jbrowse-plugin-gwas 1.0.3 → 1.0.5

package/CHANGELOG.md

@@ -1,3 +1,11 @@
+# v1.0.5
+
+- Fix ability to configure the renderer on the display, see sample config.json for custom coloring
+
+# 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

@@ -1,89 +1,103 @@
-# `jbrowse-plugin-gwas` (work in progress)
+# jbrowse-plugin-gwas
 
 Plugin for displaying GWAS results such as manhattan plot renderings
 
-## Install
+## Screenshot
 
-### For use in [JBrowse Web](https://jbrowse.org/jb2/docs/quickstart_web)
+![](img/1.png)
+![](img/2.png)
 
-No installation required
+## Data format
 
-### For use in [`@jbrowse/react-linear-view`](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view)
+jbrowse-plugin-gwas will render any features with a "score". A common format is a BED-like file, perhaps with tabix added. Example with plain BED, where the score is in column 5
 
 ```
-yarn add jbrowse-plugin-gwas
+chr22 1000 5000 rs123 84.141
+chr22 2000 6000 rs456 40.12312
 ```
 
-## Usage
+Sometimes, the file format is not a strict BED but something with just one coordinate instead of a start and end. Example with BED-like data (only one coordinate column)
 
-### In [JBrowse Web](https://jbrowse.org/jb2/docs/quickstart_web)
+```
+#chrom  pos     rsid    ref     alt     neg_log_pvalue  beta    stderr_beta     alt_allele_freq
+1       721290  rs12565286      G       C       0.275233        .       .       .
+1       752566  rs3094315       G       A       0.0315638       .       .       .
+1       775659  rs2905035       A       G       0.183626        .       .       .
+1       777122  rs2980319       A       T       0.207258        .       .       .
+1       779322  rs4040617       A       G       0.0326393       .       .       .
+1       780785  rs2977612       T       A       0.0225965       .       .       .
+```
 
-#### Development
+This file format can be indexed using tabix with something BED-like
 
 ```
-git clone https://github.com/cmdcolin/jbrowse-plugin-gwas.git
-cd jbrowse-plugin-gwas
-yarn
-yarn start
+tabix -0 -b 2 -s 1 -e 2 -f out.bed.gz
 ```
 
-Then open JBrowse Web to (assuming it is running on port 3000):
+The beginning (-b) and end (-e) coordinates of the features are set to the same
+column (2), and the sequence column (-s) is 1. Also assumes zero-based
+coordinates (-0)
 
-http://localhost:3000/?config=http://localhost:9000/config.json
+Note that this is just one format that can be used for the plugin, any adapter
+can be used that provides features with a score attribute, and it assumes the
+score is already -log10(p) transformed (this means if your file has raw
+p-values, you may need to modify them or add a -log10(p) to the file)
 
-#### Demo
+## Example config
 
-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
+The below config uses the "scoreColumn" attribute to set neg_log_pvalue (as
+seen in above section) to be the score that is plotted
 
-#### Production
+```json
+{
+  "type": "FeatureTrack",
+  "trackId": "gwas_track",
+  "name": "GWAS",
+  "category": ["Annotation"],
+  "assemblyNames": ["hg19"],
+  "adapter": {
+    "type": "BedTabixAdapter",
+    "scoreColumn": "neg_log_pvalue",
+    "bedGzLocation": {
+      "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz"
+    },
+    "index": {
+      "location": {
+        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz.tbi"
+      },
+      "indexType": "TBI"
+    }
+  },
+  "displays": [
+    {
+      "displayId": "gwas_display",
+      "type": "LinearManhattanDisplay"
+    }
+  ]
+}
+```
+
+## 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)
-
-```tsx
-import React from "react";
-import "fontsource-roboto";
-import {
-  createViewState,
-  createJBrowseTheme,
-  JBrowseLinearGenomeView,
-  ThemeProvider,
-} from "@jbrowse/react-linear-view";
-import GWAS from "jbrowse-plugin-gwas";
-
-const theme = createJBrowseTheme();
-
-function View() {
-  const state = createViewState({
-    assembly: {
-      /* assembly */
-    },
-    tracks: [
-      /* tracks */
-    ],
-    plugins: [GWAS],
-  });
-  return (
-    <ThemeProvider theme={theme}>
-      <JBrowseLinearGenomeView viewState={state} />
-    </ThemeProvider>
-  );
-}
-```
+This plugin is currently quite basic, and there is no mouseover interactivity or drawn labels on features
 
-## Screenshot
+#### Demo
 
-![](img/1.png)
-![](img/2.png)
+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
+
+### For use in jbrowse/react-linear-genome-view
+
+See [DEVELOPMENT](DEVELOPMENT.md)

package/dist/LinearManhattanDisplay/configSchemaFactory.d.ts

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

package/dist/LinearManhattanDisplay/index.d.ts

@@ -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

@@ -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

@@ -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 +358,26 @@ 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", {
+  var LinearManhattanRendererConfigSchema = pluginManager.getRendererType("LinearManhattanRenderer").configSchema;
+  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 +397,7 @@ 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"
     },
@@ -410,14 +408,18 @@ function configSchemaFactory$1(pluginManager) {
     },
     defaultRendering: {
       type: "stringEnum",
-      model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
+      model: mobxStateTree.types.enumeration("Rendering", ["density", "xyplot", "line"]),
       defaultValue: "xyplot"
-    }
+    },
+    renderers: configuration.ConfigurationSchema("RenderersConfiguration", {
+      LinearManhattanRenderer: LinearManhattanRendererConfigSchema
+    })
   }, {
     baseConfiguration: baseLinearDisplayConfigSchema,
     explicitlyTyped: true
   });
 }
+
 function stateModelFactory(pluginManager, configSchema) {
   var types = pluginManager.lib["mobx-state-tree"].types;
   var WigglePlugin = pluginManager.getPlugin("WigglePlugin"); //@ts-ignore
@@ -433,6 +435,10 @@ function stateModelFactory(pluginManager, configSchema) {
 
       get needsScalebar() {
         return true;
+      },
+
+      get regionTooLarge() {
+        return false;
       }
 
