@mstone6969/graph 0.0.0-stage → 0.2.0

package/dist/charts/genomics/GenomeSamples.js

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+import { SampleData } from "../../data/SampleData.js";
+import { GenomeCytobands } from "./GenomeCytobands.js";
+// src/charts/genomics/GenomeSamples.ts
+var BIN = 1e7;
+var Mb = 1e6;
+/** Approximate protein-coding genes per chromosome, which sets each one's density. */
+var GENES = {
+	1: 2050,
+	2: 1300,
+	3: 1080,
+	4: 750,
+	5: 880,
+	6: 1040,
+	7: 900,
+	8: 680,
+	9: 780,
+	10: 730,
+	11: 1290,
+	12: 1030,
+	13: 320,
+	14: 650,
+	15: 590,
+	16: 860,
+	17: 1180,
+	18: 270,
+	19: 1470,
+	20: 540,
+	21: 230,
+	22: 440,
+	X: 840,
+	Y: 63
+};
+var ONCOGENE = "Oncogene";
+var SUPPRESSOR = "Tumor suppressor";
+/** Cancer census genes at their GRCh38 positions, in Mb. */
+var GENE_LOCI = [
+	[
+		"NRAS",
+		"1",
+		114.7,
+		ONCOGENE
+	],
+	[
+		"ALK",
+		"2",
+		29.2,
+		ONCOGENE
+	],
+	[
+		"IDH1",
+		"2",
+		208.2,
+		ONCOGENE
+	],
+	[
+		"VHL",
+		"3",
+		10.1,
+		SUPPRESSOR
+	],
+	[
+		"PIK3CA",
+		"3",
+		179.1,
+		ONCOGENE
+	],
+	[
+		"FGFR3",
+		"4",
+		1.8,
+		ONCOGENE
+	],
+	[
+		"KIT",
+		"4",
+		54.7,
+		ONCOGENE
+	],
+	[
+		"APC",
+		"5",
+		112.7,
+		SUPPRESSOR
+	],
+	[
+		"EGFR",
+		"7",
+		55,
+		ONCOGENE
+	],
+	[
+		"MET",
+		"7",
+		116.7,
+		ONCOGENE
+	],
+	[
+		"BRAF",
+		"7",
+		140.7,
+		ONCOGENE
+	],
+	[
+		"MYC",
+		"8",
+		127.7,
+		ONCOGENE
+	],
+	[
+		"CDKN2A",
+		"9",
+		22,
+		SUPPRESSOR
+	],
+	[
+		"ABL1",
+		"9",
+		130.7,
+		ONCOGENE
+	],
+	[
+		"RET",
+		"10",
+		43.1,
+		ONCOGENE
+	],
+	[
+		"PTEN",
+		"10",
+		87.9,
+		SUPPRESSOR
+	],
+	[
+		"WT1",
+		"11",
+		32.4,
+		SUPPRESSOR
+	],
+	[
+		"CCND1",
+		"11",
+		69.6,
+		ONCOGENE
+	],
+	[
+		"ATM",
+		"11",
+		108.2,
+		SUPPRESSOR
+	],
+	[
+		"KRAS",
+		"12",
+		25.2,
+		ONCOGENE
+	],
+	[
+		"MDM2",
+		"12",
+		68.8,
+		ONCOGENE
+	],
+	[
+		"BRCA2",
+		"13",
+		32.3,
+		SUPPRESSOR
+	],
+	[
+		"RB1",
+		"13",
+		48.3,
+		SUPPRESSOR
+	],
+	[
+		"TP53",
+		"17",
+		7.7,
+		SUPPRESSOR
+	],
+	[
+		"NF1",
+		"17",
+		31.1,
+		SUPPRESSOR
+	],
+	[
+		"ERBB2",
+		"17",
+		39.7,
+		ONCOGENE
+	],
+	[
+		"BRCA1",
+		"17",
+		43.1,
+		SUPPRESSOR
+	],
+	[
+		"RNF43",
+		"17",
+		58.4,
+		SUPPRESSOR
+	],
+	[
+		"SMAD4",
+		"18",
+		51.1,
+		SUPPRESSOR
+	],
+	[
+		"STK11",
+		"19",
+		1.2,
+		SUPPRESSOR
+	],
+	[
+		"GNAS",
+		"20",
+		58.9,
+		ONCOGENE
+	],
+	[
+		"NF2",
+		"22",
