@genome-spy/core 0.36.0 → 0.37.0

package/dist/src/view/facetView.js

@@ -0,0 +1,492 @@
+// @ts-nocheck
+// TODO: Enable when this is taken to use again
+
+import { isFacetFieldDef, isFacetMapping } from "./viewUtils";
+import ContainerView from "./containerView";
+import UnitView from "./unitView";
+import { cross } from "d3-array";
+import { mapToPixelCoords } from "../utils/layout/flexLayout";
+import { OrdinalDomain } from "../utils/domainArray";
+import Rectangle from "../utils/layout/rectangle";
+import coalesce from "../utils/coalesce";
+import { field as vegaField } from "vega-util";
+import DecoratorView from "./decoratorView";
+import Padding from "../utils/layout/padding";
+
+const DEFAULT_SPACING = 20;
+
+/**
+ * @typedef {"column" | "row"} FacetChannel
+ * @type {FacetChannel[]}
+ */
+const FACET_CHANNELS = ["column", "row"];
+
+/**
+ * @type {Record<FacetChannel, FacetChannel>}
+ */
+// eslint-disable-next-line no-unused-vars
+const PERPENDICULAR_FACET_CHANNELS = {
+    column: "row",
+    row: "column",
+};
+
+// https://vega.github.io/vega-lite/docs/header.html#labels
+// TODO: Configurable
+const headerConfig = {
+    labelFontSize: 12,
+    labelColor: "black",
+};
+
+/** @type {Record<FacetChannel, any>} */
+const headerConfigs = {
+    column: {
+        ...headerConfig,
+        labelAngle: 0,
+    },
+    row: {
+        ...headerConfig,
+        labelAngle: -90,
+    },
+};
+
+/**
+ * Implements (a subset of) the Vega-Lite's Facet-operator:
+ * https://vega.github.io/vega-lite/docs/facet.html
+ *
+ * TODO:
+ *  - Facet channel titles
+ *  - Suppress redundant axes
+ *  - Make this thing configurable
+ *
+ * @typedef {object} FacetDimension Stuff for working with facet dimensions
+ * @prop {function} accessor
+ * @prop {boolean[] | string[] | number[]} factors
+ * @prop {FacetFieldDef} facetFieldDef
+ *
+ */
+export default class FacetView extends ContainerView {
+    /**
+     * @typedef {import("./view").default} View
+     * @typedef {import("./layerView").default} LayerView
+     * @typedef {import("./viewUtils").FacetFieldDef} FacetFieldDef
+     * @typedef {import("./viewUtils").FacetMapping} FacetMapping
+     * @typedef {import("../utils/layout/flexLayout").LocSize} LocSize
+     * @typedef {import("../utils/layout/flexLayout").SizeDef} SizeDef
+     */
+    /**
+     *
+     * @param {import("./viewUtils").FacetSpec} spec
+     * @param {import("./viewUtils").ViewContext} context
+     * @param {ContainerView} parent
+     * @param {string} name
+     */
+    constructor(spec, context, parent, name) {
+        super(spec, context, parent, name);
+
+        this.spec = spec;
+
+        this.child = /** @type { UnitView | LayerView | DecoratorView } */ (
+            context.createView(spec.spec, this, `facet`)
+        );
+
+        /**
+         * Faceted views for displaying the facet labels
+         *
+         * @type {Record<FacetChannel, UnitView>}
+         */
+        this._labelViews = Object.fromEntries(
+            FACET_CHANNELS.map((channel) => [
+                channel,
+                new UnitView(
+                    createLabelViewSpec(headerConfigs[channel]),
+                    this.context,
+                    this,
+                    `facetLabel-${channel}`
+                ),
+            ])
+        );
+
+        /**  @type {Record<FacetChannel, FacetDimension>} */
+        this._facetDimensions = { column: undefined, row: undefined };
+    }
+
+    /**
+     * @returns {IterableIterator<View>}
+     */
+    *[Symbol.iterator]() {
+        yield this.child;
+        for (const view of Object.values(this._labelViews)) {
+            yield view;
+        }
+    }
+
+    /**
+     * @param {import("./view").default} child
+     * @param {import("./view").default} replacement
+     */
+    replaceChild(child, replacement) {
+        if (child !== this.child) {
+            throw new Error("Not my child!");
+        }
+
+        this.child = /** @type {UnitView | LayerView | DecoratorView} */ (
+            replacement
+        );
+    }
+
+    transformData() {
+        super.transformData();
+        // A hacky solution for updating facets. TODO: Something more robust.
