@genome-spy/core 0.72.0 → 0.74.0

package/dist/src/config/resolveConfig.js

@@ -0,0 +1,32 @@
+import { mergeConfigScopes } from "./mergeConfig.js";
+
+/**
+ * @param {object} options
+ * @param {import("../spec/config.js").GenomeSpyConfig} options.defaultConfig
+ * @param {import("../spec/config.js").GenomeSpyConfig} [options.builtInTheme]
+ * @param {import("../spec/config.js").GenomeSpyConfig} [options.theme]
+ * @returns {import("../spec/config.js").GenomeSpyConfig}
+ */
+export function resolveBaseConfig({ defaultConfig, builtInTheme, theme }) {
+    return /** @type {import("../spec/config.js").GenomeSpyConfig} */ (
+        mergeConfigScopes([defaultConfig, builtInTheme, theme])
+    );
+}
+
+/**
+ * Merges import-site config with imported root config.
+ * Imported config has higher precedence.
+ *
+ * @param {import("../spec/config.js").GenomeSpyConfig} [importConfig]
+ * @param {import("../spec/config.js").GenomeSpyConfig} [importedConfig]
+ * @returns {import("../spec/config.js").GenomeSpyConfig | undefined}
+ */
+export function resolveImportedSpecConfig(importConfig, importedConfig) {
+    if (!importConfig && !importedConfig) {
+        return undefined;
+    }
+
+    return /** @type {import("../spec/config.js").GenomeSpyConfig} */ (
+        mergeConfigScopes([importConfig, importedConfig])
+    );
+}

package/dist/src/config/scaleConfig.d.ts

@@ -0,0 +1,40 @@
+/**
+ * @param {string} rangeName
+ * @returns {rangeName is keyof import("../spec/config.js").RangeConfig}
+ */
+export function isConfigRangeName(rangeName: string): rangeName is keyof import("../spec/config.js").RangeConfig;
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {string} rangeName
+ * @returns {import("../spec/config.js").RangeConfig[keyof import("../spec/config.js").RangeConfig] | undefined}
+ */
+export function getConfiguredNamedRange(scopes: import("../spec/config.js").GenomeSpyConfig[], rangeName: string): import("../spec/config.js").RangeConfig[keyof import("../spec/config.js").RangeConfig] | undefined;
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {import("../spec/channel.js").Type} dataType
+ * @returns {import("../spec/config.js").ScaleConfig}
+ */
+export function getConfiguredScaleConfig(scopes: import("../spec/config.js").GenomeSpyConfig[], dataType: import("../spec/channel.js").Type): import("../spec/config.js").ScaleConfig;
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @returns {import("../spec/config.js").RangeConfig}
+ */
+export function getConfiguredRangeConfig(scopes: import("../spec/config.js").GenomeSpyConfig[]): import("../spec/config.js").RangeConfig;
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {object} options
+ * @param {import("../spec/channel.js").Channel} options.channel
+ * @param {import("../spec/channel.js").Type} options.dataType
+ * @param {boolean} options.isExplicitDomain
+ * @param {import("../spec/mark.js").MarkType[]} [options.markTypes]
+ * @param {boolean} [options.hasDomainMid]
+ * @returns {import("../spec/scale.js").Scale}
+ */
+export function getConfiguredScaleDefaults(scopes: import("../spec/config.js").GenomeSpyConfig[], { channel, dataType, isExplicitDomain, markTypes, hasDomainMid }: {
+    channel: import("../spec/channel.js").Channel;
+    dataType: import("../spec/channel.js").Type;
+    isExplicitDomain: boolean;
+    markTypes?: import("../spec/mark.js").MarkType[];
+    hasDomainMid?: boolean;
+}): import("../spec/scale.js").Scale;
+//# sourceMappingURL=scaleConfig.d.ts.map

package/dist/src/config/scaleConfig.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/config/scaleConfig.js