+		29.6,
+		SUPPRESSOR
+	]
+];
+/** Well-known recurrent rearrangements, at their partner genes' GRCh38 positions in Mb. */
+var FUSIONS = [
+	[
+		"BCR–ABL1",
+		"9",
+		130.7,
+		"22",
+		23.2,
+		"Translocation"
+	],
+	[
+		"IGH–MYC",
+		"8",
+		127.7,
+		"14",
+		105.6,
+		"Translocation"
+	],
+	[
+		"PML–RARA",
+		"15",
+		74,
+		"17",
+		40.3,
+		"Translocation"
+	],
+	[
+		"RUNX1–RUNX1T1",
+		"8",
+		92,
+		"21",
+		34.8,
+		"Translocation"
+	],
+	[
+		"KMT2A–AFF1",
+		"4",
+		87,
+		"11",
+		118.4,
+		"Translocation"
+	],
+	[
+		"ETV6–RUNX1",
+		"12",
+		11.9,
+		"21",
+		34.8,
+		"Translocation"
+	],
+	[
+		"NPM1–ALK",
+		"2",
+		29.2,
+		"5",
+		171.4,
+		"Translocation"
+	],
+	[
+		"EWSR1–FLI1",
+		"11",
+		128.7,
+		"22",
+		29.3,
+		"Translocation"
+	],
+	[
+		"SS18–SSX1",
+		"18",
+		26,
+		"X",
+		48.2,
+		"Translocation"
+	],
+	[
+		"PAX3–FOXO1",
+		"2",
+		222.2,
+		"13",
+		40.6,
+		"Translocation"
+	],
+	[
+		"IGH–BCL2",
+		"14",
+		105.6,
+		"18",
+		63.1,
+		"Translocation"
+	],
+	[
+		"IGH–CCND1",
+		"11",
+		69.6,
+		"14",
+		105.6,
+		"Translocation"
+	],
+	[
+		"EML4–ALK",
+		"2",
+		29.2,
+		"2",
+		42.3,
+		"Inversion"
+	],
+	[
+		"CCDC6–RET",
+		"10",
+		43.1,
+		"10",
+		59.8,
+		"Inversion"
+	],
+	[
+		"TMPRSS2–ERG",
+		"21",
+		38.4,
+		"21",
+		41.5,
+		"Deletion"
+	],
+	[
+		"FIP1L1–PDGFRA",
+		"4",
+		53.4,
+		"4",
+		54.2,
+		"Deletion"
+	],
+	[
+		"KIAA1549–BRAF",
+		"7",
+		138.8,
+		"7",
+		140.7,
+		"Duplication"
+	]
+];
+/** Focal log2 ratios: amplified oncogenes and homozygously deleted suppressors. */
+var FOCAL = [
+	[
+		"7",
+		55,
+		2.1
+	],
+	[
+		"8",
+		127.7,
+		2.4
+	],
+	[
+		"11",
+		69.6,
+		1.8
+	],
+	[
+		"17",
+		39.7,
+		2.6
+	],
+	[
+		"9",
+		22,
+		-1.8
+	],
+	[
+		"10",
+		87.9,
+		-1.5
+	],
+	[
+		"13",
+		48.3,
+		-1.4
+	]
+];
+var PURITY = .7;
+/** A cancer-genome sample: the real GRCh38 reference, with measurements reshaped from `SampleData`. */
+var GenomeSamples = class {
+	/** Standard normal draws from `SampleData`, since its generators are the only seeded source. */
+	static #normals(seed, count) {
+		const values = SampleData.distribution(seed, count, 1).map((row) => (row.value - 40) / 8);
+		let i = 0;
+		return () => values[i++ % values.length];
+	}
+	static #tracks(seed) {
+		const z = this.#normals(seed, 900);
+		return [...new Set(GenomeCytobands.rows.map((row) => row.chrom))].flatMap((chrom) => {
