){var e;return i(this,u),(e=o.apply(this,arguments)).name="GWASPlugin",e}return l(u,[{key:"install",value:function(e){var t=e.getPlugin("WigglePlugin").exports,o=t.LinearWiggleDisplayReactComponent,i=t.XYPlotRendererReactComponent;e.addDisplayType((function(){var t=function(e){var t=e.getPlugin("LinearGenomeViewPlugin").exports.baseLinearDisplayConfigSchema;return n.ConfigurationSchema("LinearManhattanDisplay",{autoscale:{type:"stringEnum",defaultValue:"local",model:a.types.enumeration("Autoscale type",["global","local","globalsd","localsd","zscore"]),description:"global/local using their min/max values or w/ standard deviations (globalsd/localsd)"},minScore:{type:"number",defaultValue:Number.MIN_VALUE,description:"minimum value for the y-scale"},maxScore:{type:"number",description:"maximum value for the y-scale",defaultValue:Number.MAX_VALUE},numStdDev:{type:"number",description:"number of standard deviations to use for autoscale types globalsd or localsd",defaultValue:3},scaleType:{type:"stringEnum",model:a.types.enumeration("Scale type",["linear","log"]),description:"The type of scale to use",defaultValue:"linear"},inverted:{type:"boolean",description:"draw upside down",defaultValue:!1},defaultRendering:{type:"stringEnum",model:a.types.enumeration("Rendering",["density","xyplot","line"]),defaultValue:"xyplot"}},{baseConfiguration:t,explicitlyTyped:!0})}(e);return new r({name:"LinearManhattanDisplay",configSchema:t,stateModel:O(e,t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:o})})),e.addRendererType((function(){return new new v(e)({name:"LinearManhattanRenderer",ReactComponent:i,configSchema:w,pluginManager:e})}))}}]),u}();
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1	- {"version":3,"file":"jbrowse-plugin-gwas.cjs.production.min.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanDisplay/index.ts","../src/index.ts","../src/LinearManhattanRenderer/index.js"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n const { featureSpanPx } = pluginManager.lib[\"@jbrowse/core/util\"];\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: 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pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport rendererFactory, {\n configSchemaFactory as linearManhattanRendererConfigSchemaFactory,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as linearManhattanDisplayConfigSchemaFactory,\n stateModelFactory as linearManhattanDisplayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const DisplayType =\n pluginManager.lib[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = linearManhattanDisplayConfigSchemaFactory(\n pluginManager,\n );\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: linearManhattanDisplayModelFactory(\n pluginManager,\n configSchema,\n ),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = linearManhattanRendererConfigSchemaFactory(\n pluginManager,\n );\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n }\n}\n","export { default } from \"./LinearManhattanRenderer\";\n\nexport function configSchemaFactory(pluginManager) {\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n return ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n 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1	+ {"version":3,"file":"jbrowse-plugin-gwas.cjs.production.min.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.ts","../src/LinearManhattanDisplay/index.ts","../src/index.ts","../src/LinearManhattanDisplay/configSchemaFactory.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\nimport { featureSpanPx } from \"@jbrowse/core/util\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport const configSchema = ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n);\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nexport { configSchemaFactory } from \"./configSchemaFactory\";\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n get regionTooLarge() {\n return false;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport DisplayType from \"@jbrowse/core/pluggableElementTypes/DisplayType\";\nimport rendererFactory, {\n configSchema as rendererConfigSchema,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as displayConfigSchemaFactory,\n stateModelFactory as displayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = displayConfigSchemaFactory(pluginManager);\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: displayModelFactory(pluginManager, configSchema),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = rendererConfigSchema;\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n }\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { types } from \"mobx-state-tree\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n"],"names":["rendererFactory","pluginManager","getPlugin","exports","getScale","utils","ctx","props","features","bpPerPx","config","scaleOpts","unadjustedHeight","height","displayCrossHatches","values","ticks","region","regions","YSCALEBAR_LABEL_OFFSET","opts","range","width","end","start","scale","toY","n","feature","leftPx","featureSpanPx","score","get","fillStyle","readConfObject","beginPath","arc","Math","PI","fill","lineWidth","strokeStyle","forEach","tick","moveTo","round","lineTo","stroke","WiggleBaseRenderer","configSchema","ConfigurationSchema","color","type","description","defaultValue","explicitlyTyped","stateModelFactory","types","lib","WigglePlugin","compose","linearWiggleDisplayModelFactory","model","literal","views","Plugin","LinearWiggleDisplayReactComponent","XYPlotRendererReactComponent","addDisplayType","baseLinearDisplayConfigSchema","autoscale","enumeration","minScore","Number","MIN_VALUE","maxScore","MAX_VALUE","numStdDev","scaleType","inverted","defaultRendering","baseConfiguration","displayConfigSchemaFactory","DisplayType","name","stateModel","displayModelFactory","trackType","viewType","ReactComponent","addRendererType","rendererConfigSchema"],"mappings":"ixGAIwBA,EAAgBC,SACjBA,EAAcC,UACjC,gBAMeC,QAHNC,IAATC,MAASD,2IAMJE,EAA+BC,SAEhCC,EAQED,EARFC,SAEAC,EAMEF,EANFE,QACAC,EAKEH,EALFG,OACAC,EAIEJ,EAJFI,UACQC,EAGNL,EAHFM,OACAC,EAEEP,EAFFO,oBACSC,EACPR,EADFS,MAASD,OAEJE,IADHV,EAPFW,cAUIL,EAASD,EAAmBO,GAC5BC,SAAYT,OAAWU,MAAO,CAAC,EAAGR,KAClCS,GAASL,EAAOM,IAAMN,EAAOO,OAASf,EAEtCgB,EAAQrB,EAASgB,GACjBM,EAAM,SAACC,UAAcd,EAASY,EAAME,GANX,kmBAQTnB,EAASO,yCAAU,KAA9Ba,UACFC,IAAUC,gBAAcF,EAASX,EAAQR,SAC1CsB,EAAQH,EAAQI,IAAI,SAC1B1B,EAAI2B,UAAYC,iBAAexB,EAAQ,QAAS,CAACkB,IACjDtB,EAAI6B,YACJ7B,EAAI8B,IAAIP,EAAQH,EAAIK,GAAQ,EAAG,EAAG,EAAIM,KAAKC,IAC3ChC,EAAIiC,sCAGFzB,IACFR,EAAIkC,UAAY,EAChBlC,EAAImC,YAAc,wBAClB1B,EAAO2B,SAAQ,SAACC,GACdrC,EAAI6B,YACJ7B,EAAIsC,OAAO,EAAGP,KAAKQ,MAAMnB,EAAIiB,KAC7BrC,EAAIwC,OAAOxB,EAAOe,KAAKQ,MAAMnB,EAAIiB,KACjCrC,EAAIyC,sBAzCVC,oBCPG,IAAMC,EAAeC,sBAC1B,0BACA,CACEC,MAAO,CACLC,KAAM,QACNC,YAAa,yBACbC,aAAc,aAGlB,CAAEC,iBAAiB,aCTLC,EACdvD,EACAgD,OAEQQ,EAAUxD,EAAcyD,IAAI,mBAA5BD,MACFE,EAAe1D,EAAcC,UACjC,uBAIKuD,EAAMG,QACX,0BACAC,EAH0CF,EAAaxD,QAAjD0D,iCAG0B5D,EAAegD,GAC/CQ,EACGK,MAAM,CACLV,KAAMK,EAAMM,QAAQ,4BAErBC,OAAM,iBAAO,8BAEH,sDAGA,+BAGA,wCCjB6BC,mFACrC,yDAEChE,SACeA,EAAcC,UACjC,gBAOeC,QAHf+D,IAAAA,kCACAC,IAAAA,6BAIFlE,EAAcmE,gBAAe,eACrBnB,WCtBwBhD,OAK1BoE,EAJUpE,EAAcC,UAC9B,0BAGkDC,QAA5CkE,qCAEDnB,sBACL,yBACA,CACEoB,UAAW,CACTlB,KAAM,aACNE,aAAc,QACdQ,MAAOL,QAAMc,YAAY,iBAAkB,CACzC,SACA,QACA,WACA,UACA,WAEFlB,YACE,wFAEJmB,SAAU,CACRpB,KAAM,SACNE,aAAcmB,OAAOC,UACrBrB,YAAa,iCAEfsB,SAAU,CACRvB,KAAM,SACNC,YAAa,gCACbC,aAAcmB,OAAOG,WAEvBC,UAAW,CACTzB,KAAM,SACNC,YACE,+EACFC,aAAc,GAEhBwB,UAAW,CACT1B,KAAM,aACNU,MAAOL,QAAMc,YAAY,aAAc,CAAC,SAAU,QAClDlB,YAAa,2BACbC,aAAc,UAEhByB,SAAU,CACR3B,KAAM,UACNC,YAAa,mBACbC,cAAc,GAGhB0B,iBAAkB,CAChB5B,KAAM,aACNU,MAAOL,QAAMc,YAAY,YAAa,CAAC,UAAW,SAAU,SAC5DjB,aAAc,WAGlB,CAAE2B,kBAAmBZ,EAA+Bd,iBAAiB,IDnC9C2B,CAA2BjF,UACzC,IAAIkF,EAAY,CACrBC,KAAM,yBACNnC,aAAAA,EACAoC,WAAYC,EAAoBrF,EAAegD,GAC/CsC,UAAW,eACXC,SAAU,mBACVC,eAAgBvB,OAIpBjE,EAAcyF,iBAAgB,kBAIrB,IAFmB,IAAI1F,EAAgBC,EAEvC,CAAsB,CAC3BmF,KAAM,0BACNK,eAAgBtB,EAChBlB,aAJmB0C,EAKnB1F,cAAAA"}