@@ -0,0 +1,220 @@
+import {
+    isColorChannel,
+    isDiscreteChannel,
+    isPositionalChannel,
+} from "../encoder/encoder.js";
+import { mergeConfigScopes } from "./mergeConfig.js";
+
+/** @type {Record<string, keyof import("../spec/config.js").ScaleConfig>} */
+const COLOR_SCHEME_KEYS = {
+    nominal: "nominalColorScheme",
+    ordinal: "ordinalColorScheme",
+    quantitative: "quantitativeColorScheme",
+};
+
+const HEATMAP_MARK_TYPES = new Set(["rect"]);
+const NAMED_RANGE_KEYS = new Set([
+    "shape",
+    "size",
+    "angle",
+    "heatmap",
+    "ramp",
+    "diverging",
+]);
+
+/**
+ * @param {unknown} scheme
+ * @returns {scheme is import("../spec/scale.js").SchemeParams | string}
+ */
+function isConfiguredScheme(scheme) {
+    return (
+        typeof scheme == "string" ||
+        (scheme != null && typeof scheme == "object")
+    );
+}
+
+/**
+ * @param {string} rangeName
+ * @returns {rangeName is keyof import("../spec/config.js").RangeConfig}
+ */
+export function isConfigRangeName(rangeName) {
+    return NAMED_RANGE_KEYS.has(rangeName);
+}
+
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {string} rangeName
+ * @returns {import("../spec/config.js").RangeConfig[keyof import("../spec/config.js").RangeConfig] | undefined}
+ */
+export function getConfiguredNamedRange(scopes, rangeName) {
+    if (!isConfigRangeName(rangeName)) {
+        return undefined;
+    }
+
+    const rangeConfig = getConfiguredRangeConfig(scopes);
+    return rangeConfig[rangeName];
+}
+
+/**
+ * @param {import("../spec/channel.js").Type} dataType
+ * @returns {keyof import("../spec/config.js").ScaleConfig | undefined}
+ */
+function getDataTypeBucket(dataType) {
+    if (
+        ["nominal", "ordinal", "quantitative", "index", "locus"].includes(
+            dataType
+        )
+    ) {
+        return /** @type {keyof import("../spec/config.js").ScaleConfig} */ (
+            dataType
+        );
+    }
+}
+
+/**
+ * @param {import("../spec/config.js").ScaleConfig | undefined} scaleConfig
+ */
+function getBaseScaleConfig(scaleConfig) {
+    if (!scaleConfig) {
+        return {};
+    }
+
+    const base = /** @type {Record<string, any>} */ ({ ...scaleConfig });
+    for (const key of [
+        "nominal",
+        "ordinal",
+        "quantitative",
+        "index",
+        "locus",
+        "nominalColorScheme",
+        "ordinalColorScheme",
+        "quantitativeColorScheme",
+        // Deprecated aliases kept out of the resolved base scale object.
+        "indexColorScheme",
+        "locusColorScheme",
+    ]) {
+        delete base[key];
+    }
+
+    return base;
+}
+
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {import("../spec/channel.js").Type} dataType
+ * @returns {import("../spec/config.js").ScaleConfig}
+ */
+export function getConfiguredScaleConfig(scopes, dataType) {
+    const dataTypeBucket = getDataTypeBucket(dataType);
+
+    return /** @type {import("../spec/config.js").ScaleConfig} */ (
+        mergeConfigScopes(
+            scopes.flatMap((scope) => {
+                const scale = /** @type {Record<string, any> | undefined} */ (
+                    scope.scale
+                );
+                const typedScale =
+                    scale && dataTypeBucket
+                        ? /** @type {Record<string, any> | undefined} */ (
+                              scale[dataTypeBucket]
+                          )
+                        : undefined;
+
+                return [scale, typedScale];
+            })
+        )
+    );
+}
+
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @returns {import("../spec/config.js").RangeConfig}
+ */
+export function getConfiguredRangeConfig(scopes) {
+    return /** @type {import("../spec/config.js").RangeConfig} */ (
+        mergeConfigScopes(
+            scopes.map(
+                (scope) =>
+                    /** @type {Record<string, any> | undefined} */ (scope.range)
+            )
+        )
+    );
+}
+
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {object} options
+ * @param {import("../spec/channel.js").Channel} options.channel
+ * @param {import("../spec/channel.js").Type} options.dataType
+ * @param {boolean} options.isExplicitDomain
+ * @param {import("../spec/mark.js").MarkType[]} [options.markTypes]
+ * @param {boolean} [options.hasDomainMid]
+ * @returns {import("../spec/scale.js").Scale}
+ */
+export function getConfiguredScaleDefaults(
+    scopes,
+    { channel, dataType, isExplicitDomain, markTypes, hasDomainMid }
+) {
+    const scaleConfig = getConfiguredScaleConfig(scopes, dataType);
+    const rangeConfig = getConfiguredRangeConfig(scopes);
+
+    /** @type {import("../spec/scale.js").Scale} */
+    const props = {
+        ...getBaseScaleConfig(scaleConfig),
+    };
+
+    if (isExplicitDomain) {
+        props.zero = false;
+    } else if (props.zero === undefined && scaleConfig.zero !== undefined) {
+        props.zero = scaleConfig.zero;
+    }
+
+    if (isPositionalChannel(channel) && props.nice === undefined) {
+        props.nice =
+            scaleConfig.nice !== undefined
+                ? scaleConfig.nice
+                : !isExplicitDomain;
+    }
+
+    if (isColorChannel(channel) && props.scheme === undefined) {
+        if (dataType == "quantitative") {
+            const useDiverging =
+                hasDomainMid || scaleConfig.domainMid !== undefined;
+
+            // Mirror Vega-Lite defaults for quantitative color scales:
+            // domainMid -> diverging, rect-like marks -> heatmap, others -> ramp.
+            const rangeScheme = useDiverging
+                ? rangeConfig.diverging
+                : markTypes?.length &&
+                    markTypes.every((markType) =>
+                        HEATMAP_MARK_TYPES.has(markType)
+                    )
+                  ? rangeConfig.heatmap
+                  : rangeConfig.ramp;
+
+            const configuredScheme = isConfiguredScheme(rangeScheme)
+                ? rangeScheme
+                : scaleConfig.quantitativeColorScheme;
+
+            if (isConfiguredScheme(configuredScheme)) {
+                props.scheme = configuredScheme;
+            }
+        } else {
+            const schemeKey =
+                COLOR_SCHEME_KEYS[dataType] ?? COLOR_SCHEME_KEYS.quantitative;
+            const configuredScheme = scaleConfig[schemeKey];
+
+            if (isConfiguredScheme(configuredScheme)) {
+                props.scheme = configuredScheme;
+            }
+        }
+    } else if (isDiscreteChannel(channel) && props.range === undefined) {
+        props.range = channel == "shape" ? (rangeConfig.shape ?? []) : [];
+    } else if (channel == "size" && props.range === undefined) {
+        props.range = rangeConfig.size;
+    } else if (channel == "angle" && props.range === undefined) {
+        props.range = rangeConfig.angle;
+    }
+
+    return props;
+}