+        this.updateFacets();
+    }
+
+    /**
+     *
+     * @param {"row" | "column"} channel
+     */
+    getAccessor(channel) {
+        /** @type {import("./viewUtils").FacetMapping} */
+        let facetMapping;
+        if (isFacetMapping(this.spec.facet)) {
+            facetMapping = this.spec.facet; // Mark provides encodings with defaults and possible modifications
+        } else if (isFacetFieldDef(this.spec.facet)) {
+            // TODO: Check "columns"
+            facetMapping = {
+                column: this.spec.facet,
+            };
+        } else {
+            throw new Error(
+                "Invalid facet specification: " +
+                    JSON.stringify(this.spec.facet)
+            );
+        }
+
+        if (facetMapping[channel]) {
+            return this.context.accessorFactory.createAccessor(
+                facetMapping[channel]
+            );
+        }
+    }
+
+    updateFacets() {
+        /** @type {import("./viewUtils").FacetMapping} */
+        let facetMapping;
+        if (isFacetMapping(this.spec.facet)) {
+            facetMapping = this.spec.facet; // Mark provides encodings with defaults and possible modifications
+        } else if (isFacetFieldDef(this.spec.facet)) {
+            // TODO: Check "columns"
+            facetMapping = {
+                column: this.spec.facet,
+            };
+        } else {
+            throw new Error(
+                "Invalid facet specification: " +
+                    JSON.stringify(this.spec.facet)
+            );
+        }
+
+        for (const channel of FACET_CHANNELS) {
+            const facetFieldDef = facetMapping[channel];
+            if (!facetFieldDef) {
+                continue;
+            }
+
+            const accessor = this.context.accessorFactory.createAccessor(
+                facetMapping[channel]
+            );
+
+            const factors = new OrdinalDomain().extendAllWithAccessor(
+                this.getData(),
+                accessor
+            );
+
+            // TODO: Configurable sorting
+            factors.sort();
+
+            this._facetDimensions[channel] = {
+                accessor,
+                factors,
+                facetFieldDef,
+            };
+        }
+    }
+
+    updateLabels() {
+        for (const channel of FACET_CHANNELS) {
+            const facetDimension = this._facetDimensions[channel];
+            this._labelViews[channel].updateData(
+                facetDimension
+                    ? facetDimension.factors.map((d) => ({ data: d }))
+                    : []
+            );
+        }
+    }
+
+    /**
+     * Returns an accessor that returns a (composite) key for partitioning the data
+     *
+     * @param {View} [whoIsAsking] Passed to the immediate parent. Allows for
+     *      selectively breaking the inheritance.
+     * @return {function(object):any}
+     */
+    getFacetAccessor(whoIsAsking) {
+        const { column, row } = this._facetDimensions;
+
+        if (Object.values(this._labelViews).includes(whoIsAsking)) {
+            // Label views are faceted by the facet labels
+            return vegaField("data");
+        } else if (column && row) {
+            const columnField = vegaField(column.facetFieldDef.field);
+            const rowField = vegaField(row.facetFieldDef.field);
+            return /** @param {object} d */ (d) =>
+                columnField(d) + "," + rowField(d);
+        } else if (column) {
+            return vegaField(column.facetFieldDef.field);
+        } else if (row) {
+            return vegaField(row.facetFieldDef.field);
+        } else {
+            throw new Error("updateFacets() must be called first!");
+        }
+    }
+
+    getFacetGroups() {
+        const { column, row } = this._facetDimensions;
+
+        if (column && row) {
+            return cross(
+                column.factors,
+                row.factors,
+                (col, row) => col + "," + row
+            );
+        } else if (column) {
+            return column.factors;
+        } else if (row) {
+            return row.factors;
+        } else {
+            throw new Error("updateFacets() must be called first!");
+        }
+    }
+
+    getSize() {
+        // TODO: IMPLEMENT!