package/dist/jbrowse-plugin-gwas.esm.js CHANGED Viewed

@@ -1,5 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { readConfObject } from '@jbrowse/core/configuration';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import { readConfObject, ConfigurationSchema } from '@jbrowse/core/configuration';
+import { featureSpanPx } from '@jbrowse/core/util';
+import { types } from 'mobx-state-tree';
 function _classCallCheck(instance, Constructor) {
   if (!(instance instanceof Constructor)) {
@@ -269,7 +272,6 @@ function rendererFactory(pluginManager) {
   var _WigglePlugin$exports = WigglePlugin.exports,
       getScale = _WigglePlugin$exports.utils.getScale,
       WiggleBaseRenderer = _WigglePlugin$exports.WiggleBaseRenderer;
-  var featureSpanPx = pluginManager.lib["@jbrowse/core/util"].featureSpanPx;
   return /*#__PURE__*/function (_WiggleBaseRenderer) {
     _inherits(ManhattanPlotRenderer, _WiggleBaseRenderer);
@@ -350,22 +352,17 @@ function rendererFactory(pluginManager) {
   }(WiggleBaseRenderer);
 }
-function configSchemaFactory(pluginManager) {
-  var ConfigurationSchema = pluginManager.lib["@jbrowse/core/configuration"].ConfigurationSchema;
-  return ConfigurationSchema("LinearManhattanRenderer", {
-    color: {
-      type: "color",
-      description: "the color of the marks",
-      defaultValue: "darkblue"
-    }
-  }, {
-    explicitlyTyped: true
-  });
-}
+var configSchema = /*#__PURE__*/ConfigurationSchema("LinearManhattanRenderer", {
+  color: {
+    type: "color",
+    description: "the color of the marks",
+    defaultValue: "darkblue"
+  }
+}, {
+  explicitlyTyped: true
+});
-function configSchemaFactory$1(pluginManager) {
-  var types = pluginManager.lib["mobx-state-tree"].types;
-  var ConfigurationSchema = pluginManager.lib["@jbrowse/core/configuration"].ConfigurationSchema;
+function configSchemaFactory(pluginManager) {
   var LGVPlugin = pluginManager.getPlugin("LinearGenomeViewPlugin"); //@ts-ignore
   var baseLinearDisplayConfigSchema = LGVPlugin.exports.baseLinearDisplayConfigSchema;
@@ -412,6 +409,7 @@ function configSchemaFactory$1(pluginManager) {
     explicitlyTyped: true
   });
 }
 function stateModelFactory(pluginManager, configSchema) {
   var types = pluginManager.lib["mobx-state-tree"].types;
   var WigglePlugin = pluginManager.getPlugin("WigglePlugin"); //@ts-ignore
@@ -427,6 +425,10 @@ function stateModelFactory(pluginManager, configSchema) {
       get needsScalebar() {
         return true;
+      },
+      get regionTooLarge() {
+        return false;
       }
     };
@@ -452,12 +454,11 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
     key: "install",
     value: function install(pluginManager) {
       var WigglePlugin = pluginManager.getPlugin("WigglePlugin");
-      var DisplayType = pluginManager.lib["@jbrowse/core/pluggableElementTypes/DisplayType"];
       var _WigglePlugin$exports = WigglePlugin.exports,
           LinearWiggleDisplayReactComponent = _WigglePlugin$exports.LinearWiggleDisplayReactComponent,
           XYPlotRendererReactComponent = _WigglePlugin$exports.XYPlotRendererReactComponent;
       pluginManager.addDisplayType(function () {
-        var configSchema = configSchemaFactory$1(pluginManager);
+        var configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
           name: "LinearManhattanDisplay",
           configSchema: configSchema,
@@ -470,11 +471,11 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
       pluginManager.addRendererType(function () {
         //@ts-ignore
         var ManhattanRenderer = new rendererFactory(pluginManager);
-        var configSchema = configSchemaFactory(pluginManager);
+        var configSchema$1 = configSchema;
         return new ManhattanRenderer({
           name: "LinearManhattanRenderer",
           ReactComponent: XYPlotRendererReactComponent,
-          configSchema: configSchema,
+          configSchema: configSchema$1,
           pluginManager: pluginManager
         });
       });

