@jbrowse/plugin-variants 2.18.0 → 3.0.0

package/esm/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -1,6 +1,4 @@
-import type { Source } from '../util';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
 import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
 import type { Instance } from 'mobx-state-tree';
 export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
@@ -23,7 +21,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -38,7 +36,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -84,10 +82,16 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
-    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
+    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
     configuration: AnyConfigurationSchemaType;
-    mafFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
+    rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -179,32 +183,32 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
-    contextMenuFeature: undefined | Feature;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
-    readonly featureUnderMouse: Feature | undefined;
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
-    navToFeature(feature: Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
-    setContextMenuFeature(feature?: Feature): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -212,7 +216,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     readonly rendererConfig: {
@@ -231,35 +235,113 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
-    featureUnderMouseVolatile: Feature | undefined;
-    sourcesVolatile: Source[] | undefined;
-    featuresVolatile: Feature[] | undefined;
-    lineZoneHeight: number;
-} & {
-    setFeatures(f: Feature[]): void;
-    setLayout(layout: Source[]): void;
+    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
+    sourcesVolatile: import("../types").Source[] | undefined;
+    featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
+    hasPhased: boolean;
+    sampleInfo: undefined | Record<string, import("../types").SampleInfo>;
+    hoveredGenotype: string | undefined;
+} & {
+    setRowHeight(arg: number): void;
+    setHoveredGenotype(arg: string): void;
+    setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
+    setLayout(layout: import("../types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
-    setSources(sources: Source[]): void;
+    setSources(sources: import("../types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
+    setPhasedMode(arg: string): void;
+    setAutoHeight(arg: boolean): void;
+    setHasPhased(arg: boolean): void;
+    setSampleInfo(arg: Record<string, import("../types").SampleInfo>): void;
 } & {
-    readonly preSources: Source[] | undefined;
+    readonly preSources: import("../types").Source[] | undefined;
     readonly sources: {
-        color: string;
+        label: string;
+        id: string;
         baseUri?: string;
         name: string;
+        color?: string;
         group?: string;
+        HP?: number;
     }[] | undefined;
 } & {
+    readonly rowHeight: number;
     adapterProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         type: string;
         checked: boolean;
         onClick: () => void;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: ({
+            label: string;
+            disabled: boolean;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+        } | {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+            disabled?: undefined;
+        })[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+            disabled?: undefined;
+        } | {
+            label: string;
+            disabled: boolean;
+            checked: boolean;
+            type: string;
+            onClick: () => void;
+        })[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     })[];
 } & {
+    readonly canDisplayLabels: boolean;
+    readonly totalHeight: number;
+} & {
+    renderProps(): any;
+} & {
+    lineZoneHeight: number;
+} & {
+    readonly nrow: number;
     readonly blockType: string;
     readonly totalHeight: number;
     readonly rowHeight: number;
@@ -268,7 +350,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly canDisplayLabels: boolean;
 } & {
     afterAttach(): void;
-    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type MultiLinearVariantMatrixDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type MultiLinearVariantMatrixDisplayModel = Instance<MultiLinearVariantMatrixDisplayStateModel>;