package/dist/src/config/styleUtils.d.ts

@@ -0,0 +1,6 @@
+/**
+ * @param {string | string[] | undefined} style
+ * @returns {string[]}
+ */
+export function normalizeStyle(style: string | string[] | undefined): string[];
+//# sourceMappingURL=styleUtils.d.ts.map

package/dist/src/config/styleUtils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"styleUtils.d.ts","sourceRoot":"","sources":["../../../src/config/styleUtils.js"],"names":[],"mappings":"AAAA;;;GAGG;AACH,sCAHW,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAC3B,MAAM,EAAE,CAOpB"}

package/dist/src/config/styleUtils.js

@@ -0,0 +1,10 @@
+/**
+ * @param {string | string[] | undefined} style
+ * @returns {string[]}
+ */
+export function normalizeStyle(style) {
+    if (!style) {
+        return [];
+    }
+    return Array.isArray(style) ? style : [style];
+}

package/dist/src/config/themes.d.ts

@@ -0,0 +1,15 @@
+/**
+ * @param {import("../spec/config.js").BuiltInThemeName} name
+ * @returns {string | undefined}
+ */
+export function getBuiltInThemeBackground(name: import("../spec/config.js").BuiltInThemeName): string | undefined;
+/**
+ * @param {import("../spec/config.js").BuiltInThemeName | import("../spec/config.js").BuiltInThemeName[] | undefined} selection
+ * @returns {import("../spec/config.js").GenomeSpyConfig | undefined}
+ */
+export function resolveThemeSelection(selection: import("../spec/config.js").BuiltInThemeName | import("../spec/config.js").BuiltInThemeName[] | undefined): import("../spec/config.js").GenomeSpyConfig | undefined;
+/**
+ * @type {import("../spec/config.js").BuiltInThemeName}
+ */
+export const DEFAULT_THEME_NAME: import("../spec/config.js").BuiltInThemeName;
+//# sourceMappingURL=themes.d.ts.map

package/dist/src/config/themes.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"themes.d.ts","sourceRoot":"","sources":["../../../src/config/themes.js"],"names":[],"mappings":"AA+QA;;;GAGG;AACH,gDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAC1C,MAAM,GAAG,SAAS,CAI9B;AAED;;;GAGG;AACH,iDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAAG,OAAO,mBAAmB,EAAE,gBAAgB,EAAE,GAAG,SAAS,GACvG,OAAO,mBAAmB,EAAE,eAAe,GAAG,SAAS,CAWnE;AA1BD;;GAEG;AACH,iCAFU,OAAO,mBAAmB,EAAE,gBAAgB,CAER"}