package/dist/jbrowse-plugin-gwas.esm.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"jbrowse-plugin-gwas.esm.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.js","../src/LinearManhattanDisplay/index.ts","../src/index.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n const { featureSpanPx } = pluginManager.lib[\"@jbrowse/core/util\"];\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\n\nexport function configSchemaFactory(pluginManager) {\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n return ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n );\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport rendererFactory, {\n configSchemaFactory as linearManhattanRendererConfigSchemaFactory,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as linearManhattanDisplayConfigSchemaFactory,\n stateModelFactory as linearManhattanDisplayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const DisplayType =\n pluginManager.lib[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = linearManhattanDisplayConfigSchemaFactory(\n pluginManager,\n );\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: linearManhattanDisplayModelFactory(\n pluginManager,\n configSchema,\n ),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = linearManhattanRendererConfigSchemaFactory(\n pluginManager,\n );\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n 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1	+ {"version":3,"file":"jbrowse-plugin-gwas.esm.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.ts","../src/LinearManhattanDisplay/configSchemaFactory.ts","../src/LinearManhattanDisplay/index.ts","../src/index.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\nimport { featureSpanPx } from \"@jbrowse/core/util\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport const configSchema = ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n);\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { types } from \"mobx-state-tree\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nexport { configSchemaFactory } from \"./configSchemaFactory\";\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n get regionTooLarge() {\n return false;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport DisplayType from \"@jbrowse/core/pluggableElementTypes/DisplayType\";\nimport rendererFactory, {\n configSchema as rendererConfigSchema,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as displayConfigSchemaFactory,\n stateModelFactory as displayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = displayConfigSchemaFactory(pluginManager);\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: displayModelFactory(pluginManager, configSchema),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = rendererConfigSchema;\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n 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package/dist/jbrowse-plugin-gwas.umd.development.js CHANGED Viewed

