@jbrowse/plugin-wiggle 2.0.1 → 2.1.0

package/esm/XYPlotRenderer/configSchema.js

@@ -0,0 +1,26 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from '../configSchema';
+import { types } from 'mobx-state-tree';
+const configSchema = ConfigurationSchema('XYPlotRenderer', {
+    filled: {
+        type: 'boolean',
+        defaultValue: true,
+    },
+    displayCrossHatches: {
+        type: 'boolean',
+        description: 'choose to draw cross hatches (sideways lines)',
+        defaultValue: false,
+    },
+    summaryScoreMode: {
+        type: 'stringEnum',
+        model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
+        description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
+        defaultValue: 'whiskers',
+    },
+    minSize: {
+        type: 'number',
+        defaultValue: 0,
+    },
+}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/XYPlotRenderer/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/XYPlotRenderer/index.d.ts

@@ -1,3 +1,7 @@
-export { default as ReactComponent } from '../WiggleRendering';
-export { default } from './XYPlotRenderer';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import ReactComponent from '../WiggleRendering';
+import PluginManager from '@jbrowse/core/PluginManager';
+import XYPlotRenderer from './XYPlotRenderer';
+import configSchema from './configSchema';
+export { XYPlotRenderer, configSchema, ReactComponent };
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/XYPlotRenderer/index.js

@@ -1,23 +1,13 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import ConfigSchema from '../configSchema';
-import { types } from 'mobx-state-tree';
-export { default as ReactComponent } from '../WiggleRendering';
-export { default } from './XYPlotRenderer';
-export const configSchema = ConfigurationSchema('XYPlotRenderer', {
-    filled: {
-        type: 'boolean',
-        defaultValue: true,
-    },
-    displayCrossHatches: {
-        type: 'boolean',
-        description: 'choose to draw cross hatches (sideways lines)',
-        defaultValue: false,
-    },
-    summaryScoreMode: {
-        type: 'stringEnum',
-        model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
-        description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
-        defaultValue: 'whiskers',
-    },
-}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+import ReactComponent from '../WiggleRendering';
+import XYPlotRenderer from './XYPlotRenderer';
+import configSchema from './configSchema';
+export { XYPlotRenderer, configSchema, ReactComponent };
+export default (pluginManager) => {
+    pluginManager.addRendererType(() => new XYPlotRenderer({
+        name: 'XYPlotRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/XYPlotRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/XYPlotRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,cAAc,EAAE,CAAA;AAEvD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,cAAc,CAAC;QACjB,IAAI,EAAE,gBAAgB;QACtB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/configSchema.js

@@ -16,11 +16,6 @@ export default ConfigurationSchema('WiggleRenderer', {
         description: 'the color to use when the score is negative',
         defaultValue: 'red',
     },
-    highlightColor: {
-        type: 'color',
-        description: 'the color of highlights over the wiggle track',
-        defaultValue: 'rgba(255,255,0,0.5)',
-    },
     clipColor: {
         type: 'color',
         description: 'the color of the clipping marker',

package/esm/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../src/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,mBAAmB,CAChC,gBAAgB,EAChB;IACE,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,MAAM;KACrB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,MAAM;KACrB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,KAAK;KACpB;IACD,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,YAAY,EAAE;YACrC,SAAS;YACT,MAAM;YACN,SAAS;YACT,MAAM;SACP,CAAC;QACF,WAAW,EAAE,uBAAuB;QACpC,YAAY,EAAE,SAAS;KACxB;IACD,iBAAiB,EAAE;QACjB,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;QACf,WAAW,EAAE,gCAAgC;KAC9C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/drawxy.d.ts

