jbrowse-plugin-gwas 1.0.6 → 2.0.1

package/CHANGELOG.md

@@ -1,10 +1,16 @@
+# v2.0.0
+
+- Add clickable features
+- Add click map
+
 # 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
+- Fix ability to configure the renderer on the display, see sample config.json
+  for custom coloring
 
 # v1.0.4
 
@@ -12,7 +18,8 @@
 
 # v1.0.3
 
-- Fix for v1.1.0 of jbrowse-web requires passing pluginManager to renderer constructor
+- Fix for v1.1.0 of jbrowse-web requires passing pluginManager to renderer
+  constructor
 
 # v1.0.2
 

package/README.md

@@ -4,19 +4,22 @@ Plugin for displaying GWAS results such as manhattan plot renderings
 
 ## Screenshot
 
-![](img/1.png)
-![](img/2.png)
+![](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
+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)
+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
@@ -45,8 +48,8 @@ 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
+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
 {
@@ -79,7 +82,8 @@ seen in above section) to be the score that is plotted
 
 ## 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
+Add to the "plugins" of your JBrowse Web config. The unpkg CDN should be stable,
+or you can download the js file to your server
 
 ```json
 {
@@ -92,7 +96,8 @@ Add to the "plugins" of your JBrowse Web config. The unpkg CDN should be stable,
 }
 ```
 
-This plugin is currently quite basic, and there is no mouseover interactivity or drawn labels on features
+This plugin is currently quite basic, and there is no mouseover interactivity or
+drawn labels on features
 
 #### Demo
 

package/dist/LinearManhattanDisplay/TooltipComponent.d.ts

@@ -0,0 +1,15 @@
+import React from 'react';
+import type { Feature } from '@jbrowse/core/util';
+import type { TooltipContentsComponent } from '@jbrowse/plugin-wiggle';
+type Coord = [number, number];
+declare const TooltipComponent: (props: {
+    model: {
+        featureUnderMouse?: Feature;
+    };
+    height: number;
+    offsetMouseCoord: Coord;
+    clientMouseCoord: Coord;
+    clientRect?: DOMRect;
+    TooltipContents?: TooltipContentsComponent;
+}) => React.JSX.Element;
+export default TooltipComponent;

package/dist/LinearManhattanDisplay/TooltipComponent.js

@@ -0,0 +1,31 @@
+import React from 'react';
+import { Tooltip } from '@jbrowse/plugin-wiggle';
+import { observer } from 'mobx-react';
+const en = (n) => n.toLocaleString('en-US');
+function toP(s = 0) {
+    return +(+s).toPrecision(6);
+}
+const TooltipContents = React.forwardRef(function TooltipContents2({ feature }, ref) {
+    const start = feature.get('start') + 1;
+    const end = feature.get('end');
+    const refName = feature.get('refName');
+    const name = feature.get('name');
+    const rsid = feature.get('rsid');
+    const loc = [
+        refName,
+        start === end ? en(start) : `${en(start)}..${en(end)}`,
+    ]
+        .filter(f => !!f)
+        .join(':');
+    return (React.createElement("div", { ref: ref },
+        loc,
+        React.createElement("br", null),
+        `${toP(feature.get('score'))}`,
+        React.createElement("br", null),
+        name || rsid));
+});
+const TooltipComponent = observer(function (props) {
+    return React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props });
+});
+export default TooltipComponent;
+//# sourceMappingURL=TooltipComponent.js.map

package/dist/LinearManhattanDisplay/TooltipComponent.js.map

@@ -0,0 +1 @@
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package/dist/LinearManhattanDisplay/configSchemaFactory.d.ts

@@ -1,2 +1,70 @@
-import PluginManager from "@jbrowse/core/PluginManager";
-export declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    numStdDev: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        LinearManhattanRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/LinearManhattanDisplay/configSchemaFactory.js

@@ -0,0 +1,59 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+export function configSchemaFactory(pluginManager) {
+    const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
+    const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;
+    const LinearManhattanRendererConfigSchema = pluginManager.getRendererType('LinearManhattanRenderer').configSchema;
+    return ConfigurationSchema('LinearManhattanDisplay', {
+        autoscale: {
+            type: 'stringEnum',
+            defaultValue: 'local',
+            model: types.enumeration('Autoscale type', [
+                'global',
+                'local',
+                'globalsd',
+                'localsd',
+                'zscore',
+            ]),
+            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
+        },
+        minScore: {
+            type: 'number',
+            defaultValue: Number.MIN_VALUE,
+            description: 'minimum value for the y-scale',
+        },
+        maxScore: {
+            type: 'number',
+            description: 'maximum value for the y-scale',
+            defaultValue: Number.MAX_VALUE,
+        },
+        numStdDev: {
+            type: 'number',
+            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
+            defaultValue: 3,
+        },
+        scaleType: {
+            type: 'stringEnum',
+            model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+            description: 'The type of scale to use',
+            defaultValue: 'linear',
+        },
+        inverted: {
+            type: 'boolean',
+            description: 'draw upside down',
+            defaultValue: false,
+        },
+        defaultRendering: {
+            type: 'stringEnum',
+            model: types.enumeration('Rendering', ['density', 'xyplot', 'line']),
+            defaultValue: 'xyplot',
+        },
+        renderers: ConfigurationSchema('RenderersConfiguration', {
+            LinearManhattanRenderer: LinearManhattanRendererConfigSchema,
+        }),
+    }, {
+        baseConfiguration: baseLinearDisplayConfigSchema,
+        explicitlyTyped: true,
+    });
+}
+//# sourceMappingURL=configSchemaFactory.js.map

package/dist/LinearManhattanDisplay/configSchemaFactory.js.map

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package/dist/LinearManhattanDisplay/index.d.ts

@@ -1,10 +1,2 @@
-import PluginManager from "@jbrowse/core/PluginManager";
-export { configSchemaFactory } from "./configSchemaFactory";
-export declare function stateModelFactory(pluginManager: PluginManager, configSchema: any): import("mobx-state-tree").IModelType<import("mobx-state-tree").ModelProperties & {
-    type: import("mobx-state-tree").ISimpleType<"LinearManhattanDisplay">;
-}, {
-    readonly rendererTypeName: string;
-    readonly needsScalebar: boolean;
-    readonly regionTooLarge: boolean;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type LinearManhattanDisplayModel = ReturnType<typeof stateModelFactory>;
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function LinearManhattanDisplayF(pluginManager: PluginManager): void;

package/dist/LinearManhattanDisplay/index.js

@@ -0,0 +1,19 @@
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
+import { configSchemaFactory } from './configSchemaFactory';
+import { stateModelFactory } from './stateModelFactory';
+export default function LinearManhattanDisplayF(pluginManager) {
+    const WigglePlugin = pluginManager.getPlugin('WigglePlugin');
+    const { LinearWiggleDisplayReactComponent } = WigglePlugin.exports;
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'LinearManhattanDisplay',
+            configSchema,
+            stateModel: stateModelFactory(pluginManager, configSchema),
+            trackType: 'FeatureTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: LinearWiggleDisplayReactComponent,
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/LinearManhattanDisplay/index.js.map

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