@@ -1,10 +1,11 @@
 (function (global, factory) {
-  typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports, require('@jbrowse/core/Plugin'), require('@jbrowse/core/configuration')) :
-  typeof define === 'function' && define.amd ? define(['exports', '@jbrowse/core/Plugin', '@jbrowse/core/configuration'], factory) :
-  (global = global || self, factory(global.JBrowsePluginGWAS = {}, global.JBrowseExports['@jbrowse/core/Plugin'], global.JBrowseExports['@jbrowse/core/configuration']));
-}(this, (function (exports, Plugin, configuration) { 'use strict';
+  typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports, require('@jbrowse/core/Plugin'), require('@jbrowse/core/pluggableElementTypes/DisplayType'), require('@jbrowse/core/configuration'), require('@jbrowse/core/util'), require('mobx-state-tree')) :
+  typeof define === 'function' && define.amd ? define(['exports', '@jbrowse/core/Plugin', '@jbrowse/core/pluggableElementTypes/DisplayType', '@jbrowse/core/configuration', '@jbrowse/core/util', 'mobx-state-tree'], factory) :
+  (global = global || self, factory(global.JBrowsePluginGWAS = {}, global.JBrowseExports['@jbrowse/core/Plugin'], global.JBrowseExports['@jbrowse/core/pluggableElementTypes/DisplayType'], global.JBrowseExports['@jbrowse/core/configuration'], global.JBrowseExports['@jbrowse/core/util'], global.JBrowseExports['mobx-state-tree']));
+}(this, (function (exports, Plugin, DisplayType, configuration, util, mobxStateTree) { 'use strict';
   Plugin = Plugin && Object.prototype.hasOwnProperty.call(Plugin, 'default') ? Plugin['default'] : Plugin;
+  DisplayType = DisplayType && Object.prototype.hasOwnProperty.call(DisplayType, 'default') ? DisplayType['default'] : DisplayType;
   function _classCallCheck(instance, Constructor) {
     if (!(instance instanceof Constructor)) {
@@ -274,7 +275,6 @@
     var _WigglePlugin$exports = WigglePlugin.exports,
         getScale = _WigglePlugin$exports.utils.getScale,
         WiggleBaseRenderer = _WigglePlugin$exports.WiggleBaseRenderer;
-    var featureSpanPx = pluginManager.lib["@jbrowse/core/util"].featureSpanPx;
     return /*#__PURE__*/function (_WiggleBaseRenderer) {
       _inherits(ManhattanPlotRenderer, _WiggleBaseRenderer);
@@ -322,7 +322,7 @@
             for (_iterator.s(); !(_step = _iterator.n()).done;) {
               var feature = _step.value;
-              var _featureSpanPx = featureSpanPx(feature, region, bpPerPx),
+              var _featureSpanPx = util.featureSpanPx(feature, region, bpPerPx),
                   _featureSpanPx2 = _slicedToArray(_featureSpanPx, 1),
                   leftPx = _featureSpanPx2[0];
@@ -355,30 +355,25 @@
     }(WiggleBaseRenderer);
   }
-  function configSchemaFactory(pluginManager) {
-    var ConfigurationSchema = pluginManager.lib["@jbrowse/core/configuration"].ConfigurationSchema;
-    return ConfigurationSchema("LinearManhattanRenderer", {
-      color: {
-        type: "color",
-        description: "the color of the marks",
-        defaultValue: "darkblue"
-      }
-    }, {
-      explicitlyTyped: true
-    });
-  }
+  var configSchema = /*#__PURE__*/configuration.ConfigurationSchema("LinearManhattanRenderer", {
+    color: {
+      type: "color",
+      description: "the color of the marks",
+      defaultValue: "darkblue"
+    }
+  }, {
+    explicitlyTyped: true
+  });
-  function configSchemaFactory$1(pluginManager) {
-    var types = pluginManager.lib["mobx-state-tree"].types;
-    var ConfigurationSchema = pluginManager.lib["@jbrowse/core/configuration"].ConfigurationSchema;
+  function configSchemaFactory(pluginManager) {
     var LGVPlugin = pluginManager.getPlugin("LinearGenomeViewPlugin"); //@ts-ignore
     var baseLinearDisplayConfigSchema = LGVPlugin.exports.baseLinearDisplayConfigSchema;
-    return ConfigurationSchema("LinearManhattanDisplay", {
+    return configuration.ConfigurationSchema("LinearManhattanDisplay", {
       autoscale: {
         type: "stringEnum",
         defaultValue: "local",
-        model: types.enumeration("Autoscale type", ["global", "local", "globalsd", "localsd", "zscore"]),
+        model: mobxStateTree.types.enumeration("Autoscale type", ["global", "local", "globalsd", "localsd", "zscore"]),
         description: "global/local using their min/max values or w/ standard deviations (globalsd/localsd)"
       },
       minScore: {
@@ -398,7 +393,7 @@
       },
       scaleType: {
         type: "stringEnum",
-        model: types.enumeration("Scale type", ["linear", "log"]),
+        model: mobxStateTree.types.enumeration("Scale type", ["linear", "log"]),
         description: "The type of scale to use",
         defaultValue: "linear"
       },
@@ -409,7 +404,7 @@
       },
       defaultRendering: {
         type: "stringEnum",
-        model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
+        model: mobxStateTree.types.enumeration("Rendering", ["density", "xyplot", "line"]),
         defaultValue: "xyplot"
       }
     }, {
@@ -417,6 +412,7 @@
       explicitlyTyped: true
     });
   }
   function stateModelFactory(pluginManager, configSchema) {
     var types = pluginManager.lib["mobx-state-tree"].types;
     var WigglePlugin = pluginManager.getPlugin("WigglePlugin"); //@ts-ignore
@@ -432,6 +428,10 @@
         get needsScalebar() {
           return true;
+        },
+        get regionTooLarge() {
+          return false;
         }
       };
@@ -457,12 +457,11 @@
       key: "install",
       value: function install(pluginManager) {
         var WigglePlugin = pluginManager.getPlugin("WigglePlugin");
-        var DisplayType = pluginManager.lib["@jbrowse/core/pluggableElementTypes/DisplayType"];
         var _WigglePlugin$exports = WigglePlugin.exports,
             LinearWiggleDisplayReactComponent = _WigglePlugin$exports.LinearWiggleDisplayReactComponent,
             XYPlotRendererReactComponent = _WigglePlugin$exports.XYPlotRendererReactComponent;
         pluginManager.addDisplayType(function () {
-          var configSchema = configSchemaFactory$1(pluginManager);
+          var configSchema = configSchemaFactory(pluginManager);
           return new DisplayType({
             name: "LinearManhattanDisplay",
             configSchema: configSchema,
@@ -475,11 +474,11 @@
         pluginManager.addRendererType(function () {
           //@ts-ignore
           var ManhattanRenderer = new rendererFactory(pluginManager);
-          var configSchema = configSchemaFactory(pluginManager);
+          var configSchema$1 = configSchema;
           return new ManhattanRenderer({
             name: "LinearManhattanRenderer",
             ReactComponent: XYPlotRendererReactComponent,
-            configSchema: configSchema,
+            configSchema: configSchema$1,
             pluginManager: pluginManager
           });
         });