@@ -0,0 +1,50 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature, Region } from '@jbrowse/core/util';
+import { ScaleOpts } from './util';
+export declare function drawXY(ctx: CanvasRenderingContext2D, props: {
+    features: Map<string, Feature> | Feature[];
+    bpPerPx: number;
+    regions: Region[];
+    scaleOpts: ScaleOpts;
+    height: number;
+    ticks: {
+        values: number[];
+    };
+    config: AnyConfigurationModel;
+    displayCrossHatches: boolean;
+    offset?: number;
+    colorCallback: (f: Feature, score: number) => string;
+    Color: typeof import('color');
+}): {
+    reducedFeatures: Feature[];
+};
+export declare function drawLine(ctx: CanvasRenderingContext2D, props: {
+    features: Map<string, Feature> | Feature[];
+    regions: Region[];
+    bpPerPx: number;
+    scaleOpts: ScaleOpts;
+    height: number;
+    ticks: {
+        values: number[];
+    };
+    displayCrossHatches: boolean;
+    colorCallback: (f: Feature, score: number) => string;
+    config: AnyConfigurationModel;
+    offset?: number;
+}): {
+    reducedFeatures: Feature[];
+};
+export declare function drawDensity(ctx: CanvasRenderingContext2D, props: {
+    features: Map<string, Feature> | Feature[];
+    regions: Region[];
+    bpPerPx: number;
+    scaleOpts: ScaleOpts;
+    height: number;
+    ticks: {
+        values: number[];
+    };
+    displayCrossHatches: boolean;
+    config: AnyConfigurationModel;
+}): {
+    reducedFeatures: Feature[];
+};