package/esm/MultiLinearVariantMatrixDisplay/model.js

@@ -1,148 +1,32 @@
-import { lazy } from 'react';
-import { ConfigurationReference } from '@jbrowse/core/configuration';
-import { set1 } from '@jbrowse/core/ui/colors';
 import { getSession } from '@jbrowse/core/util';
-import { stopStopToken } from '@jbrowse/core/util/stopToken';
-import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view';
-import deepEqual from 'fast-deep-equal';
 import { isAlive, types } from 'mobx-state-tree';
-import { randomColor } from '../util';
-const SetColorDialog = lazy(() => import('../shared/SetColorDialog'));
-const MAFFilterDialog = lazy(() => import('../shared/MAFFilterDialog'));
-const ClusterDialog = lazy(() => import('../shared/ClusterDialog'));
+import MultiVariantBaseModelF from '../shared/MultiVariantBaseModel';
 export default function stateModelFactory(configSchema) {
     return types
-        .compose('LinearVariantMatrixDisplay', linearBareDisplayStateModelFactory(configSchema), types.model({
+        .compose('LinearVariantMatrixDisplay', MultiVariantBaseModelF(configSchema), types.model({
         type: types.literal('LinearVariantMatrixDisplay'),
-        layout: types.optional(types.frozen(), []),
-        configuration: ConfigurationReference(configSchema),
-        mafFilter: types.optional(types.number, 0.1),
-        showSidebarLabelsSetting: true,
+        rowHeightSetting: types.optional(types.number, 1),
     }))
         .volatile(() => ({
-        sourcesLoadingStopToken: undefined,
-        featureUnderMouseVolatile: undefined,
-        sourcesVolatile: undefined,
-        featuresVolatile: undefined,
         lineZoneHeight: 20,
-    }))
-        .actions(self => ({
-        setFeatures(f) {
-            self.featuresVolatile = f;
-        },
-        setLayout(layout) {
-            self.layout = layout;
-        },
-        clearLayout() {
-            self.layout = [];
-        },
-        setSourcesLoading(str) {
-            if (self.sourcesLoadingStopToken) {
-                stopStopToken(self.sourcesLoadingStopToken);
-            }
-            self.sourcesLoadingStopToken = str;
-        },
-        setSources(sources) {
-            if (!deepEqual(sources, self.sourcesVolatile)) {
-                self.sourcesVolatile = sources;
-            }
-        },
-        setMafFilter(arg) {
-            self.mafFilter = arg;
-        },
-        setShowSidebarLabels(arg) {
-            self.showSidebarLabelsSetting = arg;
-        },
     }))
         .views(self => ({
-        get preSources() {
-            return self.layout.length ? self.layout : self.sourcesVolatile;
-        },
-        get sources() {
-            var _a, _b;
-            const sources = Object.fromEntries(((_a = self.sourcesVolatile) === null || _a === void 0 ? void 0 : _a.map(s => [s.name, s])) || []);
-            return (_b = this.preSources) === null || _b === void 0 ? void 0 : _b.map(s => ({
-                ...sources[s.name],
-                ...s,
-            })).map((s, i) => ({
-                ...s,
-                color: s.color || set1[i] || randomColor(s.name),
-            }));
+        get nrow() {
+            var _a;
+            return ((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1;
         },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-        return {
-            adapterProps() {
-                const superProps = superRenderProps();
-                return {
-                    ...superProps,
-                    rpcDriverName: self.rpcDriverName,
-                    displayModel: self,
-                    config: self.rendererConfig,
-                };
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Show sidebar labels',
-                        type: 'checkbox',
-                        checked: self.showSidebarLabelsSetting,
-                        onClick: () => {
-                            self.setShowSidebarLabels(!self.showSidebarLabelsSetting);
-                        },
-                    },
-                    {
-                        label: 'Minimum allele frequency',
-                        onClick: () => {
-                            getSession(self).queueDialog(handleClose => [
-                                MAFFilterDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                    {
-                        label: 'Cluster by genotype',
-                        onClick: () => {
-                            getSession(self).queueDialog(handleClose => [
-                                ClusterDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                    {
-                        label: 'Edit colors/arrangement...',
-                        onClick: () => {
-                            getSession(self).queueDialog(handleClose => [
-                                SetColorDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                ];
-            },
-        };
-    })
-        .views(self => ({
         get blockType() {
             return 'dynamicBlocks';
         },
         get totalHeight() {
-            return self.height - self.lineZoneHeight;
+            return self.autoHeight
+                ? self.height - self.lineZoneHeight
+                : this.nrow * self.rowHeightSetting;
         },
         get rowHeight() {
-            var _a;
-            return this.totalHeight / (((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1);
+            return self.autoHeight
+                ? self.totalHeight / this.nrow
+                : self.rowHeightSetting;
         },
     }))
         .views(self => ({
@@ -151,7 +35,8 @@ export default function stateModelFactory(configSchema) {
             return {
                 ...superProps,
                 notReady: superProps.notReady || !self.sources || !self.featuresVolatile,
-                mafFilter: self.mafFilter,
+                renderingMode: self.renderingMode,
+                minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
                 height: self.totalHeight,
                 sources: self.sources,
             };