package/dist/src/config/themes.js

@@ -0,0 +1,293 @@
+import { mergeConfigScopes } from "./mergeConfig.js";
+
+/** @type {import("../spec/config.js").GenomeSpyConfig} */
+const VEGALITE_THEME = {
+    mark: {
+        color: "#4c78a8",
+    },
+    point: {
+        filled: false,
+        size: 30,
+    },
+    rule: {
+        color: "black",
+    },
+    text: {
+        color: "black",
+    },
+    view: {
+        stroke: "#ddd",
+        strokeWidth: 1,
+    },
+    axis: {
+        grid: false,
+        domain: true,
+        tickColor: "gray",
+        domainColor: "gray",
+        gridColor: "#ddd",
+        labelColor: "#333",
+        titleColor: "#333",
+        titleFontSize: 11,
+        titleFontWeight: "normal",
+    },
+    axisQuantitative: {
+        grid: true,
+    },
+    scale: {
+        nominalColorScheme: "tableau10",
+        ordinalColorScheme: "blues",
+        quantitativeColorScheme: "blues",
+    },
+    range: {
+        heatmap: "viridis",
+        ramp: "blues",
+        diverging: "blueorange",
+    },
+};
+
+/**
+ * Built-in themes. These can be selected with the `theme` property
+ * in view specs.
+ *
+ * TODO: Vega themes include additional properties (for example legend config,
+ * top-level background, and custom categorical range arrays) that are not yet
+ * configurable through GenomeSpy's theme/config surface.
+ *
+ * `background` mirrors Vega(-Lite) theme shape. GenomeSpy uses it only for
+ * root canvas clear color; subtree config resolution ignores it.
+ *
+ * @type {Record<import("../spec/config.js").BuiltInThemeName, import("../spec/config.js").GenomeSpyConfig & { background?: string}>}
+ */
+const BUILT_IN_THEME_DEFINITIONS = {
+    genomespy: {},
+    vegalite: VEGALITE_THEME,
+    quartz: mergeConfigScopes([
+        VEGALITE_THEME,
+        {
+            background: "#f9f9f9",
+            view: {
+                fill: "#f9f9f9",
+            },
+            mark: {
+                color: "#ab5787",
+            },
+            point: {
+                size: 30,
+            },
+            axis: {
+                domainColor: "#979797",
+                domainWidth: 0.5,
+                gridWidth: 0.2,
+                labelColor: "#979797",
+                tickColor: "#979797",
+                tickWidth: 0.2,
+                titleColor: "#979797",
+            },
+            axisX: {
+                grid: true,
+                tickSize: 10,
+            },
+            axisY: {
+                domain: false,
+                grid: true,
+                tickSize: 0,
+            },
+        },
+    ]),
+    dark: mergeConfigScopes([
+        VEGALITE_THEME,
+        {
+            background: "#333",
+            view: {
+                fill: "#333",
+                stroke: "#888",
+            },
+            title: {
+                color: "#fff",
+            },
+            axis: {
+                domainColor: "#fff",
+                gridColor: "#888",
+                tickColor: "#fff",
+                labelColor: "#fff",
+                titleColor: "#fff",
+            },
+            text: {
+                color: "#fff",
+            },
+            rule: {
+                color: "#fff",
+            },
+        },
+    ]),
+    fivethirtyeight: mergeConfigScopes([
+        VEGALITE_THEME,
+        {
+            background: "#f0f0f0",
+            view: {
+                fill: "#f0f0f0",
+            },
+            mark: {
+                color: "#30a2da",
+            },
+            point: {
+                filled: true,
+                shape: "circle",
+            },
+            axis: {
+                domainColor: "#cbcbcb",
+                grid: true,
+                gridColor: "#cbcbcb",
+                gridWidth: 1,
+                labelColor: "#999",
+                labelFontSize: 10,
+                titleColor: "#333",
+                tickColor: "#cbcbcb",
+                tickSize: 10,
+                titleFontSize: 14,
+                titlePadding: 10,
+                labelPadding: 4,
+            },
+            axisNominal: {
+                grid: false,
+            },
+            axisOrdinal: {