package/esm/drawxy.js

@@ -0,0 +1,286 @@
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { clamp, featureSpanPx } from '@jbrowse/core/util';
+import { getOrigin, getScale } from './util';
+function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+const fudgeFactor = 0.4;
+const clipHeight = 2;
+export function drawXY(ctx, props) {
+    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, Color, } = props;
+    const [region] = regions;
+    const width = (region.end - region.start) / bpPerPx;
+    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+    // wiggle display, and makes the height of the actual drawn area add
+    // "padding" to the top and bottom of the display
+    const height = unadjustedHeight - offset * 2;
+    const filled = readConfObject(config, 'filled');
+    const clipColor = readConfObject(config, 'clipColor');
+    const summaryScoreMode = readConfObject(config, 'summaryScoreMode');
+    const pivotValue = readConfObject(config, 'bicolorPivotValue');
+    const minSize = readConfObject(config, 'minSize');
+    const scale = getScale({ ...scaleOpts, range: [0, height] });
+    const originY = getOrigin(scaleOpts.scaleType);
+    const [niceMin, niceMax] = scale.domain();
+    const toY = (n) => clamp(height - (scale(n) || 0), 0, height) + offset;
+    const toOrigin = (n) => toY(originY) - toY(n);
+    const getHeight = (n) => (filled ? toOrigin(n) : Math.max(minSize, 1));
+    let hasClipping = false;
+    let prevLeftPx = 0;
+    const reducedFeatures = [];
+    const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
+    // we handle whiskers separately to render max row, min row, and avg in three
+    // passes. this reduces subpixel rendering issues. note: for stylistic
+    // reasons, clipping indicator is only drawn for score, not min/max score
+    if (summaryScoreMode === 'whiskers') {
+        let lastCol;
+        let lastMix;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            if (feature.get('summary')) {
+                const w = rightPx - leftPx + fudgeFactor;
+                const max = feature.get('maxScore');
+                const c = colorCallback(feature, max);
+                const effectiveC = crossingOrigin
+                    ? c
+                    : c === lastCol
+                        ? lastMix
+                        : (lastMix = Color(c).lighten(0.4).toString());
+                fillRectCtx(leftPx, toY(max), w, getHeight(max), ctx, effectiveC);
+                lastCol = c;
+            }
+        }
+        lastMix = undefined;
+        lastCol = undefined;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const score = feature.get('score');
+            const max = feature.get('maxScore');
+            const min = feature.get('minScore');
+            const summary = feature.get('summary');
+            const c = colorCallback(feature, score);
+            const effectiveC = crossingOrigin && summary
+                ? c === lastCol
+                    ? lastMix
+                    : (lastMix = Color(colorCallback(feature, max))
+                        .mix(Color(colorCallback(feature, min)))
+                        .toString())
+                : c;
+            const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
+            // create reduced features, avoiding multiple features per px
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+                reducedFeatures.push(feature);
+                prevLeftPx = leftPx;
+            }
+            hasClipping = hasClipping || score < niceMin || score > niceMax;
+            fillRectCtx(leftPx, toY(score), w, getHeight(score), ctx, effectiveC);
+            lastCol = c;
+        }
+        lastMix = undefined;
+        lastCol = undefined;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            if (feature.get('summary')) {
+                const min = feature.get('minScore');
+                const c = colorCallback(feature, min);
+                const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
+                const effectiveC = crossingOrigin
+                    ? c
+                    : c === lastCol
+                        ? lastMix
+                        : (lastMix = Color(c).darken(0.4).toString());
+                fillRectCtx(leftPx, toY(min), w, getHeight(min), ctx, effectiveC);
+                lastCol = c;
+            }
+        }
+    }
+    else {
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            // create reduced features, avoiding multiple features per px
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+                reducedFeatures.push(feature);
+                prevLeftPx = leftPx;
+            }
+            const score = feature.get('score');
+            const c = colorCallback(feature, score);
+            hasClipping = hasClipping || score < niceMin || score > niceMax;
+            const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
+            if (summaryScoreMode === 'max') {
+                const s = feature.get('summary') ? feature.get('maxScore') : score;
+                fillRectCtx(leftPx, toY(s), w, getHeight(s), ctx, c);
+            }
+            else if (summaryScoreMode === 'min') {
+                const s = feature.get('summary') ? feature.get('minScore') : score;
+                fillRectCtx(leftPx, toY(s), w, getHeight(s), ctx, c);
+            }
+            else {
+                fillRectCtx(leftPx, toY(score), w, getHeight(score), ctx, c);
+            }
+        }
+    }
+    // second pass: draw clipping
+    // avoid persisting the red fillstyle with save/restore
+    ctx.save();
+    if (hasClipping) {
+        ctx.fillStyle = clipColor;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const w = rightPx - leftPx + fudgeFactor;
