@jbrowse/plugin-variants 4.0.3 → 4.1.1

package/esm/LDRenderer/makeImageData.js

@@ -0,0 +1,158 @@
+import Flatbush from '@jbrowse/core/util/flatbush';
+import { checkStopToken2, checkStopToken, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
+import { scaleSequential } from '@mui/x-charts-vendor/d3-scale';
+const colorSchemes = {
+    r2: interpolateRgbBasis([
+        'rgb(255, 255, 255)',
+        'rgb(255, 224, 224)',
+        'rgb(255, 192, 192)',
+        'rgb(255, 128, 128)',
+        'rgb(255, 64, 64)',
+        'rgb(255, 0, 0)',
+        'rgb(208, 0, 0)',
+        'rgb(160, 0, 0)',
+    ]),
+    dprime: interpolateRgbBasis([
+        'rgb(255, 255, 255)',
+        'rgb(224, 224, 255)',
+        'rgb(192, 192, 255)',
+        'rgb(128, 128, 255)',
+        'rgb(64, 64, 255)',
+        'rgb(0, 0, 255)',
+        'rgb(0, 0, 208)',
+        'rgb(0, 0, 160)',
+    ]),
+    rSigned: interpolateRgbBasis([
+        'rgb(0, 0, 160)',
+        'rgb(0, 0, 208)',
+        'rgb(0, 0, 255)',
+        'rgb(64, 64, 255)',
+        'rgb(128, 128, 255)',
+        'rgb(192, 192, 255)',
+        'rgb(224, 224, 255)',
+        'rgb(255, 255, 255)',
+        'rgb(255, 224, 224)',
+        'rgb(255, 192, 192)',
+        'rgb(255, 128, 128)',
+        'rgb(255, 64, 64)',
+        'rgb(255, 0, 0)',
+        'rgb(208, 0, 0)',
+        'rgb(160, 0, 0)',
+    ]),
+    dprimeSigned: interpolateRgbBasis([
+        'rgb(0, 100, 0)',
+        'rgb(0, 128, 0)',
+        'rgb(0, 160, 0)',
+        'rgb(64, 192, 64)',
+        'rgb(128, 224, 128)',
+        'rgb(192, 240, 192)',
+        'rgb(224, 248, 224)',
+        'rgb(255, 255, 255)',
+        'rgb(224, 224, 255)',
+        'rgb(192, 192, 255)',
+        'rgb(128, 128, 255)',
+        'rgb(64, 64, 255)',
+        'rgb(0, 0, 255)',
+        'rgb(0, 0, 208)',
+        'rgb(0, 0, 160)',
+    ]),
+};
+export function makeImageData(ctx, props) {
+    const { ldData, regions, bpPerPx, stopToken, yScalar, useGenomicPositions = false, signedLD = false, } = props;
+    const lastCheck = createStopTokenChecker(stopToken);
+    const { snps, ldValues, metric } = ldData;
+    const n = snps.length;
+    if (n === 0) {
+        return undefined;
+    }
+    checkStopToken(stopToken);
+    const region = regions[0];
+    if (!region) {
+        return undefined;
+    }
+    let colorInterpolator;
+    if (signedLD) {
+        colorInterpolator =
+            metric === 'dprime' ? colorSchemes.dprimeSigned : colorSchemes.rSigned;
+    }
+    else {
+        colorInterpolator =
+            metric === 'dprime' ? colorSchemes.dprime : colorSchemes.r2;
+    }
+    const scale = scaleSequential(colorInterpolator).domain(signedLD ? [-1, 1] : [0, 1]);
+    const viewWidthPx = (region.end - region.start) / bpPerPx;
+    const sqrt2 = Math.sqrt(2);
+    const uniformW = viewWidthPx / (n * sqrt2);
+    const boundaries = [];
+    if (useGenomicPositions) {
+        for (let i = 0; i < n; i++) {
+            const snpPos = snps[i].start;
+            const prevPos = i > 0 ? snps[i - 1].start : region.start;
+            const boundaryPos = (prevPos + snpPos) / 2;
+            const pixelPos = (boundaryPos - region.start) / bpPerPx / sqrt2;
+            boundaries.push(pixelPos);
+        }
+        const lastSnpPos = snps[n - 1].start;
+        const finalBoundary = lastSnpPos + 50 * bpPerPx;
+        boundaries.push((finalBoundary - region.start) / bpPerPx / sqrt2);
+    }
+    if (yScalar) {
+        ctx.scale(1, yScalar);
+    }
+    ctx.save();
+    ctx.rotate(-Math.PI / 4);
+    const coords = [];
+    const items = [];
+    let ldIdx = 0;
+    for (let i = 1; i < n; i++) {
+        for (let j = 0; j < i; j++) {
+            const ldVal = ldValues[ldIdx] ?? 0;
+            ctx.fillStyle = scale(ldVal);
+            let x;
+            let y;
+            let cellW;
+            let cellH;
+            if (useGenomicPositions) {
+                x = boundaries[j];
+                y = boundaries[i];
+                cellW = boundaries[j + 1] - x;
+                cellH = boundaries[i + 1] - y;
+            }
+            else {
+                x = j * uniformW;
+                y = i * uniformW;
+                cellW = uniformW;
+                cellH = uniformW;
+            }
+            ctx.fillRect(x, y, cellW, cellH);
+            coords.push(x, y, x + cellW, y + cellH);
+            items.push({
+                i,
+                j,
+                ldValue: ldVal,
+                snp1: snps[i],
+                snp2: snps[j],
+            });
+            ldIdx++;
+            checkStopToken2(lastCheck);
+        }
+    }
+    ctx.restore();
+    const flatbush = new Flatbush(Math.max(items.length, 1));
+    if (coords.length) {
+        for (let k = 0; k < coords.length; k += 4) {
+            flatbush.add(coords[k], coords[k + 1], coords[k + 2], coords[k + 3]);
+        }
+    }
+    else {
+        flatbush.add(0, 0, 0, 0);
+    }
+    flatbush.finish();
+    return {
+        flatbush: flatbush.data,
+        items,
+        maxScore: signedLD ? 1 : 1,
+        w: uniformW,
+    };
+}

package/esm/LDRenderer/types.d.ts

@@ -0,0 +1,8 @@
+import type { LDMatrixResult } from '../VariantRPC/getLDMatrix.ts';
+export interface LDFlatbushItem {
+    i: number;
+    j: number;
+    ldValue: number;
+    snp1: LDMatrixResult['snps'][0];
+    snp2: LDMatrixResult['snps'][0];
+}

package/esm/LDRenderer/types.js

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

package/esm/LDTrack/configSchema.d.ts

@@ -0,0 +1,85 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: (pluginManager: PluginManager) => import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+export default configSchema;

package/esm/LDTrack/configSchema.js

@@ -0,0 +1,7 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+function x() { }
+const configSchema = (pluginManager) => ConfigurationSchema('LDTrack', {}, {
+    baseConfiguration: createBaseTrackConfig(pluginManager),
+});
+export default configSchema;

package/esm/LDTrack/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function LDTrackF(pm: PluginManager): void;

package/esm/LDTrack/index.js

@@ -0,0 +1,14 @@
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import configSchemaF from "./configSchema.js";
+export default function LDTrackF(pm) {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
+        return new TrackType({
+            name: 'LDTrack',
+            displayName: 'LD track',
+            configSchema,
+            stateModel: createBaseTrackModel(pm, 'LDTrack', configSchema),
+        });
+    });
+}