+			const bands = GenomeCytobands.rows.filter((row) => row.chrom === chrom);
+			const length = bands.at(-1).end, centromere = bands.find((row) => row.stain === "acen").end;
+			const armState = () => {
+				const draw = z();
+				return draw > 1.1 ? 3 : draw < -1.1 ? 1 : 2;
+			};
+			const p = armState(), q = armState(), density = (GENES[chrom] ?? 0) / (length / Mb);
+			return Array.from({ length: Math.ceil(length / BIN) }, (_, i) => {
+				const start = i * BIN, end = Math.min(length, start + BIN), middle = (start + end) / 2;
+				const silent = bands.some((row) => middle >= row.start && middle < row.end && /acen|gvar|stalk/.test(row.stain));
+				const copies = middle < centromere ? p : q;
+				return [{
+					chrom,
+					start,
+					end,
+					track: "log2 CN",
+					value: +(FOCAL.find(([c, at]) => c === chrom && at * Mb >= start && at * Mb < end)?.[2] ?? Math.log2((.6000000000000001 + copies * PURITY) / 2) + z() * .07).toFixed(3)
+				}, {
+					chrom,
+					start,
+					end,
+					track: "Genes/Mb",
+					value: silent ? 0 : +(density * Math.exp(z() * .35)).toFixed(2)
+				}];
+			}).flat();
+		});
+	}
+	/** Every gene and rearrangement above, with tracks, on the published bands. Values are illustrative. */
+	static cancerGenome(seed) {
+		const score = SampleData.categories(seed, GENE_LOCI.length, 1).map((row) => row.value);
+		const recurrence = SampleData.categories(seed + 1, FUSIONS.length, 1).map((row) => row.value);
+		return {
+			bands: GenomeCytobands.rows,
+			tracks: this.#tracks(seed),
+			annotations: GENE_LOCI.map(([label, chrom, at, group], i) => ({
+				chrom,
+				start: at * Mb,
+				end: at * Mb,
+				label,
+				group,
+				value: score[i % score.length]
+			})),
+			links: FUSIONS.map(([name, chrom1, at1, chrom2, at2, kind], i) => {
+				const half = recurrence[i % recurrence.length] * .08 * Mb;
+				return {
+					name,
+					kind,
+					value: recurrence[i % recurrence.length],
+					chrom1,
+					start1: at1 * Mb - half,
+					end1: at1 * Mb + half,
+					chrom2,
+					start2: at2 * Mb - half,
+					end2: at2 * Mb + half
+				};
+			})
+		};
+	}
+};
+export { GenomeSamples };

package/dist/charts/genomics/GenomeStainScale.js

@@ -0,0 +1,24 @@
+import { hsl, interpolateRgb } from "d3";
+// src/charts/genomics/GenomeStainScale.ts
+/**
+* Giemsa stain colours. G-dark bands stay darker than G-light ones in both themes,
+* so a dark theme does not read as reverse banding.