package/dist/jbrowse-plugin-gwas.umd.development.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"jbrowse-plugin-gwas.umd.development.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.js","../src/LinearManhattanDisplay/index.ts","../src/index.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n const { featureSpanPx } = pluginManager.lib[\"@jbrowse/core/util\"];\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\n\nexport function configSchemaFactory(pluginManager) {\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n return ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n );\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport rendererFactory, {\n configSchemaFactory as linearManhattanRendererConfigSchemaFactory,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as linearManhattanDisplayConfigSchemaFactory,\n stateModelFactory as linearManhattanDisplayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const DisplayType =\n pluginManager.lib[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = linearManhattanDisplayConfigSchemaFactory(\n pluginManager,\n );\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: linearManhattanDisplayModelFactory(\n pluginManager,\n configSchema,\n ),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = linearManhattanRendererConfigSchemaFactory(\n pluginManager,\n );\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n 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1	+ {"version":3,"file":"jbrowse-plugin-gwas.umd.development.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.ts","../src/LinearManhattanDisplay/configSchemaFactory.ts","../src/LinearManhattanDisplay/index.ts","../src/index.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\nimport { featureSpanPx } from \"@jbrowse/core/util\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport const configSchema = ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n);\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { types } from \"mobx-state-tree\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nexport { configSchemaFactory } from \"./configSchemaFactory\";\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n get regionTooLarge() {\n return 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t=b(a);function a(){return i(this,a),t.apply(this,arguments)}return u(a,[{key:"draw",value:function(e,t){var a,i=t.features,l=t.bpPerPx,u=t.config,c=t.scaleOpts,s=t.height,p=t.displayCrossHatches,y=t.ticks.values,d=g(t.regions,1)[0],b=s-10,h=f(f({},c),{},{range:[0,b]}),v=(d.end-d.start)/l,w=r(h),j=function(e){return b-w(e)+5},O=function(e,t){var r;if("undefined"==typeof Symbol||null==e[Symbol.iterator]){if(Array.isArray(e)||(r=m(e))){r&&(e=r);var n=0,o=function(){};return{s:o,n:function(){return n>=e.length?{done:!0}:{done:!1,value:e[n++]}},e:function(e){throw e},f:o}}throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}var a,i=!0,l=!1;return{s:function(){r=e[Symbol.iterator]()},n:function(){var e=r.next();return i=e.done,e},e:function(e){l=!0,a=e},f:function(){try{i||null==r.return||r.return()}finally{if(l)throw a}}}}(i.values());try{for(O.s();!(a=O.n()).done;){var P=a.value,S=g(o.featureSpanPx(P,d,l),1)[0],x=P.get("score");e.fillStyle=n.readConfObject(u,"color",[P]),e.beginPath(),e.arc(S,j(x),2,0,2*Math.PI),e.fill()}}catch(e){O.e(e)}finally{O.f()}p&&(e.lineWidth=1,e.strokeStyle="rgba(200,200,200,0.8)",y.forEach((function(t){e.beginPath(),e.moveTo(0,Math.round(j(t))),e.lineTo(v,Math.round(j(t))),e.stroke()})))}}]),a}(t.WiggleBaseRenderer)}t=t&&Object.prototype.hasOwnProperty.call(t,"default")?t.default:t,r=r&&Object.prototype.hasOwnProperty.call(r,"default")?r.default:r;var w=n.ConfigurationSchema("LinearManhattanRenderer",{color:{type:"color",description:"the color of the marks",defaultValue:"darkblue"}},{explicitlyTyped:!0});function j(e,t){var r=e.lib["mobx-state-tree"].types,n=e.getPlugin("WigglePlugin");return r.compose("LinearManhattanDisplay",(0,n.exports.linearWiggleDisplayModelFactory)(e,t),r.model({type:r.literal("LinearManhattanDisplay")}).views((function(){return{get rendererTypeName(){return"LinearManhattanRenderer"},get needsScalebar(){return!0},get regionTooLarge(){return!1}}})))}e.default=function(e){p(o,e);var t=b(o);function o(){var e;return i(this,o),(e=t.apply(this,arguments)).name="GWASPlugin",e}return u(o,[{key:"install",value:function(e){var t=e.getPlugin("WigglePlugin").exports,o=t.LinearWiggleDisplayReactComponent,i=t.XYPlotRendererReactComponent;e.addDisplayType((function(){var t=function(e){var t=e.getPlugin("LinearGenomeViewPlugin").exports.baseLinearDisplayConfigSchema;return n.ConfigurationSchema("LinearManhattanDisplay",{autoscale:{type:"stringEnum",defaultValue:"local",model:a.types.enumeration("Autoscale type",["global","local","globalsd","localsd","zscore"]),description:"global/local using their min/max values or w/ standard deviations (globalsd/localsd)"},minScore:{type:"number",defaultValue:Number.MIN_VALUE,description:"minimum value for the y-scale"},maxScore:{type:"number",description:"maximum value for the y-scale",defaultValue:Number.MAX_VALUE},numStdDev:{type:"number",description:"number of standard deviations to use for autoscale types globalsd or localsd",defaultValue:3},scaleType:{type:"stringEnum",model:a.types.enumeration("Scale type",["linear","log"]),description:"The type of scale to use",defaultValue:"linear"},inverted:{type:"boolean",description:"draw upside down",defaultValue:!1},defaultRendering:{type:"stringEnum",model:a.types.enumeration("Rendering",["density","xyplot","line"]),defaultValue:"xyplot"}},{baseConfiguration:t,explicitlyTyped:!0})}(e);return new r({name:"LinearManhattanDisplay",configSchema:t,stateModel:j(e,t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:o})})),e.addRendererType((function(){return new new v(e)({name:"LinearManhattanRenderer",ReactComponent:i,configSchema:w,pluginManager:e})}))}}]),o}(t),Object.defineProperty(e,"__esModule",{value:!0})}));
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pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport rendererFactory, {\n configSchemaFactory as linearManhattanRendererConfigSchemaFactory,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as linearManhattanDisplayConfigSchemaFactory,\n stateModelFactory as linearManhattanDisplayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const DisplayType =\n pluginManager.lib[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = linearManhattanDisplayConfigSchemaFactory(\n pluginManager,\n );\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: linearManhattanDisplayModelFactory(\n pluginManager,\n configSchema,\n ),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = linearManhattanRendererConfigSchemaFactory(\n pluginManager,\n );\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n }\n}\n","export { default } from \"./LinearManhattanRenderer\";\n\nexport function configSchemaFactory(pluginManager) {\n const { ConfigurationSchema } = pluginManager.lib[\n \"@jbrowse/core/configuration\"\n ];\n\n return ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n 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1	+ {"version":3,"file":"jbrowse-plugin-gwas.umd.production.min.js","sources":["../src/LinearManhattanRenderer/LinearManhattanRenderer.ts","../src/LinearManhattanRenderer/index.ts","../src/LinearManhattanDisplay/index.ts","../src/index.ts","../src/LinearManhattanDisplay/configSchemaFactory.ts"],"sourcesContent":["import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { readConfObject } from \"@jbrowse/core/configuration\";\nimport { featureSpanPx } from \"@jbrowse/core/util\";\n\nexport default function rendererFactory(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n const {\n utils: { getScale },\n WiggleBaseRenderer,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n return class ManhattanPlotRenderer extends WiggleBaseRenderer {\n draw(ctx: CanvasRenderingContext2D, props: any) {\n const {\n features,\n regions,\n bpPerPx,\n config,\n scaleOpts,\n height: unadjustedHeight,\n displayCrossHatches,\n ticks: { values },\n } = props;\n const [region] = regions;\n const YSCALEBAR_LABEL_OFFSET = 5;\n const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;\n const opts = { ...scaleOpts, range: [0, height] };\n const width = (region.end - region.start) / bpPerPx;\n\n const scale = getScale(opts);\n const toY = (n: number) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx);\n