+                grid: false,
+            },
+            title: {
+                anchor: "start",
+                fontSize: 24,
+                fontWeight: 600,
+                offset: 20,
+            },
+        },
+    ]),
+    urbaninstitute: mergeConfigScopes([
+        VEGALITE_THEME,
+        {
+            background: "#FFFFFF",
+            view: {
+                fill: "#FFFFFF",
+                // Vega theme uses "transparent". GenomeSpy color channels are RGB-only,
+                // so represent a transparent stroke via zero opacity.
+                stroke: "#000000",
+                strokeOpacity: 0,
+            },
+            mark: {
+                color: "#1696d2",
+            },
+            point: {
+                filled: true,
+            },
+            text: {
+                font: "Lato",
+                color: "#1696d2",
+                size: 11,
+                align: "center",
+                fontWeight: 400,
+            },
+            title: {
+                anchor: "start",
+                fontSize: 18,
+                font: "Lato",
+            },
+            axisX: {
+                domain: true,
+                domainColor: "#000000",
+                domainWidth: 1,
+                grid: false,
+                labelFontSize: 12,
+                labelFont: "Lato",
+                labelAngle: 0,
+                tickColor: "#000000",
+                tickSize: 5,
+                titleFontSize: 12,
+                titlePadding: 10,
+                titleFont: "Lato",
+            },
+            axisY: {
+                domain: false,
+                domainWidth: 1,
+                grid: true,
+                gridColor: "#DEDDDD",
+                gridWidth: 1,
+                labelFontSize: 12,
+                labelFont: "Lato",
+                labelPadding: 8,
+                ticks: false,
+                titleFontSize: 12,
+                titlePadding: 10,
+                titleFont: "Lato",
+            },
+        },
+    ]),
+};
+
+/** @type {import("../spec/config.js").BuiltInThemeName[]} */
+const BUILT_IN_THEME_NAMES =
+    /** @type {import("../spec/config.js").BuiltInThemeName[]} */ (
+        Object.keys(BUILT_IN_THEME_DEFINITIONS)
+    );
+
+/**
+ * @param {import("../spec/config.js").BuiltInThemeName} name
+ * @returns {import("../spec/config.js").GenomeSpyConfig}
+ */
+function getThemeConfig(name) {
+    const config = { ...BUILT_IN_THEME_DEFINITIONS[name] };
+    delete config.background;
+    return /** @type {import("../spec/config.js").GenomeSpyConfig} */ (config);
+}
+
+/**
+ * @param {import("../spec/config.js").BuiltInThemeName | import("../spec/config.js").BuiltInThemeName[] | undefined} selection
+ * @returns {import("../spec/config.js").BuiltInThemeName[]}
+ */
+function resolveThemeNames(selection) {
+    if (!selection) {
+        return [];
+    }
+
+    const names = Array.isArray(selection) ? selection : [selection];
+    const unknown = names.filter(
+        (name) => !(name in BUILT_IN_THEME_DEFINITIONS)
+    );
+    if (unknown.length > 0) {
+        throw new Error(
+            'Unknown theme "' +
+                unknown[0] +
+                '". Available themes: ' +
+                BUILT_IN_THEME_NAMES.join(", ")
+        );
+    }
+
+    return names;
+}
+
+/**
+ * @type {import("../spec/config.js").BuiltInThemeName}
+ */
+export const DEFAULT_THEME_NAME = "genomespy";
+
+/**
+ * @param {import("../spec/config.js").BuiltInThemeName} name
+ * @returns {string | undefined}
+ */
+export function getBuiltInThemeBackground(name) {
+    return BUILT_IN_THEME_DEFINITIONS[name].background;
+}
+
+/**
+ * @param {import("../spec/config.js").BuiltInThemeName | import("../spec/config.js").BuiltInThemeName[] | undefined} selection
+ * @returns {import("../spec/config.js").GenomeSpyConfig | undefined}
+ */
+export function resolveThemeSelection(selection) {
+    const names = resolveThemeNames(selection);
+    if (names.length == 0) {
+        return undefined;
+    }
+
+    return /** @type {import("../spec/config.js").GenomeSpyConfig} */ (
+        mergeConfigScopes(names.map((name) => getThemeConfig(name)))
+    );
+}