+*/
+var GenomeStainScale = class {
+	#ramp;
+	#low;
+	#centromere;
+	constructor(theme) {
+		const [paper, carbon] = hsl(theme.surface).l > hsl(theme.ink).l ? [theme.surface, theme.ink] : [theme.ink, theme.surface];
+		this.#ramp = interpolateRgb(paper, carbon);
+		this.#low = theme.divergingLow;
+		this.#centromere = theme.divergingHigh;
+	}
+	fill = (band) => {
+		if (band.stain === "acen") return this.#centromere;
+		if (band.stain === "stalk") return this.#low;
+		if (band.stain === "gvar") return interpolateRgb(this.#ramp(.05), this.#low)(.45);
+		return this.#ramp(.05 + band.density * .82);
+	};
+};
+export { GenomeStainScale };

package/dist/charts/genomics/genomicsEnums.js

@@ -0,0 +1,67 @@
+// src/charts/genomics/genomicsEnums.ts
+/** ISCN level bands are shown at: as published, merged to sub-bands (p36.3), or merged to bands (p36). */
+var GenomeBandLevel = /* @__PURE__ */ function(GenomeBandLevel) {
+	GenomeBandLevel["Published"] = "published";
+	GenomeBandLevel["SubBand"] = "sub-band";
+	GenomeBandLevel["Band"] = "band";
+	return GenomeBandLevel;
+}({});
+/** `Karyogram` is the ISCN four-row arrangement; `Single` is one chromosome with its band names. */
+var GenomeIdeogramLayout = /* @__PURE__ */ function(GenomeIdeogramLayout) {
+	GenomeIdeogramLayout["Columns"] = "columns";
+	GenomeIdeogramLayout["Rows"] = "rows";
+	GenomeIdeogramLayout["Karyogram"] = "karyogram";
+	GenomeIdeogramLayout["Single"] = "single";
+	return GenomeIdeogramLayout;
+}({});
+/** What chromosomes line up on: the centromere, or the p-arm telomere. */
+var GenomeAlign = /* @__PURE__ */ function(GenomeAlign) {
+	GenomeAlign["Centromere"] = "centromere";
+	GenomeAlign["Telomere"] = "telomere";
+	return GenomeAlign;
+}({});
+/** `Constricted` draws the primary constriction and capped telomeres; `Block` is a plain band strip. */
+var GenomeOutline = /* @__PURE__ */ function(GenomeOutline) {
+	GenomeOutline["Constricted"] = "constricted";
+	GenomeOutline["Block"] = "block";
+	return GenomeOutline;
+}({});
+var GenomeAnnotationMark = /* @__PURE__ */ function(GenomeAnnotationMark) {
+	GenomeAnnotationMark["Triangle"] = "triangle";
+	GenomeAnnotationMark["Tick"] = "tick";
+	GenomeAnnotationMark["Lollipop"] = "lollipop";
+	GenomeAnnotationMark["None"] = "none";
+	return GenomeAnnotationMark;
+}({});
+var CircosIdeogram = /* @__PURE__ */ function(CircosIdeogram) {
+	CircosIdeogram["Banded"] = "banded";
+	CircosIdeogram["Plain"] = "plain";
+	return CircosIdeogram;
+}({});
+var CircosTrackMark = /* @__PURE__ */ function(CircosTrackMark) {
+	CircosTrackMark["Histogram"] = "histogram";
+	CircosTrackMark["Heatmap"] = "heatmap";
+	CircosTrackMark["Line"] = "line";
+	CircosTrackMark["Scatter"] = "scatter";
+	return CircosTrackMark;
+}({});
+/** `Ribbon` keeps both genomic spans in view; `Bezier` is a single line between loci. */
+var CircosLinkMark = /* @__PURE__ */ function(CircosLinkMark) {
+	CircosLinkMark["Ribbon"] = "ribbon";
+	CircosLinkMark["Bezier"] = "bezier";
+	CircosLinkMark["None"] = "none";
+	return CircosLinkMark;
+}({});
+var CircosLinkScope = /* @__PURE__ */ function(CircosLinkScope) {
+	CircosLinkScope["All"] = "all";
+	CircosLinkScope["Inter"] = "inter";
+	CircosLinkScope["Intra"] = "intra";
+	return CircosLinkScope;
+}({});
+/** `Focus` magnifies one chromosome, as Circos `chromosomes_scale` does. */