package/esm/MultiLinearVariantMatrixDisplay/renderSvg.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { MultiLinearVariantMatrixDisplayModel } from './model';
 import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
-export declare function renderSvg(model: MultiLinearVariantMatrixDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<React.JSX.Element>;
+export declare function renderSvg(model: MultiLinearVariantMatrixDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<import("react/jsx-runtime").JSX.Element>;

package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
 import { when } from 'mobx';
 import LegendBar from '../shared/LegendBar';
@@ -6,10 +6,6 @@ import LinesConnectingMatrixToGenomicPosition from './components/LinesConnecting
 export async function renderSvg(model, opts, superRenderSvg) {
     await when(() => !!model.regionCannotBeRenderedText);
     const { offsetPx } = getContainingView(model);
-    return (React.createElement(React.Fragment, null,
-        React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
-            React.createElement(LinesConnectingMatrixToGenomicPosition, { exportSVG: true, model: model }),
-            React.createElement("g", { transform: `translate(0,${model.lineZoneHeight})` },
-                React.createElement("g", null, await superRenderSvg(opts)),
-                React.createElement(LegendBar, { model: model, orientation: "left", exportSVG: true })))));
+    const { lineZoneHeight } = model;
+    return (_jsx(_Fragment, { children: _jsxs("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: [_jsx(LinesConnectingMatrixToGenomicPosition, { exportSVG: true, model: model }), _jsxs("g", { transform: `translate(0,${lineZoneHeight})`, children: [_jsx("g", { children: await superRenderSvg(opts) }), _jsx(LegendBar, { model: model, orientation: "left", exportSVG: true })] })] }) }));
 }

package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.d.ts

@@ -1,36 +1,8 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import type { Source } from '../util';
-import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { RenderArgsDeserialized } from './types';
 import type { Feature } from '@jbrowse/core/util';
-export interface SortParams {
-    type: string;
-    pos: number;
-    refName: string;
-    assemblyName: string;
-    tag?: string;
-}
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    sources: {
-        name: string;
-    }[];
-    mafFilter: number;
-    highResolutionScaling: number;
-    height: number;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    sources: Source[];
-    features: Map<string, Feature>;
-}
 export default class LinearVariantMatrixRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }: {
-        ctx: CanvasRenderingContext2D;
-        canvasWidth: number;
-        canvasHeight: number;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-    }): {
-        mafs: Feature[];
-    };
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<any, any>;
         simplifiedFeatures: any;
@@ -38,14 +10,14 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         width: number;
         canvasRecordedData: any;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
         simplifiedFeatures: any;
         height: number;
         width: number;
-        reactElement: React.JSX.Element;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
         html?: string;
     } | {
@@ -55,7 +27,7 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         width: number;
         imageData: any;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     }>;
 }