+        return super.getSize();
+    }
+
+    /**
+     * @param {import("./renderingContext/viewRenderingContext").default} context
+     * @param {import("../utils/layout/rectangle").default} coords
+     * @param {import("./view").RenderingOptions} [options]
+     */
+    render(context, coords, options = {}) {
+        if (!this.isConfiguredVisible()) {
+            return;
+        }
+
+        coords = coords.shrink(this.getPadding());
+        context.pushView(this, coords);
+
+        // Size of the view that is being repeated for all the facets
+        const childSize = this.child.getSize();
+
+        // Fugly hack. TODO: Figure out a systematic phase for doing this
+        if (!this._labelsUpdated) {
+            this.updateLabels();
+            this._labelsUpdated = true;
+        }
+
+        // TODO: Validate. Columns is not compatible with row channel
+        const wrap = this.spec.columns && this._facetDimensions.column;
+
+        // We use two flexLayouts to create a grid for the facets.
+        // Stride and offset control how the cells in the grid are allocated
+        // for the facets and the intervening facet labels.
+        const xStride = 1;
+        const xOffset = wrap ? 0 : this._facetDimensions.row ? 1 : 0;
+        const yStride = wrap ? 2 : 1;
+        const yOffset = this._facetDimensions.column ? 1 : 0;
+
+        /**
+         * @param {SizeDef} childSize
+         * @param {number} count
+         * @param {number} stride
+         * @param {number} offset
+         */
+        const calculateCellSizes = (childSize, count, stride, offset) => {
+            // TODO: take the channel into account
+            const labelSize = { px: headerConfig.labelFontSize };
+
+            /** @type {SizeDef[]} */
+            const cellSizes = [];
+
+            for (let i = 0; i < offset; i++) {
+                cellSizes.push(labelSize);
+            }
+
+            for (let i = 0; i < count; i++) {
+                for (let j = 1; j < stride; j++) {
+                    cellSizes.push(labelSize);
+                }
+                cellSizes.push(childSize);
+            }
+
+            return cellSizes;
+        };
+
+        /**
+         *
+         * @param {FacetChannel} channel
+         * @param {number} count Number of factors
+         */
+        const computeFlexCoords = (channel, count) => {
+            const dimension = this._facetDimensions[channel];
+
+            const spacing = coalesce(
+                dimension ? dimension.facetFieldDef.spacing : undefined,
+                this.spec.spacing,
+                DEFAULT_SPACING
+            );
+
+            const cellSizes =
+                channel == "column"
+                    ? calculateCellSizes(
+                          childSize.width,
+                          count,
+                          xStride,
+                          xOffset
+                      )
+                    : calculateCellSizes(
+                          childSize.height,
+                          count,
+                          yStride,
+                          wrap ? 0 : yOffset
+                      );
+
+            return mapToPixelCoords(
+                cellSizes,
+                coords[channel == "column" ? "width" : "height"],
+                {
+                    spacing,
+                    devicePixelRatio: window.devicePixelRatio,
+                }
+            );
+        };
+
+        let nCols = 0;
+        let nRows = 0;
+        let n = 0;
+
+        if (wrap) {
+            // Wrapping layout
+            n = this._facetDimensions.column.factors.length;
+            nCols = this.spec.columns;
+            nRows = Math.ceil(n / nCols);
+        } else {
+            /** @param {FacetDimension} facetDimension */
+            const getCount = (facetDimension) =>
+                facetDimension ? facetDimension.factors.length : 1;
+
+            nCols = getCount(this._facetDimensions.column);
+            nRows = getCount(this._facetDimensions.row);
+            n = nCols * nRows;
+        }
+
+        const columnFlexCoords = computeFlexCoords("column", nCols);
+        const rowFlexCoords = computeFlexCoords("row", nRows);
+
+        const axisSizes =
+            this.child instanceof DecoratorView
+                ? this.child.getAxisSizes()
+                : Padding.createUniformPadding(0);
+
+        const facetIds = this.getFacetGroups();
+
+        // Render column labels
+        if (this._facetDimensions.column) {
+            const factors = this._facetDimensions.column.factors;