+var CircosScale = /* @__PURE__ */ function(CircosScale) {
+	CircosScale["Proportional"] = "proportional";
+	CircosScale["Focus"] = "focus";
+	return CircosScale;
+}({});
+export { CircosIdeogram, CircosLinkMark, CircosLinkScope, CircosScale, CircosTrackMark, GenomeAlign, GenomeAnnotationMark, GenomeBandLevel, GenomeIdeogramLayout, GenomeOutline };

package/dist/charts/genomics/index.js

@@ -0,0 +1,11 @@
+import { CircosFrame } from "./CircosFrame.js";
+import { CircosIdeogram, CircosLinkMark, CircosLinkScope, CircosScale, CircosTrackMark, GenomeAlign, GenomeAnnotationMark, GenomeBandLevel, GenomeIdeogramLayout, GenomeOutline } from "./genomicsEnums.js";
+import { GenomeAssembly } from "./GenomeAssembly.js";
+import { GenomeCytobands } from "./GenomeCytobands.js";
+import { GenomeSamples } from "./GenomeSamples.js";
+import { GenomeStainScale } from "./GenomeStainScale.js";
+import { CircosPlot } from "./CircosPlot.js";
+import { GenomeIdeogram } from "./GenomeIdeogram.js";
+// src/charts/genomics/index.ts
+var genomicsCatalog = [CircosPlot, GenomeIdeogram];
+export { CircosFrame, CircosIdeogram, CircosLinkMark, CircosLinkScope, CircosPlot, CircosScale, CircosTrackMark, GenomeAlign, GenomeAnnotationMark, GenomeAssembly, GenomeBandLevel, GenomeCytobands, GenomeIdeogram, GenomeIdeogramLayout, GenomeOutline, GenomeSamples, GenomeStainScale, genomicsCatalog };

package/dist/charts/geoflows/ConnectionMap.js

@@ -0,0 +1,137 @@
+import { ChartFamily, DataShape, Dimension } from "../../core/enums.js";
+import { FlowGeometry } from "./FlowGeometry.js";
+import { GeoFlowProjection } from "./GeoFlowFrame.js";
+import { GeoFlowSample } from "./GeoFlowSample.js";
+import { GeoFlowRoute, GeoLinkChart } from "./GeoLinkChart.js";
+import { scaleSqrt } from "d3";
+// src/charts/geoflows/ConnectionMap.ts
+/** Which links stay on the map. */
+var ConnectionMapTopology = /* @__PURE__ */ function(ConnectionMapTopology) {
+	ConnectionMapTopology["Full"] = "full";
+	ConnectionMapTopology["Spanning"] = "spanning-tree";
+	ConnectionMapTopology["Nearest"] = "nearest-neighbours";
+	ConnectionMapTopology["Backbone"] = "backbone";
+	return ConnectionMapTopology;
+}({});
+/** What sizes a node. */
+var ConnectionMapNode = /* @__PURE__ */ function(ConnectionMapNode) {
+	ConnectionMapNode["Degree"] = "degree";
+	ConnectionMapNode["Uniform"] = "uniform";
+	return ConnectionMapNode;
+}({});
+/** Show who is linked to whom, as an airline map does: reach and structure matter, not volume. */
+var ConnectionMap = class extends GeoLinkChart {
+	static meta = {
+		id: "connection-map",
+		name: "Connection map",
+		family: ChartFamily.Geospatial,
+		dimension: Dimension.Two,
+		shape: DataShape.Table,
+		description: "Draws thin links between places to reveal network reach, optionally reduced to a tree or backbone.",
+		tags: [
+			"airline",
+			"network",
+			"links"
+		],
+		sample: (seed) => GeoFlowSample.flows(seed, 90),
+		variants: {
+			projection: [
+				GeoFlowProjection.NaturalEarth,
+				GeoFlowProjection.Orthographic,
+				GeoFlowProjection.Mercator,
+				GeoFlowProjection.AzimuthalEquidistant
+			],
+			topology: [
+				"full",
+				"spanning-tree",
+				"nearest-neighbours",
+				"backbone"
+			],
+			route: [
+				GeoFlowRoute.Geodesic,
+				GeoFlowRoute.Arc,
+				GeoFlowRoute.Straight,
+				GeoFlowRoute.Bundled
+			],
