jbrowse-plugin-gwas 1.0.4 → 1.0.6

package/CHANGELOG.md

@@ -1,6 +1,14 @@
+# v1.0.6
+
+- Fix passing feature context variable to the color callback
+
+# 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)
+- Make the code always try to render (never produce the force load)
 
 # v1.0.3
 

package/README.md

@@ -7,6 +7,76 @@ Plugin for displaying GWAS results such as manhattan plot renderings
 ![](img/1.png)
 ![](img/2.png)
 
+## Data format
+
+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
+
+```
+chr22 1000 5000 rs123 84.141
+chr22 2000 6000 rs456 40.12312
+```
+
+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)
+
+```
+#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       .       .       .
+```
+
+This file format can be indexed using tabix with something BED-like
+
+```
+tabix -0 -b 2 -s 1 -e 2 -f out.bed.gz
+```
+
+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)
+
+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)
+
+## Example config
+
+The below config uses the "scoreColumn" attribute to set neg_log_pvalue (as
+seen in above section) to be the score that is plotted
+
+```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. The unpkg CDN should be stable, or you can download the js file to your server
@@ -28,7 +98,6 @@ This plugin is currently quite basic, and there is no mouseover interactivity or
 
 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/jbrowse-plugin-gwas.cjs.development.js

@@ -329,8 +329,11 @@ function rendererFactory(pluginManager) {
                 _featureSpanPx2 = _slicedToArray(_featureSpanPx, 1),
                 leftPx = _featureSpanPx2[0];
 
-            var score = feature.get("score");
-            ctx.fillStyle = configuration.readConfObject(config, "color", [feature]);
+            var score = feature.get("score"); // @ts-ignore
+
+            ctx.fillStyle = configuration.readConfObject(config, "color", {
+              feature: feature
+            });
             ctx.beginPath();
             ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);
             ctx.fill();
@@ -362,7 +365,8 @@ var configSchema = /*#__PURE__*/configuration.ConfigurationSchema("LinearManhatt
   color: {
     type: "color",
     description: "the color of the marks",
-    defaultValue: "darkblue"
+    defaultValue: "darkblue",
+    contextVariable: ["feature"]
   }
 }, {
   explicitlyTyped: true
@@ -372,6 +376,7 @@ function configSchemaFactory(pluginManager) {
   var LGVPlugin = pluginManager.getPlugin("LinearGenomeViewPlugin"); //@ts-ignore
 
   var baseLinearDisplayConfigSchema = LGVPlugin.exports.baseLinearDisplayConfigSchema;
+  var LinearManhattanRendererConfigSchema = pluginManager.getRendererType("LinearManhattanRenderer").configSchema;
   return configuration.ConfigurationSchema("LinearManhattanDisplay", {
     autoscale: {
       type: "stringEnum",
@@ -409,7 +414,10 @@ function configSchemaFactory(pluginManager) {
       type: "stringEnum",
       model: mobxStateTree.types.enumeration("Rendering", ["density", "xyplot", "line"]),
       defaultValue: "xyplot"
-    }
+    },
+    renderers: configuration.ConfigurationSchema("RenderersConfiguration", {
+      LinearManhattanRenderer: LinearManhattanRendererConfigSchema
+    })
   }, {
     baseConfiguration: baseLinearDisplayConfigSchema,
     explicitlyTyped: true

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

@@ -1 +1 @@
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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     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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) 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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        // @ts-ignore\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 = 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\"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    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},\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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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=b(o.featureSpanPx(j,d,u),1)[0],x=j.get("score");e.fillStyle=n.readConfObject(l,"color",{feature: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",contextVariable:["feature"]}},{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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package/dist/jbrowse-plugin-gwas.cjs.production.min.js.map