const score = feature.get(\"score\") as number;\n ctx.fillStyle = readConfObject(config, \"color\", [feature]);\n ctx.beginPath();\n ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);\n ctx.fill();\n }\n\n if (displayCrossHatches) {\n ctx.lineWidth = 1;\n ctx.strokeStyle = \"rgba(200,200,200,0.8)\";\n values.forEach((tick: number) => {\n ctx.beginPath();\n ctx.moveTo(0, Math.round(toY(tick)));\n ctx.lineTo(width, Math.round(toY(tick)));\n ctx.stroke();\n });\n }\n }\n };\n}\n","export { default } from \"./LinearManhattanRenderer\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport const configSchema = ConfigurationSchema(\n \"LinearManhattanRenderer\",\n {\n color: {\n type: \"color\",\n description: \"the color of the marks\",\n defaultValue: \"darkblue\",\n },\n },\n { explicitlyTyped: true },\n);\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nexport { configSchemaFactory } from \"./configSchemaFactory\";\n\nexport function stateModelFactory(\n pluginManager: PluginManager,\n configSchema: any,\n) {\n const { types } = pluginManager.lib[\"mobx-state-tree\"];\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n //@ts-ignore\n const { linearWiggleDisplayModelFactory } = WigglePlugin.exports;\n return types.compose(\n \"LinearManhattanDisplay\",\n linearWiggleDisplayModelFactory(pluginManager, configSchema),\n types\n .model({\n type: types.literal(\"LinearManhattanDisplay\"),\n })\n .views(() => ({\n get rendererTypeName() {\n return \"LinearManhattanRenderer\";\n },\n get needsScalebar() {\n return true;\n },\n get regionTooLarge() {\n return false;\n },\n })),\n );\n}\n\nexport type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;\n","import Plugin from \"@jbrowse/core/Plugin\";\nimport PluginManager from \"@jbrowse/core/PluginManager\";\nimport DisplayType from \"@jbrowse/core/pluggableElementTypes/DisplayType\";\nimport rendererFactory, {\n configSchema as rendererConfigSchema,\n} from \"./LinearManhattanRenderer\";\nimport {\n configSchemaFactory as displayConfigSchemaFactory,\n stateModelFactory as displayModelFactory,\n} from \"./LinearManhattanDisplay\";\n\nexport default class AlignmentsPlugin extends Plugin {\n name = \"GWASPlugin\";\n\n install(pluginManager: PluginManager) {\n const WigglePlugin = pluginManager.getPlugin(\n \"WigglePlugin\",\n ) as import(\"@jbrowse/plugin-wiggle\").default;\n\n const {\n LinearWiggleDisplayReactComponent,\n XYPlotRendererReactComponent,\n //@ts-ignore\n } = WigglePlugin.exports;\n\n pluginManager.addDisplayType(() => {\n const configSchema = displayConfigSchemaFactory(pluginManager);\n return new DisplayType({\n name: \"LinearManhattanDisplay\",\n configSchema,\n stateModel: displayModelFactory(pluginManager, configSchema),\n trackType: \"FeatureTrack\",\n viewType: \"LinearGenomeView\",\n ReactComponent: LinearWiggleDisplayReactComponent,\n });\n });\n\n pluginManager.addRendererType(() => {\n //@ts-ignore\n const ManhattanRenderer = new rendererFactory(pluginManager);\n const configSchema = rendererConfigSchema;\n return new ManhattanRenderer({\n name: \"LinearManhattanRenderer\",\n ReactComponent: XYPlotRendererReactComponent,\n configSchema,\n pluginManager,\n });\n });\n }\n}\n","import PluginManager from \"@jbrowse/core/PluginManager\";\nimport { types } from \"mobx-state-tree\";\nimport { ConfigurationSchema } from \"@jbrowse/core/configuration\";\n\nexport function configSchemaFactory(pluginManager: PluginManager) {\n const LGVPlugin = pluginManager.getPlugin(\n \"LinearGenomeViewPlugin\",\n ) as import(\"@jbrowse/plugin-linear-genome-view\").default;\n //@ts-ignore\n const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;\n\n return ConfigurationSchema(\n \"LinearManhattanDisplay\",\n {\n autoscale: {\n type: \"stringEnum\",\n defaultValue: \"local\",\n model: types.enumeration(\"Autoscale type\", [\n \"global\",\n \"local\",\n \"globalsd\",\n \"localsd\",\n \"zscore\",\n ]),\n description:\n \"global/local using their min/max values or w/ standard deviations (globalsd/localsd)\",\n },\n minScore: {\n type: \"number\",\n defaultValue: Number.MIN_VALUE,\n description: \"minimum value for the y-scale\",\n },\n maxScore: {\n type: \"number\",\n description: \"maximum value for the y-scale\",\n defaultValue: Number.MAX_VALUE,\n },\n numStdDev: {\n type: \"number\",\n description:\n \"number of standard deviations to use for autoscale types globalsd or localsd\",\n defaultValue: 3,\n },\n scaleType: {\n type: \"stringEnum\",\n model: types.enumeration(\"Scale type\", [\"linear\", \"log\"]), // todo zscale\n description: \"The type of scale to use\",\n defaultValue: \"linear\",\n },\n inverted: {\n type: \"boolean\",\n description: \"draw upside down\",\n defaultValue: false,\n },\n\n defaultRendering: {\n type: \"stringEnum\",\n model: types.enumeration(\"Rendering\", [\"density\", \"xyplot\", \"line\"]),\n defaultValue: \"xyplot\",\n },\n },\n { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n );\n}\n"],"names":["rendererFactory","pluginManager","getPlugin","exports","getScale","utils","ctx","props","features","bpPerPx","config","scaleOpts","unadjustedHeight","height","displayCrossHatches","values","ticks","region","regions","YSCALEBAR_LABEL_OFFSET","opts","range","width","end","start","scale","toY","n","feature","leftPx","featureSpanPx","score","get","fillStyle","readConfObject","beginPath","arc","Math","PI","fill","lineWidth","strokeStyle","forEach","tick","moveTo","round","lineTo","stroke","WiggleBaseRenderer","configSchema","ConfigurationSchema","color","type","description","defaultValue","explicitlyTyped","stateModelFactory","types","lib","WigglePlugin","compose","linearWiggleDisplayModelFactory","model","literal","views","LinearWiggleDisplayReactComponent","XYPlotRendererReactComponent","addDisplayType","baseLinearDisplayConfigSchema","autoscale","enumeration","minScore","Number","MIN_VALUE","maxScore","MAX_VALUE","numStdDev","scaleType","inverted","defaultRendering","baseConfiguration","displayConfigSchemaFactory","DisplayType","name","stateModel","displayModelFactory","trackType","viewType","ReactComponent","addRendererType","rendererConfigSchema","Plugin"],"mappings":"ksHAIwBA,EAAgBC,SACjBA,EAAcC,UACjC,gBAMeC,QAHNC,IAATC,MAASD,2IAMJE,EAA+BC,SAEhCC,EAQED,EARFC,SAEAC,EAMEF,EANFE,QACAC,EAKEH,EALFG,OACAC,EAIEJ,EAJFI,UACQC,EAGNL,EAHFM,OACAC,EAEEP,EAFFO,oBACSC,EACPR,EADFS,MAASD,OAEJE,IADHV,EAPFW,cAUIL,EAASD,EAAmBO,GAC5BC,SAAYT,OAAWU,MAAO,CAAC,EAAGR,KAClCS,GAASL,EAAOM,IAAMN,EAAOO,OAASf,EAEtCgB,EAAQrB,EAASgB,GACjBM,EAAM,SAACC,UAAcd,EAASY,EAAME,GANX,kmBAQTnB,EAASO,yCAAU,KAA9Ba,UACFC,IAAUC,gBAAcF,EAASX,EAAQR,SAC1CsB,EAAQH,EAAQI,IAAI,SAC1B1B,EAAI2B,UAAYC,iBAAexB,EAAQ,QAAS,CAACkB,IACjDtB,EAAI6B,YACJ7B,EAAI8B,IAAIP,EAAQH,EAAIK,GAAQ,EAAG,EAAG,EAAIM,KAAKC,IAC3ChC,EAAIiC,sCAGFzB,IACFR,EAAIkC,UAAY,EAChBlC,EAAImC,YAAc,wBAClB1B,EAAO2B,SAAQ,SAACC,GACdrC,EAAI6B,YACJ7B,EAAIsC,OAAO,EAAGP,KAAKQ,MAAMnB,EAAIiB,KAC7BrC,EAAIwC,OAAOxB,EAAOe,KAAKQ,MAAMnB,EAAIiB,KACjCrC,EAAIyC,sBAzCVC,0JCPG,IAAMC,EAAeC,sBAC1B,0BACA,CACEC,MAAO,CACLC,KAAM,QACNC,YAAa,yBACbC,aAAc,aAGlB,CAAEC,iBAAiB,aCTLC,EACdvD,EACAgD,OAEQQ,EAAUxD,EAAcyD,IAAI,mBAA5BD,MACFE,EAAe1D,EAAcC,UACjC,uBAIKuD,EAAMG,QACX,0BACAC,EAH0CF,EAAaxD,QAAjD0D,iCAG0B5D,EAAegD,GAC/CQ,EACGK,MAAM,CACLV,KAAMK,EAAMM,QAAQ,4BAErBC,OAAM,iBAAO,8BAEH,sDAGA,+BAGA,qHChBR,yDAEC/D,SACeA,EAAcC,UACjC,gBAOeC,QAHf8D,IAAAA,kCACAC,IAAAA,6BAIFjE,EAAckE,gBAAe,eACrBlB,WCtBwBhD,OAK1BmE,EAJUnE,EAAcC,UAC9B,0BAGkDC,QAA5CiE,qCAEDlB,sBACL,yBACA,CACEmB,UAAW,CACTjB,KAAM,aACNE,aAAc,QACdQ,MAAOL,QAAMa,YAAY,iBAAkB,CACzC,SACA,QACA,WACA,UACA,WAEFjB,YACE,wFAEJkB,SAAU,CACRnB,KAAM,SACNE,aAAckB,OAAOC,UACrBpB,YAAa,iCAEfqB,SAAU,CACRtB,KAAM,SACNC,YAAa,gCACbC,aAAckB,OAAOG,WAEvBC,UAAW,CACTxB,KAAM,SACNC,YACE,+EACFC,aAAc,GAEhBuB,UAAW,CACTzB,KAAM,aACNU,MAAOL,QAAMa,YAAY,aAAc,CAAC,SAAU,QAClDjB,YAAa,2BACbC,aAAc,UAEhBwB,SAAU,CACR1B,KAAM,UACNC,YAAa,mBACbC,cAAc,GAGhByB,iBAAkB,CAChB3B,KAAM,aACNU,MAAOL,QAAMa,YAAY,YAAa,CAAC,UAAW,SAAU,SAC5DhB,aAAc,WAGlB,CAAE0B,kBAAmBZ,EAA+Bb,iBAAiB,IDnC9C0B,CAA2BhF,UACzC,IAAIiF,EAAY,CACrBC,KAAM,yBACNlC,aAAAA,EACAmC,WAAYC,EAAoBpF,EAAegD,GAC/CqC,UAAW,eACXC,SAAU,mBACVC,eAAgBvB,OAIpBhE,EAAcwF,iBAAgB,kBAIrB,IAFmB,IAAIzF,EAAgBC,EAEvC,CAAsB,CAC3BkF,KAAM,0BACNK,eAAgBtB,EAChBjB,aAJmByC,EAKnBzF,cAAAA,cAlCsC0F"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-gwas",
-  "version": "1.0.3",
+  "version": "1.0.4",
   "description": "JBrowse 2 GWAS API plugin",
   "repository": "github:cmdcolin/jbrowse-plugin-gwas",
   "jbrowse-plugin": {

