@jbrowse/plugin-wiggle 3.0.5 → 3.1.0

package/dist/BigWigAdapter/configSchema.js

@@ -20,5 +20,18 @@ const BigWigAdapter = (0, configuration_1.ConfigurationSchema)('BigWigAdapter',
         defaultValue: 1,
         description: 'Initial resolution multiplier',
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                bigWigLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = BigWigAdapter;

package/dist/MultiLinearWiggleDisplay/components/ClusterDialog.d.ts

@@ -0,0 +1,11 @@
+import type { Source } from '../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function ClusterDialog({ model, handleClose, }: {
+    model: {
+        sources?: Source[];
+        minorAlleleFrequencyFilter?: number;
+        adapterConfig: AnyConfigurationModel;
+        setLayout: (arg: Source[]) => void;
+    };
+    handleClose: () => void;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/MultiLinearWiggleDisplay/components/ClusterDialog.js

@@ -0,0 +1,115 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ClusterDialog;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const material_1 = require("@mui/material");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const file_saver_1 = require("file-saver");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    mgap: {
+        display: 'flex',
+        flexDirection: 'column',
+        gap: theme.spacing(4),
+    },
+}));
+function ClusterDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const [results, setResults] = (0, react_1.useState)();
+    const [error, setError] = (0, react_1.useState)();
+    const [paste, setPaste] = (0, react_1.useState)('');
+    const [useCompleteMethod, setUseCompleteMethod] = (0, react_1.useState)(false);
+    (0, react_1.useEffect)(() => {
+        ;
+        (async () => {
+            try {
+                setError(undefined);
+                const view = (0, util_1.getContainingView)(model);
+                if (!view.initialized) {
+                    return;
+                }
+                const { rpcManager } = (0, util_1.getSession)(model);
+                const { sources, minorAlleleFrequencyFilter, adapterConfig } = model;
+                const sessionId = (0, tracks_1.getRpcSessionId)(model);
+                const { bpPerPx } = view;
+                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                    bpPerPx,
+                }));
+                const entries = Object.values(ret);
+                const keys = Object.keys(ret);
+                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
+                const text = `try(library(fastcluster), silent=TRUE)
+inputMatrix<-matrix(c(${entries.map(val => val.scores.join(',')).join(',\n')}
+),nrow=${entries.length},byrow=TRUE)
+rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
+resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
+cat(resultClusters$order,sep='\\n')`;
+                setResults(text);
+            }
+            catch (e) {
+                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+        })();
+    }, [model, useCompleteMethod]);
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Cluster by score", onClose: handleClose, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsxs)("div", { className: classes.mgap, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible score data using `hclust`." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsxs)("div", { children: ["Step 1:", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                            (0, file_saver_1.saveAs)(new Blob([results || ''], {
+                                                type: 'text/plain;charset=utf-8',
+                                            }), 'cluster.R');
+                                        }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                            (0, copy_to_clipboard_1.default)(results || '');
+                                        }, children: "Copy Rscript to clipboard" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useCompleteMethod, onChange: e => {
+                                                setUseCompleteMethod(e.target.checked);
+                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
+                                                setPaste(event.target.value);
+                                            }, slotProps: {
+                                                input: {
+                                                    classes: {
+                                                        input: classes.textAreaFont,
+                                                    },
+                                                },
+                                            } }) })] }) })) : ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", title: "Generating score matrix" })), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null] }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !results, variant: "contained", onClick: () => {
+                            const { sources } = model;
+                            if (sources) {
+                                try {
+                                    model.setLayout(paste
+                                        .split('\n')
+                                        .map(t => t.trim())
+                                        .filter(f => !!f)
+                                        .map(r => +r)
+                                        .map(idx => {
+                                        const ret = sources[idx - 1];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    setError(e);
+                                }
+                            }
+                            handleClose();
+                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
+}

package/dist/MultiLinearWiggleDisplay/model.js

@@ -50,6 +50,7 @@ const util_2 = require("../util");
 const randomColor = () => '#000000'.replaceAll('0', () => (~~(Math.random() * 16)).toString(16));
 const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
 const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
+const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ClusterDialog'))));
 const rendererTypes = new Map([
     ['xyplot', 'MultiXYPlotRenderer'],
     ['multirowxy', 'MultiRowXYPlotRenderer'],
@@ -326,12 +327,27 @@ function stateModelFactory(_pluginManager, configSchema) {
                             },
                         ]
                         : []),
+                    {
+                        label: 'Cluster by score',
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                ClusterDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
                     {
                         label: 'Edit colors/arrangement...',
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 SetColorDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/dist/MultiLinearWiggleDisplay/types.d.ts