@@ -1 +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"}
+{"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        // @ts-ignore\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      contextVariable: [\"feature\"],\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","contextVariable","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,SAE1B1B,EAAI2B,UAAYC,iBAAexB,EAAQ,QAAS,CAAEkB,QAAAA,IAClDtB,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,sBA1CVC,oBCPG,IAAMC,EAAeC,sBAC1B,0BACA,CACEC,MAAO,CACLC,KAAM,QACNC,YAAa,yBACbC,aAAc,WACdC,gBAAiB,CAAC,aAGtB,CAAEC,iBAAiB,aCVLC,EACdxD,EACAgD,OAEQS,EAAUzD,EAAc0D,IAAI,mBAA5BD,MACFE,EAAe3D,EAAcC,UACjC,uBAIKwD,EAAMG,QACX,0BACAC,EAH0CF,EAAazD,QAAjD2D,iCAG0B7D,EAAegD,GAC/CS,EACGK,MAAM,CACLX,KAAMM,EAAMM,QAAQ,4BAErBC,OAAM,iBAAO,8BAEH,sDAGA,+BAGA,wCCjB6BC,mFACrC,yDAECjE,SACeA,EAAcC,UACjC,gBAOeC,QAHfgE,IAAAA,kCACAC,IAAAA,6BAIFnE,EAAcoE,gBAAe,eACrBpB,WCtBwBhD,OAK1BqE,EAJUrE,EAAcC,UAC9B,0BAGkDC,QAA5CmE,8BAEFC,EAAsCtE,EAAcuE,gBACxD,2BACAvB,oBACKC,sBACL,yBACA,CACEuB,UAAW,CACTrB,KAAM,aACNE,aAAc,QACdS,MAAOL,QAAMgB,YAAY,iBAAkB,CACzC,SACA,QACA,WACA,UACA,WAEFrB,YACE,wFAEJsB,SAAU,CACRvB,KAAM,SACNE,aAAcsB,OAAOC,UACrBxB,YAAa,iCAEfyB,SAAU,CACR1B,KAAM,SACNC,YAAa,gCACbC,aAAcsB,OAAOG,WAEvBC,UAAW,CACT5B,KAAM,SACNC,YACE,+EACFC,aAAc,GAEhB2B,UAAW,CACT7B,KAAM,aACNW,MAAOL,QAAMgB,YAAY,aAAc,CAAC,SAAU,QAClDrB,YAAa,2BACbC,aAAc,UAEhB4B,SAAU,CACR9B,KAAM,UACNC,YAAa,mBACbC,cAAc,GAGhB6B,iBAAkB,CAChB/B,KAAM,aACNW,MAAOL,QAAMgB,YAAY,YAAa,CAAC,UAAW,SAAU,SAC5DpB,aAAc,UAEhB8B,UAAWlC,sBAAoB,yBAA0B,CACvDmC,wBAAyBd,KAG7B,CAAEe,kBAAmBhB,EAA+Bd,iBAAiB,IDzC9C+B,CAA2BtF,UACzC,IAAIuF,EAAY,CACrBC,KAAM,yBACNxC,aAAAA,EACAyC,WAAYC,EAAoB1F,EAAegD,GAC/C2C,UAAW,eACXC,SAAU,mBACVC,eAAgB3B,OAIpBlE,EAAc8F,iBAAgB,kBAIrB,IAFmB,IAAI/F,EAAgBC,EAEvC,CAAsB,CAC3BwF,KAAM,0BACNK,eAAgB1B,EAChBnB,aAJmB+C,EAKnB/F,cAAAA"}

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

@@ -323,8 +323,11 @@ function rendererFactory(pluginManager) {
                 _featureSpanPx2 = _slicedToArray(_featureSpanPx, 1),
                 leftPx = _featureSpanPx2[0];
 
-            var score = feature.get("score");
-            ctx.fillStyle = readConfObject(config, "color", [feature]);
+            var score = feature.get("score"); // @ts-ignore
+
+            ctx.fillStyle = readConfObject(config, "color", {
+              feature: feature
+            });
             ctx.beginPath();
             ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);
             ctx.fill();
@@ -356,7 +359,8 @@ var configSchema = /*#__PURE__*/ConfigurationSchema("LinearManhattanRenderer", {
   color: {
     type: "color",
     description: "the color of the marks",
-    defaultValue: "darkblue"
+    defaultValue: "darkblue",
+    contextVariable: ["feature"]
   }
 }, {
   explicitlyTyped: true
@@ -366,6 +370,7 @@ 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",
@@ -403,7 +408,10 @@ function configSchemaFactory(pluginManager) {
       type: "stringEnum",
       model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
       defaultValue: "xyplot"
-    }
+    },
+    renderers: ConfigurationSchema("RenderersConfiguration", {
+      LinearManhattanRenderer: LinearManhattanRendererConfigSchema
+    })
   }, {
     baseConfiguration: baseLinearDisplayConfigSchema,
     explicitlyTyped: true

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

@@ -1 +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 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   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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+{"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        // @ts-ignore\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      contextVariable: [\"feature\"],\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    } = 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

@@ -326,8 +326,11 @@
                   _featureSpanPx2 = _slicedToArray(_featureSpanPx, 1),
                   leftPx = _featureSpanPx2[0];
 
-              var score = feature.get("score");
-              ctx.fillStyle = configuration.readConfObject(config, "color", [feature]);
+              var score = feature.get("score"); // @ts-ignore
+
+              ctx.fillStyle = configuration.readConfObject(config, "color", {
+                feature: feature
+              });
               ctx.beginPath();
               ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);
               ctx.fill();
@@ -359,7 +362,8 @@
     color: {
       type: "color",
       description: "the color of the marks",
-      defaultValue: "darkblue"
+      defaultValue: "darkblue",
+      contextVariable: ["feature"]
     }
   }, {
     explicitlyTyped: true
@@ -369,6 +373,7 @@
     var LGVPlugin = pluginManager.getPlugin("LinearGenomeViewPlugin"); //@ts-ignore
 
     var baseLinearDisplayConfigSchema = LGVPlugin.exports.baseLinearDisplayConfigSchema;
+    var LinearManhattanRendererConfigSchema = pluginManager.getRendererType("LinearManhattanRenderer").configSchema;
     return configuration.ConfigurationSchema("LinearManhattanDisplay", {
       autoscale: {
         type: "stringEnum",
@@ -406,7 +411,10 @@
         type: "stringEnum",
         model: mobxStateTree.types.enumeration("Rendering", ["density", "xyplot", "line"]),
         defaultValue: "xyplot"
-      }
+      },
+      renderers: configuration.ConfigurationSchema("RenderersConfiguration", {
+        LinearManhattanRenderer: LinearManhattanRendererConfigSchema
+      })
     }, {
       baseConfiguration: baseLinearDisplayConfigSchema,
       explicitlyTyped: true