+			node: ["degree", "uniform"]
+		}
+	};
+	defaults() {
+		return {
+			...super.defaults(),
+			topology: "full",
+			route: GeoFlowRoute.Geodesic,
+			node: "degree",
+			neighbours: 2
+		};
+	}
+	categorical() {
+		return false;
+	}
+	kept() {
+		const { topology, neighbours } = this.options;
+		const links = this.links;
+		if (topology === "backbone") return [...links].sort((a, b) => b.value - a.value).slice(0, Math.ceil(links.length / 4));
+		const byLength = [...links].sort((a, b) => FlowGeometry.km(a.from, a.to) - FlowGeometry.km(b.from, b.to));
+		if (topology === "nearest-neighbours") {
+			const used = /* @__PURE__ */ new Map();
+			return byLength.filter((link) => {
+				const open = [link.source, link.target].some((name) => (used.get(name) ?? 0) < neighbours);
+				if (open) for (const name of [link.source, link.target]) used.set(name, (used.get(name) ?? 0) + 1);
+				return open;
+			});
+		}
+		if (topology !== "spanning-tree") return links;
+		const parent = /* @__PURE__ */ new Map();
+		const root = (name) => {
+			const up = parent.get(name) ?? name;
+			return up === name ? name : root(up);
+		};
+		return byLength.filter((link) => {
+			const a = root(link.source), b = root(link.target);
+			if (a !== b) parent.set(a, b);
+			return a !== b;
+		});
+	}
+	track(frame, link, bundles) {
+		const { route } = this.options;
+		if (route === GeoFlowRoute.Geodesic) return frame.line(FlowGeometry.geodesic(link.from, link.to, 24));
+		const points = route === GeoFlowRoute.Bundled ? bundles.get(link.id) : this.screenRoute(frame, link, route);
+		return points ? FlowGeometry.polyline(points) : "";
+	}
+	plotGeo(ctx, frame) {
+		const links = this.kept();
+		const degree = /* @__PURE__ */ new Map();
+		for (const link of links) for (const name of [link.source, link.target]) degree.set(name, (degree.get(name) ?? 0) + 1);
+		const top = Math.max(1, ...degree.values());
+		const area = scaleSqrt([0, top], [0, 6.5]);
+		const radius = (stop) => this.options.node === "uniform" ? 4 : Math.max(4, area(degree.get(stop.name) ?? 0));
+		const bundles = this.options.route === GeoFlowRoute.Bundled ? this.bundled(frame, links) : /* @__PURE__ */ new Map();
+		const color = ctx.palette.color("Links");
+		const shown = links.map((link) => ({
+			link,
+			d: this.track(frame, link, bundles)
+		})).filter((item) => item.d);
+		const paths = ctx.marks("links", "path", shown, (d) => d.link.id).attr("fill", "none").attr("stroke", color).attr("stroke-width", 2).attr("stroke-opacity", links.length > 40 ? .3 : .8).attr("stroke-linecap", "round");
+		ctx.set(paths, { d: (d) => d.d }, { d: (d) => d.d });
+		ctx.drawOn(paths);
+		ctx.hover(paths, (d) => ({
+			title: `${d.link.source} — ${d.link.target}`,
+			color,
+			rows: [["Distance", `${Math.round(FlowGeometry.km(d.link.from, d.link.to)).toLocaleString("en")} km`]]
+		}));
+		const stops = this.stops.filter((stop) => degree.has(stop.name));
+		this.stopDots(ctx, frame, stops, radius);
+		const busiest = [...stops].sort((a, b) => (degree.get(b.name) ?? 0) - (degree.get(a.name) ?? 0));
+		this.labels(ctx, busiest.flatMap((stop) => {
+			const at = frame.at(stop.place);
+			return at ? [{
+				text: stop.name,
+				x: at[0],
+				y: at[1],
+				gap: radius(stop)
+			}] : [];
+		}), "labels", 6);
+	}
+};
+export { ConnectionMap, ConnectionMapNode, ConnectionMapTopology };