+            const score = feature.get('score');
+            if (score > niceMax) {
+                fillRectCtx(leftPx, offset, w, clipHeight, ctx);
+            }
+            else if (score < niceMin && scaleOpts.scaleType !== 'log') {
+                fillRectCtx(leftPx, unadjustedHeight, w, clipHeight, ctx);
+            }
+        }
+    }
+    ctx.restore();
+    if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(200,200,200,0.5)';
+        ticks.values.forEach(tick => {
+            ctx.beginPath();
+            ctx.moveTo(0, Math.round(toY(tick)));
+            ctx.lineTo(width, Math.round(toY(tick)));
+            ctx.stroke();
+        });
+    }
+    return { reducedFeatures };
+}
+export function drawLine(ctx, props) {
+    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, } = props;
+    const [region] = regions;
+    const width = (region.end - region.start) / bpPerPx;
+    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+    // wiggle display, and makes the height of the actual drawn area add
+    // "padding" to the top and bottom of the display
+    const height = unadjustedHeight - offset * 2;
+    const clipColor = readConfObject(config, 'clipColor');
+    const scale = getScale({ ...scaleOpts, range: [0, height] });
+    const [niceMin, niceMax] = scale.domain();
+    const toY = (n) => clamp(height - (scale(n) || 0), 0, height) + offset;
+    let lastVal;
+    let prevLeftPx = 0;
+    const reducedFeatures = [];
+    for (const feature of features.values()) {
+        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+        // create reduced features, avoiding multiple features per px
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            reducedFeatures.push(feature);
+            prevLeftPx = leftPx;
+        }
+        const score = feature.get('score');
+        const lowClipping = score < niceMin;
+        const highClipping = score > niceMax;
+        const w = rightPx - leftPx + fudgeFactor;
+        const c = colorCallback(feature, score);
+        ctx.beginPath();
+        ctx.strokeStyle = c;
+        const startPos = typeof lastVal !== 'undefined' ? lastVal : score;
+        if (!region.reversed) {
+            ctx.moveTo(leftPx, toY(startPos));
+            ctx.lineTo(leftPx, toY(score));
+            ctx.lineTo(rightPx, toY(score));
+        }
+        else {
+            ctx.moveTo(rightPx, toY(startPos));
+            ctx.lineTo(rightPx, toY(score));
+            ctx.lineTo(leftPx, toY(score));
+        }
+        ctx.stroke();
+        lastVal = score;
+        if (highClipping) {
+            ctx.fillStyle = clipColor;
+            ctx.fillRect(leftPx, offset, w, clipHeight);
+        }
+        else if (lowClipping && scaleOpts.scaleType !== 'log') {
+            ctx.fillStyle = clipColor;
+            ctx.fillRect(leftPx, height - clipHeight, w, height);
+        }
+    }
+    if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(200,200,200,0.5)';
+        values.forEach(tick => {
+            ctx.beginPath();
+            ctx.moveTo(0, Math.round(toY(tick)));
+            ctx.lineTo(width, Math.round(toY(tick)));
+            ctx.stroke();
+        });
+    }
+    return { reducedFeatures };
+}
+export function drawDensity(ctx, props) {
+    const { features, regions, bpPerPx, scaleOpts, height, config } = props;
+    const [region] = regions;
+    const pivot = readConfObject(config, 'bicolorPivot');
+    const pivotValue = readConfObject(config, 'bicolorPivotValue');
+    const negColor = readConfObject(config, 'negColor');
+    const posColor = readConfObject(config, 'posColor');
+    const color = readConfObject(config, 'color');
+    const clipColor = readConfObject(config, 'clipColor');
+    const crossing = pivot !== 'none' && scaleOpts.scaleType !== 'log';
+    const scale = getScale({
+        ...scaleOpts,
+        pivotValue: crossing ? pivotValue : undefined,
+        range: crossing ? [negColor, 'white', posColor] : ['white', posColor],
+    });
+    const scale2 = getScale({ ...scaleOpts, range: [0, height] });
+    let cb;
+    if (color === '#f0f') {
+        cb = (_feature, score) => scale(score);
+    }
+    else {
+        cb = (feature, score) => readConfObject(config, 'color', { feature, score });
+    }
+    const [niceMin, niceMax] = scale2.domain();
+    let prevLeftPx = 0;
+    let hasClipping = false;
+    const reducedFeatures = [];
+    for (const feature of features.values()) {
+        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+        // create reduced features, avoiding multiple features per px
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            reducedFeatures.push(feature);
+            prevLeftPx = leftPx;
+        }
+        const score = feature.get('score');
+        hasClipping = hasClipping || score > niceMax || score < niceMin;
+        const w = rightPx - leftPx + fudgeFactor;
+        ctx.fillStyle = cb(feature, score);
+        ctx.fillRect(leftPx, 0, w, height);
+    }
+    // second pass: draw clipping
+    // avoid persisting the red fillstyle with save/restore
+    ctx.save();
+    if (hasClipping) {
+        ctx.fillStyle = clipColor;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const w = rightPx - leftPx + fudgeFactor;
+            const score = feature.get('score');
+            if (score > niceMax) {
+                fillRectCtx(leftPx, 0, w, clipHeight, ctx);
+            }
+            else if (score < niceMin && scaleOpts.scaleType !== 'log') {
+                fillRectCtx(leftPx, 0, w, clipHeight, ctx);
+            }
+        }
+    }
+    ctx.restore();
+    return { reducedFeatures };
+}
+//# sourceMappingURL=drawxy.js.map

package/esm/drawxy.js.map

@@ -0,0 +1 @@
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