@@ -0,0 +1,14 @@
+export interface Source {
+    baseUri?: string;
+    name: string;
+    label?: string;
+    color?: string;
+    group?: string;
+    HP?: number;
+    id?: string;
+    [key: string]: unknown;
+}
+export interface SampleInfo {
+    isPhased: boolean;
+    maxPloidy: number;
+}

package/dist/MultiLinearWiggleDisplay/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts

@@ -0,0 +1,17 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { type Region } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<Record<string, {
+        name: string;
+        scores: string[];
+    }>>;
+}

package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.js

@@ -0,0 +1,54 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiWiggleGetScoreMatrix = void 0;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+const util_1 = require("@jbrowse/core/util");
+const rxjs_1 = require("rxjs");
+class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiWiggleGetScoreMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        var _a, _b;
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { sources, regions, adapterConfig, sessionId, bpPerPx } = deserializedArgs;
+        const adapter = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        const dataAdapter = adapter.dataAdapter;
+        const resolution = 2;
+        const bpScale = bpPerPx / resolution;
+        const r0 = regions[0];
+        const r0len = r0.end - r0.start;
+        const w = Math.floor(r0len / bpScale);
+        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(r0, deserializedArgs).pipe((0, rxjs_1.toArray)()));
+        const groups = (0, util_1.groupBy)(feats, f => f.get('source'));
+        const rows = {};
+        for (const source of sources) {
+            const { name } = source;
+            const features = groups[name] || [];
+            for (const feat of features) {
+                if (!rows[name]) {
+                    rows[name] = {
+                        name,
+                        scores: new Array(w),
+                    };
+                }
+                const fstart = feat.get('start');
+                const fend = feat.get('end');
+                const score = feat.get('score');
+                for (let i = fstart; i < fend; i += bpScale) {
+                    if (i > r0.start && i < r0.end) {
+                        (_a = rows[name].scores)[_b = Math.floor((i - r0.start) / bpScale)] || (_a[_b] = score);
+                    }
+                }
+            }
+        }
+        return rows;
+    }
+}
+exports.MultiWiggleGetScoreMatrix = MultiWiggleGetScoreMatrix;

package/dist/WiggleRPC/rpcMethods.d.ts

@@ -1,3 +1,4 @@
 export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
+export * from './MultiWiggleGetScoreMatrix';

package/dist/WiggleRPC/rpcMethods.js

@@ -17,3 +17,4 @@ Object.defineProperty(exports, "__esModule", { value: true });
 __exportStar(require("./MultiWiggleGetSources"), exports);
 __exportStar(require("./WiggleGetMultiRegionQuantitativeStats"), exports);
 __exportStar(require("./WiggleGetGlobalQuantitativeStats"), exports);
+__exportStar(require("./MultiWiggleGetScoreMatrix"), exports);

package/dist/drawXY.js

@@ -9,12 +9,18 @@ const util_2 = require("./util");
 function lighten(color, amount) {
     const hslColor = color.toHsl();
     const l = hslColor.l * (1 + amount);
-    return (0, colord_1.colord)({ ...hslColor, l: (0, util_1.clamp)(l, 0, 100) });
+    return (0, colord_1.colord)({
+        ...hslColor,
+        l: (0, util_1.clamp)(l, 0, 100),
+    });
 }
 function darken(color, amount) {
     const hslColor = color.toHsl();
     const l = hslColor.l * (1 - amount);
-    return (0, colord_1.colord)({ ...hslColor, l: (0, util_1.clamp)(l, 0, 100) });
+    return (0, colord_1.colord)({
+        ...hslColor,
+        l: (0, util_1.clamp)(l, 0, 100),
+    });
 }
 const fudgeFactor = 0.3;
 const clipHeight = 2;

package/dist/index.js

@@ -96,6 +96,7 @@ class WigglePlugin extends Plugin_1.default {
         pm.addRpcMethod(() => new rpcMethods_1.WiggleGetGlobalQuantitativeStats(pm));
         pm.addRpcMethod(() => new rpcMethods_1.WiggleGetMultiRegionQuantitativeStats(pm));
         pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetSources(pm));
+        pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetScoreMatrix(pm));
     }
 }
 exports.default = WigglePlugin;

package/esm/BigWigAdapter/configSchema.js

@@ -18,5 +18,18 @@ const BigWigAdapter = ConfigurationSchema('BigWigAdapter', {
         defaultValue: 1,
         description: 'Initial resolution multiplier',
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                bigWigLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default BigWigAdapter;

package/esm/MultiLinearWiggleDisplay/components/ClusterDialog.d.ts

@@ -0,0 +1,11 @@
+import type { Source } from '../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function ClusterDialog({ model, handleClose, }: {
+    model: {
+        sources?: Source[];
+        minorAlleleFrequencyFilter?: number;
+        adapterConfig: AnyConfigurationModel;
+        setLayout: (arg: Source[]) => void;
+    };
+    handleClose: () => void;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/ClusterDialog.js