package/src/LinearManhattanDisplay/configSchemaFactory.ts ADDED Viewed

@@ -0,0 +1,64 @@
+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(
+    "LinearManhattanDisplay",
+    {
+      autoscale: {
+        type: "stringEnum",
+        defaultValue: "local",
+        model: types.enumeration("Autoscale type", [
+          "global",
+          "local",
+          "globalsd",
+          "localsd",
+          "zscore",
+        ]),
+        description:
+          "global/local using their min/max values or w/ standard deviations (globalsd/localsd)",
+      },
+      minScore: {
+        type: "number",
+        defaultValue: Number.MIN_VALUE,
+        description: "minimum value for the y-scale",
+      },
+      maxScore: {
+        type: "number",
+        description: "maximum value for the y-scale",
+        defaultValue: Number.MAX_VALUE,
+      },
+      numStdDev: {
+        type: "number",
+        description:
+          "number of standard deviations to use for autoscale types globalsd or localsd",
+        defaultValue: 3,
+      },
+      scaleType: {
+        type: "stringEnum",
+        model: types.enumeration("Scale type", ["linear", "log"]), // todo zscale
+        description: "The type of scale to use",
+        defaultValue: "linear",
+      },
+      inverted: {
+        type: "boolean",
+        description: "draw upside down",
+        defaultValue: false,
+      },
+      defaultRendering: {
+        type: "stringEnum",
+        model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
+        defaultValue: "xyplot",
+      },
+    },
+    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },
+  );
+}