     };
@@ -458,12 +464,11 @@ 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 +481,11 @@ 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

@@ -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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+{"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","import { ConfigurationSchema } from \"@jbrowse/core/configuration\";\nexport { default } from \"./LinearManhattanRenderer\";\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  const LinearManhattanRendererConfigSchema = pluginManager.getRendererType(\n    \"LinearManhattanRenderer\",\n  ).configSchema;\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      renderers: ConfigurationSchema(\"RenderersConfiguration\", {\n        LinearManhattanRenderer: LinearManhattanRendererConfigSchema,\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    } = 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package/dist/jbrowse-plugin-gwas.cjs.production.min.js

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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=g(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,r=e.getRendererType("LinearManhattanRenderer").configSchema;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"},renderers:n.ConfigurationSchema("RenderersConfiguration",{LinearManhattanRenderer:r})},{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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         \"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 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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 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+{"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","import { ConfigurationSchema } from \"@jbrowse/core/configuration\";\nexport { default } from \"./LinearManhattanRenderer\";\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  const LinearManhattanRendererConfigSchema = pluginManager.getRendererType(\n    \"LinearManhattanRenderer\",\n  ).configSchema;\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      renderers: ConfigurationSchema(\"RenderersConfiguration\", {\n        LinearManhattanRenderer: LinearManhattanRendererConfigSchema,\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","LinearManhattanRendererConfigSchema","getRendererType","autoscale","enumeration","minScore","Number","MIN_VALUE","maxScore","MAX_VALUE","numStdDev","scaleType","inverted","defaultRendering","renderers","LinearManhattanRenderer","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,8BAEFC,EAAsCrE,EAAcsE,gBACxD,2BACAtB,oBACKC,sBACL,yBACA,CACEsB,UAAW,CACTpB,KAAM,aACNE,aAAc,QACdQ,MAAOL,QAAMgB,YAAY,iBAAkB,CACzC,SACA,QACA,WACA,UACA,WAEFpB,YACE,wFAEJqB,SAAU,CACRtB,KAAM,SACNE,aAAcqB,OAAOC,UACrBvB,YAAa,iCAEfwB,SAAU,CACRzB,KAAM,SACNC,YAAa,gCACbC,aAAcqB,OAAOG,WAEvBC,UAAW,CACT3B,KAAM,SACNC,YACE,+EACFC,aAAc,GAEhB0B,UAAW,CACT5B,KAAM,aACNU,MAAOL,QAAMgB,YAAY,aAAc,CAAC,SAAU,QAClDpB,YAAa,2BACbC,aAAc,UAEhB2B,SAAU,CACR7B,KAAM,UACNC,YAAa,mBACbC,cAAc,GAGhB4B,iBAAkB,CAChB9B,KAAM,aACNU,MAAOL,QAAMgB,YAAY,YAAa,CAAC,UAAW,SAAU,SAC5DnB,aAAc,UAEhB6B,UAAWjC,sBAAoB,yBAA0B,CACvDkC,wBAAyBd,KAG7B,CAAEe,kBAAmBhB,EAA+Bd,iBAAiB,IDzC9C+B,CAA2BrF,UACzC,IAAIsF,EAAY,CACrBC,KAAM,yBACNvC,aAAAA,EACAwC,WAAYC,EAAoBzF,EAAegD,GAC/C0C,UAAW,eACXC,SAAU,mBACVC,eAAgB3B,OAIpBjE,EAAc6F,iBAAgB,kBAIrB,IAFmB,IAAI9F,EAAgBC,EAEvC,CAAsB,CAC3BuF,KAAM,0BACNK,eAAgB1B,EAChBlB,aAJmB8C,EAKnB9F,cAAAA"}

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

@@ -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);
 
@@ -350,25 +352,21 @@ 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;
+  var LinearManhattanRendererConfigSchema = pluginManager.getRendererType("LinearManhattanRenderer").configSchema;
   return ConfigurationSchema("LinearManhattanDisplay", {
     autoscale: {
       type: "stringEnum",
@@ -406,12 +404,16 @@ function configSchemaFactory$1(pluginManager) {
       type: "stringEnum",
       model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
       defaultValue: "xyplot"
-    }
+    },
+    renderers: ConfigurationSchema("RenderersConfiguration", {
+      LinearManhattanRenderer: LinearManhattanRendererConfigSchema
+    })
   }, {
     baseConfiguration: baseLinearDisplayConfigSchema,
     explicitlyTyped: true
   });
 }
+
 function stateModelFactory(pluginManager, configSchema) {
   var types = pluginManager.lib["mobx-state-tree"].types;
   var WigglePlugin = pluginManager.getPlugin("WigglePlugin"); //@ts-ignore
@@ -427,6 +429,10 @@ function stateModelFactory(pluginManager, configSchema) {
 
       get needsScalebar() {
         return true;
+      },
+
+      get regionTooLarge() {
+        return false;
       }
 
     };
@@ -452,12 +458,11 @@ 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 +475,11 @@ 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
         });
       });