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

@@ -1 +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 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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+{"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        // @ts-ignore\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      contextVariable: [\"feature\"],\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.umd.production.min.js

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P=a.value,S=g(o.featureSpanPx(P,d,u),1)[0],x=P.get("score");e.fillStyle=n.readConfObject(l,"color",{feature: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",contextVariable:["feature"]}},{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 l(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,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 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 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 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+{"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        // @ts-ignore\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      contextVariable: [\"feature\"],\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","contextVariable","explicitlyTyped","stateModelFactory","types","lib","WigglePlugin","compose","linearWiggleDisplayModelFactory","model","literal","views","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","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,SAE1B1B,EAAI2B,UAAYC,iBAAexB,EAAQ,QAAS,CAAEkB,QAAAA,IAClDtB,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,sBA1CVC,0JCPG,IAAMC,EAAeC,sBAC1B,0BACA,CACEC,MAAO,CACLC,KAAM,QACNC,YAAa,yBACbC,aAAc,WACdC,gBAAiB,CAAC,aAGtB,CAAEC,iBAAiB,aCVLC,EACdxD,EACAgD,OAEQS,EAAUzD,EAAc0D,IAAI,mBAA5BD,MACFE,EAAe3D,EAAcC,UACjC,uBAIKwD,EAAMG,QACX,0BACAC,EAH0CF,EAAazD,QAAjD2D,iCAG0B7D,EAAegD,GAC/CS,EACGK,MAAM,CACLX,KAAMM,EAAMM,QAAQ,4BAErBC,OAAM,iBAAO,8BAEH,sDAGA,+BAGA,qHChBR,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,QACdS,MAAOL,QAAMe,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,aACNW,MAAOL,QAAMe,YAAY,aAAc,CAAC,SAAU,QAClDpB,YAAa,2BACbC,aAAc,UAEhB2B,SAAU,CACR7B,KAAM,UACNC,YAAa,mBACbC,cAAc,GAGhB4B,iBAAkB,CAChB9B,KAAM,aACNW,MAAOL,QAAMe,YAAY,YAAa,CAAC,UAAW,SAAU,SAC5DnB,aAAc,UAEhB6B,UAAWjC,sBAAoB,yBAA0B,CACvDkC,wBAAyBd,KAG7B,CAAEe,kBAAmBhB,EAA+Bb,iBAAiB,IDzC9C8B,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,cAlCsC+F"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-gwas",
-  "version": "1.0.4",
+  "version": "1.0.6",
   "description": "JBrowse 2 GWAS API plugin",
   "repository": "github:cmdcolin/jbrowse-plugin-gwas",
   "jbrowse-plugin": {

package/src/LinearManhattanDisplay/configSchemaFactory.ts

@@ -9,6 +9,9 @@ export function configSchemaFactory(pluginManager: PluginManager) {
   //@ts-ignore
   const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;
 
+  const LinearManhattanRendererConfigSchema = pluginManager.getRendererType(
+    "LinearManhattanRenderer",
+  ).configSchema;
   return ConfigurationSchema(
     "LinearManhattanDisplay",
     {
@@ -58,6 +61,9 @@ export function configSchemaFactory(pluginManager: PluginManager) {
         model: types.enumeration("Rendering", ["density", "xyplot", "line"]),
         defaultValue: "xyplot",
       },
+      renderers: ConfigurationSchema("RenderersConfiguration", {
+        LinearManhattanRenderer: LinearManhattanRendererConfigSchema,
+      }),
     },
     { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },
   );

package/src/LinearManhattanRenderer/LinearManhattanRenderer.ts

@@ -36,7 +36,8 @@ export default function rendererFactory(pluginManager: PluginManager) {
       for (const feature of features.values()) {
         const [leftPx] = featureSpanPx(feature, region, bpPerPx);
         const score = feature.get("score") as number;
-        ctx.fillStyle = readConfObject(config, "color", [feature]);
+        // @ts-ignore
+        ctx.fillStyle = readConfObject(config, "color", { feature });
         ctx.beginPath();
         ctx.arc(leftPx, toY(score), 2, 0, 2 * Math.PI);
         ctx.fill();

package/src/LinearManhattanRenderer/index.ts

@@ -1,5 +1,5 @@
-export { default } from "./LinearManhattanRenderer";
 import { ConfigurationSchema } from "@jbrowse/core/configuration";
+export { default } from "./LinearManhattanRenderer";
 
 export const configSchema = ConfigurationSchema(
   "LinearManhattanRenderer",
@@ -8,6 +8,7 @@ export const configSchema = ConfigurationSchema(
       type: "color",
       description: "the color of the marks",
       defaultValue: "darkblue",
+      contextVariable: ["feature"],
     },
   },
   { explicitlyTyped: true },