+            for (let x = 0; x < factors.length; x++) {
+                // Take wrapping labels into account
+                const xCell = columnFlexCoords[(x % nCols) * xStride + xOffset];
+                const yCell = rowFlexCoords[Math.floor(x / nCols) * yStride];
+                this._labelViews.column.render(
+                    context,
+                    Rectangle.create(
+                        xCell.location + axisSizes.left,
+                        yCell.location,
+                        xCell.size - axisSizes.width,
+                        yCell.size
+                    ).translateBy(coords),
+                    { ...options, facetId: factors[x] }
+                );
+            }
+        }
+
+        // Render row labels
+        if (this._facetDimensions.row) {
+            const factors = this._facetDimensions.row.factors;
+            for (let y = 0; y < factors.length; y++) {
+                const xCell = columnFlexCoords[0];
+                const yCell = rowFlexCoords[y * yStride + yOffset];
+                this._labelViews.row.render(
+                    context,
+                    Rectangle.create(
+                        xCell.location,
+                        yCell.location + axisSizes.top,
+                        xCell.size,
+                        yCell.size - axisSizes.height
+                    ).translateBy(coords),
+                    { ...options, facetId: factors[y] }
+                );
+            }
+        }
+
+        // Render facets
+        let i = 0;
+        for (let x = 0; x < nCols; x++) {
+            for (let y = 0; y < nRows; y++) {
+                if (i >= n) break;
+
+                const xCell = columnFlexCoords[x * xStride + xOffset];
+                const yCell = rowFlexCoords[y * yStride + yOffset];
+                this.child.render(
+                    context,
+                    new Rectangle(
+                        xCell.location,
+                        yCell.location,
+                        xCell.size,
+                        yCell.size
+                    ).translateBy(coords),
+                    { ...options, facetId: facetIds[i] }
+                );
+                i++;
+            }
+        }
+
+        context.popView(this);
+    }
+}
+
+/**
+ *
+ */
+function createLabelViewSpec(headerConfig) {
+    // TODO: Support styling: https://vega.github.io/vega-lite/docs/header.html#labels
+
+    /** @type {import("./viewUtils").UnitSpec} */
+    const titleView = {
+        data: {
+            values: [],
+        },
+        mark: {
+            type: "text",
+            clip: false,
+            angle: headerConfig.labelAngle,
+        },
+        encoding: {
+            text: { field: "data", type: "nominal" },
+            size: { value: headerConfig.labelFontSize },
+            color: { value: headerConfig.labelColor },
+        },
+    };
+
+    return titleView;
+}

package/dist/src/view/flowBuilder.d.ts

@@ -0,0 +1,37 @@
+/**
+ * @param {View} root
+ * @param {DataFlow<View>} [existingFlow] Add data flow
+ *      graphs to an existing DataFlow object.
+ */
+export function buildDataFlow(root: import("./view").default, existingFlow?: DataFlow<import("./view").default>): DataFlow<import("./view").default>;
+/**
+ * Changes the ChromPos channelDefs into FieldDefs and returns
+ * LinearizeGenomicCoordinate transform(s) that should be inserted into
+ * the data flow.
+ *
+ * @param {View} view
+ */
+export function linearizeLocusAccess(view: import("./view").default): {
+    transforms: import("../data/flowNode").default[];
+    rewrittenEncoding: import("../spec/channel").Encoding<string>;
+    /**
+     * Should be called after the whole flow has been created in order to
+     * not disrupt inheritance of encodings
+     */
+    rewrite: () => void;
+};
+/**
+ * A helper function for creating linear data flows programmatically.
+ *
+ * @param {H} dataSource A data source or any other initial FlowNode.
+ * @param  {...FlowNode} transforms
+ * @template {FlowNode} H
+ */
+export function createChain<H extends import("../data/flowNode").default>(dataSource: H, ...transforms: import("../data/flowNode").default[]): {
+    dataSource: H;
+    collector: Collector;
+    loadAndCollect: () => Promise<Iterable<import("../data/flowNode").Datum>>;
+};
+import DataFlow from "../data/dataFlow";
+import Collector from "../data/collector";
+//# sourceMappingURL=flowBuilder.d.ts.map

package/dist/src/view/flowBuilder.d.ts.map

@@ -0,0 +1 @@
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