package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -1,79 +1,27 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { SimpleFeature, renderToAbstractCanvas } from '@jbrowse/core/util';
-import { getCol } from '../util';
-const fudgeFactor = 0.6;
-const f2 = fudgeFactor / 2;
 export default class LinearVariantMatrixRenderer extends BoxRendererType {
     constructor() {
         super(...arguments);
         this.supportsSVG = true;
     }
-    makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-        const { mafFilter, sources, features } = renderArgs;
-        const feats = [...features.values()];
-        const h = canvasHeight / sources.length;
-        const mafs = [];
-        for (const feat of feats) {
-            let c = 0;
-            let c2 = 0;
-            const samp = feat.get('genotypes');
-            if (feat.get('end') - feat.get('start') <= 10) {
-                for (const { name } of sources) {
-                    const s = samp[name];
-                    if (s === '0|0' || s === './.') {
-                        c2++;
-                    }
-                    else if (s === '1|0' || s === '0|1') {
-                        c++;
-                    }
-                    else if (s === '1|1') {
-                        c++;
-                        c2++;
-                    }
-                    else {
-                        c++;
-                    }
-                }
-                if (c / sources.length > mafFilter &&
-                    c2 / sources.length < 1 - mafFilter) {
-                    mafs.push(feat);
-                }
-            }
-        }
-        const w = canvasWidth / mafs.length;
-        for (let i = 0; i < mafs.length; i++) {
-            const f = mafs[i];
-            if (f.get('end') - f.get('start') <= 10) {
-                const samp = f.get('genotypes');
-                const x = (i / mafs.length) * canvasWidth;
-                for (let j = 0; j < sources.length; j++) {
-                    const y = (j / sources.length) * canvasHeight;
-                    const { name } = sources[j];
-                    ctx.fillStyle = getCol(samp[name]);
-                    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-                }
-            }
-        }
-        return { mafs };
-    }
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
         const { height, sources, regions, bpPerPx } = renderProps;
         const region = regions[0];
         const { end, start } = region;
         const width = (end - start) / bpPerPx;
-        const { mafs, ...res } = await renderToAbstractCanvas(width, height, renderProps, ctx => {
-            return this.makeImageData({
-                ctx,
-                canvasWidth: width,
-                canvasHeight: height,
-                renderArgs: {
-                    ...renderProps,
-                    features,
-                    sources,
-                },
-            });
-        });
+        const { makeImageData } = await import('./makeImageData');
+        const { mafs, ...res } = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData({
+            ctx,
+            canvasWidth: width,
+            canvasHeight: height,
+            renderArgs: {
+                ...renderProps,
+                features,
+                sources,
+            },
+        }));
         const results = await super.render({
             ...renderProps,
             ...res,

package/esm/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.d.ts

@@ -1,6 +1,7 @@
-import React from 'react';
 declare const LinearVariantMatrixRendering: (props: {
     width: number;
     height: number;
-}) => React.JSX.Element;
+    displayModel: any;
+    arr: string[];
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.js

@@ -1,7 +1,36 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useRef } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 const LinearVariantMatrixRendering = observer(function (props) {
-    return React.createElement(PrerenderedCanvas, { ...props });
+    const { arr, width, height, displayModel } = props;
+    const ref = useRef(null);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        var _a, _b;
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const dimY = arr.length;
+        const dimX = ((_a = arr[0]) === null || _a === void 0 ? void 0 : _a.length) || 0;
+        return (_b = arr[Math.floor((offsetX / width) * dimY)]) === null || _b === void 0 ? void 0 : _b[Math.floor((offsetY / height) * dimX)];
+    }
+    return (_jsx("div", { ref: ref, onMouseMove: e => {
+            var _a;
+            return (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, getFeatureUnderMouse(e.clientX, e.clientY));
+        }, onMouseLeave: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, onMouseOut: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        }, children: _jsx(PrerenderedCanvas, { ...props }) }));
 });
 export default LinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/index.js

@@ -1,5 +1,5 @@
-import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import LinearVariantMatrixRenderer from './LinearVariantMatrixRenderer';
+import PrerenderedCanvas from './components/LinearVariantMatrixRendering';
 import configSchema from './configSchema';
 export default function LinearVariantMatrixRendererF(pluginManager) {
     pluginManager.addRendererType(() => {

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -0,0 +1,10 @@
+import type { RenderArgsDeserializedWithFeaturesAndLayout } from './types';
+export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }: {
+    ctx: CanvasRenderingContext2D;
+    canvasWidth: number;
+    canvasHeight: number;
+    renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+}): {
+    mafs: import("@jbrowse/core/util").Feature[];
+    arr: string[][];
+};