package/dist/src/config/titleConfig.d.ts

@@ -0,0 +1,12 @@
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @returns {import("../spec/config.js").TitleConfig}
+ */
+export function getConfiguredTitleConfig(scopes: import("../spec/config.js").GenomeSpyConfig[]): import("../spec/config.js").TitleConfig;
+/**
+ * @param {import("../spec/config.js").GenomeSpyConfig[]} scopes
+ * @param {string | string[]} [styleName]
+ * @returns {import("../spec/config.js").StyleConfig}
+ */
+export function getConfiguredStyleConfig(scopes: import("../spec/config.js").GenomeSpyConfig[], styleName?: string | string[]): import("../spec/config.js").StyleConfig;
+//# sourceMappingURL=titleConfig.d.ts.map

package/dist/src/config/titleConfig.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"titleConfig.d.ts","sourceRoot":"","sources":["../../../src/config/titleConfig.js"],"names":[],"mappings":"AAGA;;;GAGG;AACH,iDAHW,OAAO,mBAAmB,EAAE,eAAe,EAAE,GAC3C,OAAO,mBAAmB,EAAE,WAAW,CAWnD;AAED;;;;GAIG;AACH,iDAJW,OAAO,mBAAmB,EAAE,eAAe,EAAE,cAC7C,MAAM,GAAG,MAAM,EAAE,GACf,OAAO,mBAAmB,EAAE,WAAW,CAoBnD"}