@@ -0,0 +1,109 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getContainingView, getSession, isAbortException, } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
+import copy from 'copy-to-clipboard';
+import { saveAs } from 'file-saver';
+import { isAlive } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    mgap: {
+        display: 'flex',
+        flexDirection: 'column',
+        gap: theme.spacing(4),
+    },
+}));
+export default function ClusterDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const [results, setResults] = useState();
+    const [error, setError] = useState();
+    const [paste, setPaste] = useState('');
+    const [useCompleteMethod, setUseCompleteMethod] = useState(false);
+    useEffect(() => {
+        ;
+        (async () => {
+            try {
+                setError(undefined);
+                const view = getContainingView(model);
+                if (!view.initialized) {
+                    return;
+                }
+                const { rpcManager } = getSession(model);
+                const { sources, minorAlleleFrequencyFilter, adapterConfig } = model;
+                const sessionId = getRpcSessionId(model);
+                const { bpPerPx } = view;
+                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                    bpPerPx,
+                }));
+                const entries = Object.values(ret);
+                const keys = Object.keys(ret);
+                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
+                const text = `try(library(fastcluster), silent=TRUE)
+inputMatrix<-matrix(c(${entries.map(val => val.scores.join(',')).join(',\n')}
+),nrow=${entries.length},byrow=TRUE)
+rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
+resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
+cat(resultClusters$order,sep='\\n')`;
+                setResults(text);
+            }
+            catch (e) {
+                if (!isAbortException(e) && isAlive(model)) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+        })();
+    }, [model, useCompleteMethod]);
+    return (_jsxs(Dialog, { open: true, title: "Cluster by score", onClose: handleClose, children: [_jsx(DialogContent, { children: _jsxs("div", { className: classes.mgap, children: [_jsx(Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible score data using `hclust`." }), _jsx(Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? (_jsx("div", { children: _jsxs("div", { children: ["Step 1:", ' ', _jsx(Button, { variant: "contained", onClick: () => {
+                                            saveAs(new Blob([results || ''], {
+                                                type: 'text/plain;charset=utf-8',
+                                            }), 'cluster.R');
+                                        }, children: "Download Rscript" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
+                                            copy(results || '');
+                                        }, children: "Copy Rscript to clipboard" }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: useCompleteMethod, onChange: e => {
+                                                setUseCompleteMethod(e.target.checked);
+                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), _jsx("div", { children: _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
+                                                setPaste(event.target.value);
+                                            }, slotProps: {
+                                                input: {
+                                                    classes: {
+                                                        input: classes.textAreaFont,
+                                                    },
+                                                },
+                                            } }) })] }) })) : (_jsx(LoadingEllipses, { variant: "h6", title: "Generating score matrix" })), error ? _jsx(ErrorMessage, { error: error }) : null] }) }), _jsxs(DialogActions, { children: [_jsx(Button, { disabled: !results, variant: "contained", onClick: () => {
+                            const { sources } = model;
+                            if (sources) {
+                                try {
+                                    model.setLayout(paste
+                                        .split('\n')
+                                        .map(t => t.trim())
+                                        .filter(f => !!f)
+                                        .map(r => +r)
+                                        .map(idx => {
+                                        const ret = sources[idx - 1];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    setError(e);
+                                }
+                            }
+                            handleClose();
+                        }, children: "Apply clustering" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
+}

package/esm/MultiLinearWiggleDisplay/model.js

@@ -11,6 +11,7 @@ import { YSCALEBAR_LABEL_OFFSET, getScale } from '../util';
 const randomColor = () => '#000000'.replaceAll('0', () => (~~(Math.random() * 16)).toString(16));
 const Tooltip = lazy(() => import('./components/Tooltip'));
 const SetColorDialog = lazy(() => import('./components/SetColorDialog'));
+const ClusterDialog = lazy(() => import('./components/ClusterDialog'));
 const rendererTypes = new Map([
     ['xyplot', 'MultiXYPlotRenderer'],
     ['multirowxy', 'MultiRowXYPlotRenderer'],
@@ -287,12 +288,27 @@ export function stateModelFactory(_pluginManager, configSchema) {
                             },
                         ]
                         : []),
+                    {
+                        label: 'Cluster by score',
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                ClusterDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
                     {
                         label: 'Edit colors/arrangement...',
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 SetColorDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/esm/MultiLinearWiggleDisplay/types.d.ts