package/src/LinearManhattanDisplay/index.ts CHANGED Viewed

@@ -1,70 +1,5 @@
 import PluginManager from "@jbrowse/core/PluginManager";
-export function configSchemaFactory(pluginManager: PluginManager) {
-  const { types } = pluginManager.lib["mobx-state-tree"];
-  const { ConfigurationSchema } = pluginManager.lib[
-    "@jbrowse/core/configuration"
-  ];
-  const LGVPlugin = pluginManager.getPlugin(
-    "LinearGenomeViewPlugin",
-  ) as import("@jbrowse/plugin-linear-genome-view").default;
-  //@ts-ignore
-  const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;
-  return ConfigurationSchema(
-    "LinearManhattanDisplay",
-    {
-      autoscale: {
-        type: "stringEnum",
-        defaultValue: "local",
-        model: types.enumeration("Autoscale type", [
-          "global",
-          "local",
-          "globalsd",
-          "localsd",
-          "zscore",
-        ]),
-        description:
-          "global/local using their min/max values or w/ standard deviations (globalsd/localsd)",
-      },
-      minScore: {
-        type: "number",
-        defaultValue: Number.MIN_VALUE,
-        description: "minimum value for the y-scale",
-      },
-      maxScore: {
-        type: "number",
-        description: "maximum value for the y-scale",
-        defaultValue: Number.MAX_VALUE,
-      },
-      numStdDev: {
-        type: "number",
-        description:
-          "number of standard deviations to use for autoscale types globalsd or localsd",
-        defaultValue: 3,
-      },
-      scaleType: {
-        type: "stringEnum",
-        model: types.enumeration("Scale type", ["linear", "log"]), // todo zscale
-        description: "The type of scale to use",
-        defaultValue: "linear",
-      },
-      inverted: {
-        type: "boolean",
-        description: "draw upside down",
-        defaultValue: false,
-      },
-      defaultRendering: {
-        type: "stringEnum",
-        model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
-        defaultValue: "xyplot",
-      },
-    },
-    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },
-  );
-}
+export { configSchemaFactory } from "./configSchemaFactory";
 export function stateModelFactory(
   pluginManager: PluginManager,
@@ -90,6 +25,9 @@ export function stateModelFactory(
         get needsScalebar() {
           return true;
         },
+        get regionTooLarge() {
+          return false;
+        },
       })),
   );
 }

package/src/LinearManhattanRenderer/LinearManhattanRenderer.ts CHANGED Viewed

@@ -1,5 +1,6 @@
 import PluginManager from "@jbrowse/core/PluginManager";
 import { readConfObject } from "@jbrowse/core/configuration";
+import { featureSpanPx } from "@jbrowse/core/util";
 export default function rendererFactory(pluginManager: PluginManager) {
   const WigglePlugin = pluginManager.getPlugin(
@@ -11,8 +12,6 @@ export default function rendererFactory(pluginManager: PluginManager) {
     //@ts-ignore
   } = WigglePlugin.exports;
-  const { featureSpanPx } = pluginManager.lib["@jbrowse/core/util"];
   return class ManhattanPlotRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: any) {
       const {

package/src/LinearManhattanRenderer/index.ts ADDED Viewed

@@ -0,0 +1,14 @@
+export { default } from "./LinearManhattanRenderer";
+import { ConfigurationSchema } from "@jbrowse/core/configuration";
+export const configSchema = ConfigurationSchema(
+  "LinearManhattanRenderer",
+  {
+    color: {
+      type: "color",
+      description: "the color of the marks",
+      defaultValue: "darkblue",
+    },
+  },
+  { explicitlyTyped: true },
+);

package/src/index.ts CHANGED Viewed

@@ -1,11 +1,12 @@
 import Plugin from "@jbrowse/core/Plugin";
 import PluginManager from "@jbrowse/core/PluginManager";
+import DisplayType from "@jbrowse/core/pluggableElementTypes/DisplayType";
 import rendererFactory, {
-  configSchemaFactory as linearManhattanRendererConfigSchemaFactory,
+  configSchema as rendererConfigSchema,
 } from "./LinearManhattanRenderer";
 import {
-  configSchemaFactory as linearManhattanDisplayConfigSchemaFactory,
-  stateModelFactory as linearManhattanDisplayModelFactory,
+  configSchemaFactory as displayConfigSchemaFactory,
+  stateModelFactory as displayModelFactory,
 } from "./LinearManhattanDisplay";
 export default class AlignmentsPlugin extends Plugin {
@@ -15,8 +16,7 @@ export default class AlignmentsPlugin extends Plugin {
     const WigglePlugin = pluginManager.getPlugin(
       "WigglePlugin",
     ) as import("@jbrowse/plugin-wiggle").default;
-    const DisplayType =
-      pluginManager.lib["@jbrowse/core/pluggableElementTypes/DisplayType"];
     const {
       LinearWiggleDisplayReactComponent,
       XYPlotRendererReactComponent,
@@ -24,16 +24,11 @@ export default class AlignmentsPlugin extends Plugin {
     } = WigglePlugin.exports;
     pluginManager.addDisplayType(() => {
-      const configSchema = linearManhattanDisplayConfigSchemaFactory(
-        pluginManager,
-      );
+      const configSchema = displayConfigSchemaFactory(pluginManager);
       return new DisplayType({
         name: "LinearManhattanDisplay",
         configSchema,
-        stateModel: linearManhattanDisplayModelFactory(
-          pluginManager,
-          configSchema,
-        ),
+        stateModel: displayModelFactory(pluginManager, configSchema),
         trackType: "FeatureTrack",
         viewType: "LinearGenomeView",
         ReactComponent: LinearWiggleDisplayReactComponent,
@@ -43,9 +38,7 @@ export default class AlignmentsPlugin extends Plugin {
     pluginManager.addRendererType(() => {
       //@ts-ignore
       const ManhattanRenderer = new rendererFactory(pluginManager);
-      const configSchema = linearManhattanRendererConfigSchemaFactory(
-        pluginManager,
-      );
+      const configSchema = rendererConfigSchema;
       return new ManhattanRenderer({
         name: "LinearManhattanRenderer",
         ReactComponent: XYPlotRendererReactComponent,

package/src/LinearManhattanRenderer/index.js DELETED Viewed

@@ -1,19 +0,0 @@
-export { default } from "./LinearManhattanRenderer";
-export function configSchemaFactory(pluginManager) {
-  const { ConfigurationSchema } = pluginManager.lib[
-    "@jbrowse/core/configuration"
-  ];
-  return ConfigurationSchema(
-    "LinearManhattanRenderer",
-    {
-      color: {
-        type: "color",
-        description: "the color of the marks",
-        defaultValue: "darkblue",
-      },
-    },
-    { explicitlyTyped: true },
-  );
-}