@@ -0,0 +1,14 @@
+export interface Source {
+    baseUri?: string;
+    name: string;
+    label?: string;
+    color?: string;
+    group?: string;
+    HP?: number;
+    id?: string;
+    [key: string]: unknown;
+}
+export interface SampleInfo {
+    isPhased: boolean;
+    maxPloidy: number;
+}

package/esm/MultiLinearWiggleDisplay/types.js

@@ -0,0 +1 @@
+export {};

package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts

@@ -0,0 +1,17 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { type Region } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<Record<string, {
+        name: string;
+        scores: string[];
+    }>>;
+}

package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.js

@@ -0,0 +1,47 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { groupBy } from '@jbrowse/core/util';
+import { firstValueFrom, toArray } from 'rxjs';
+export class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiWiggleGetScoreMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        var _a, _b;
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { sources, regions, adapterConfig, sessionId, bpPerPx } = deserializedArgs;
+        const adapter = await getAdapter(pm, sessionId, adapterConfig);
+        const dataAdapter = adapter.dataAdapter;
+        const resolution = 2;
+        const bpScale = bpPerPx / resolution;
+        const r0 = regions[0];
+        const r0len = r0.end - r0.start;
+        const w = Math.floor(r0len / bpScale);
+        const feats = await firstValueFrom(dataAdapter.getFeatures(r0, deserializedArgs).pipe(toArray()));
+        const groups = groupBy(feats, f => f.get('source'));
+        const rows = {};
+        for (const source of sources) {
+            const { name } = source;
+            const features = groups[name] || [];
+            for (const feat of features) {
+                if (!rows[name]) {
+                    rows[name] = {
+                        name,
+                        scores: new Array(w),
+                    };
+                }
+                const fstart = feat.get('start');
+                const fend = feat.get('end');
+                const score = feat.get('score');
+                for (let i = fstart; i < fend; i += bpScale) {
+                    if (i > r0.start && i < r0.end) {
+                        (_a = rows[name].scores)[_b = Math.floor((i - r0.start) / bpScale)] || (_a[_b] = score);
+                    }
+                }
+            }
+        }
+        return rows;
+    }
+}

package/esm/WiggleRPC/rpcMethods.d.ts

@@ -1,3 +1,4 @@
 export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
+export * from './MultiWiggleGetScoreMatrix';

package/esm/WiggleRPC/rpcMethods.js

@@ -1,3 +1,4 @@
 export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
+export * from './MultiWiggleGetScoreMatrix';

package/esm/drawXY.js

@@ -6,12 +6,18 @@ import { fillRectCtx, getOrigin, getScale } from './util';
 function lighten(color, amount) {
     const hslColor = color.toHsl();
     const l = hslColor.l * (1 + amount);
-    return colord({ ...hslColor, l: clamp(l, 0, 100) });
+    return colord({
+        ...hslColor,
+        l: clamp(l, 0, 100),
+    });
 }
 function darken(color, amount) {
     const hslColor = color.toHsl();
     const l = hslColor.l * (1 - amount);
-    return colord({ ...hslColor, l: clamp(l, 0, 100) });
+    return colord({
+        ...hslColor,
+        l: clamp(l, 0, 100),
+    });
 }
 const fudgeFactor = 0.3;
 const clipHeight = 2;

package/esm/index.js

@@ -16,7 +16,7 @@ import MultiWiggleAddTrackWorkflowF from './MultiWiggleAddTrackWorkflow';
 import MultiXYPlotRendererF from './MultiXYPlotRenderer';
 import QuantitativeTrackF from './QuantitativeTrack';
 import WiggleBaseRenderer from './WiggleBaseRenderer';
-import { MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
+import { MultiWiggleGetScoreMatrix, MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
 import XYPlotRendererF, { ReactComponent as XYPlotRendererReactComponent, XYPlotRenderer, configSchema as xyPlotRendererConfigSchema, } from './XYPlotRenderer';
 import * as utils from './util';
 export default class WigglePlugin extends Plugin {
@@ -54,6 +54,7 @@ export default class WigglePlugin extends Plugin {
         pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm));
         pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm));
         pm.addRpcMethod(() => new MultiWiggleGetSources(pm));
+        pm.addRpcMethod(() => new MultiWiggleGetScoreMatrix(pm));
     }
 }
 export * from './util';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "3.0.5",
+  "version": "3.1.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,9 +37,9 @@
   },
   "dependencies": {
     "@gmod/bbi": "^6.0.0",
-    "@jbrowse/core": "^3.0.5",
-    "@jbrowse/plugin-data-management": "^3.0.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.5",
+    "@jbrowse/core": "^3.1.0",
+    "@jbrowse/plugin-data-management": "^3.1.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "@mui/x-charts-vendor": "^7.12.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a03749efe19e51609922272b845a331897346789"
+  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
 }