@mstone6969/graph 0.0.0-stage → 0.2.0

package/dist/charts/genomics/GenomeCytobands.js

@@ -0,0 +1,157 @@
+// src/charts/genomics/GenomeCytobands.ts
+/** UCSC hg38 cytoBand: chromosome, length in bp, then `name end stain` per band, with ends in 100 kb. */
+var GRCH38 = [
+	[
+		"1",
+		248956422,
+		"p36.33 23n,p36.32 531,p36.31 71n,p36.23 911,p36.22 125n,p36.21 1592,p36.13 201n,p36.12 2361,p36.11 276n,p35.3 2991,p35.2 323n,p35.1 3431,p34.3 396n,p34.2 4371,p34.1 463n,p33 5023,p32.3 556n,p32.2 5852,p32.1 608n,p31.3 6852,p31.2 693n,p31.1 8444,p22.3 879n,p22.2 9153,p22.1 943n,p21.3 9933,p21.2 1018n,p21.1 10674,p13.3 1112n,p13.2 11552,p13.1 1172n,p12 12042,p11.2 1217n,p11.1 1234a,q11 1251a,q12 1432v,q21.1 1475n,q21.2 15062,q21.3 1551n,q22 15662,q23.1 1591n,q23.2 16052,q23.3 1655n,q24.1 16722,q24.2 1709n,q24.3 17303,q25.1 1761n,q25.2 18032,q25.3 1858n,q31.1 19084,q31.2 1938n,q31.3 19874,q32.1 2071n,q32.2 21131,q32.3 2144n,q41 22394,q42.11 2244n,q42.12 22681,q42.13 2305n,q42.2 23462,q42.3 2364n,q43 24353,q44 n"
+	],
+	[
+		"2",
+		242193529,
+		"p25.3 44n,p25.2 692,p25.1 120n,p24.3 1653,p24.2 190n,p24.1 2383,p23.3 277n,p23.2 2981,p23.1 318n,p22.3 3633,p22.2 383n,p22.1 4152,p21 475n,p16.3 5264,p16.2 547n,p16.1 6104,p15 639n,p14 6842,p13.3 713n,p13.2 7332,p13.1 748n,p12 8314,p11.2 918n,p11.1 939a,q11.1 960a,q11.2 1021n,q12.1 10532,q12.2 1067n,q12.3 10871,q13 1122n,q14.1 11812,q14.2 1216n,q14.3 12912,q21.1 1317n,q21.2 13431,q21.3 1361n,q22.1 14154,q22.2 1434n,q22.3 14794,q23.1 1490n,q23.2 14961,q23.3 1540n,q24.1 15893,q24.2 1629n,q24.3 16893,q31.1 1771n,q31.2 17972,q31.3 1821n,q32.1 18853,q32.2 1911n,q32.3 19663,q33.1 2025n,q33.2 20412,q33.3 2082n,q34 21454,q35 2207n,q36.1 22433,q36.2 2252n,q36.3 23014,q37.1 2347n,q37.2 23642,q37.3 n"
+	],
+	[
+		"3",
+		198295559,
+		"p26.3 282,p26.2 40n,p26.1 812,p25.3 116n,p25.2 1321,p25.1 163n,p24.3 2384,p24.2 263n,p24.1 3083,p23 320n,p22.3 3642,p22.2 393n,p22.1 4363,p21.33 441n,p21.32 4422,p21.31 506n,p21.2 5231,p21.1 544n,p14.3 5862,p14.2 638n,p14.1 6972,p13 741n,p12.3 7983,p12.2 835n,p12.1 8713,p11.2 878n,p11.1 909a,q11.1 940a,q11.2 986v,q12.1 1003n,q12.2 10121,q12.3 1031n,q13.11 10653,q13.12 1082n,q13.13 11162,q13.2 1137n,q13.31 11763,q13.32 1193n,q13.33 12223,q21.1 1241n,q21.2 12611,q21.3 1295n,q22.1 13401,q22.2 1360n,q22.3 13901,q23 1431n,q24 14924,q25.1 1523n,q25.2 15532,q25.31 1573n,q25.32 15932,q25.33 1610n,q26.1 16794,q26.2 1712n,q26.31 17603,q26.32 1793n,q26.33 18303,q27.1 1848n,q27.2 18631,q27.3 1882n,q28 19263,q29 n"
+	],
+	[
+		"4",
+		190214555,
+		"p16.3 45n,p16.2 601,p16.1 113n,p15.33 1502,p15.32 177n,p15.31 2133,p15.2 277n,p15.1 3584,p14 412n,p13 4462,p12 482n,p11 500a,q11 518a,q12 585n,q13.1 6554,q13.2 694n,q13.3 7533,q21.1 780n,q21.21 8152,q21.22 832n,q21.23 8601,q21.3 871n,q22.1 9283,q22.2 942n,q22.3 9793,q23 1001n,q24 10672,q25 1132n,q26 11993,q27 1228n,q28.1 12792,q28.2 1301n,q28.3 13854,q31.1 1406n,q31.21 14591,q31.22 1475n,q31.23 15021,q31.3 1546n,q32.1 16084,q32.2 1636n,q32.3 16924,q33 1710n,q34.1 17543,q34.2 1766n,q34.3 18234,q35.1 1862n,q35.2 1"
+	],
+	[
+		"5",
+		181538259,
+		"p15.33 44n,p15.32 631,p15.31 99n,p15.2 1502,p15.1 184n,p14.3 2334,p14.2 246n,p14.1 2894,p13.3 338n,p13.2 3841,p13.1 425n,p12 4612,p11 488a,q11.1 514a,q11.2 596n,q12.1 6363,q12.2 639n,q12.3 6743,q13.1 691n,q13.2 7402,q13.3 776n,q14.1 8212,q14.2 835n,q14.3 9304,q15 989n,q21.1 10344,q21.2 1051n,q21.3 11024,q22.1 1122n,q22.2 11382,q22.3 1159n,q23.1 12214,q23.2 1279n,q23.3 13124,q31.1 1369n,q31.2 14011,q31.3 1451n,q32 15043,q33.1 1533n,q33.2 15632,q33.3 1605n,q34 16904,q35.1 1733n,q35.2 17711,q35.3 n"
+	],
+	[
+		"6",
+		170805979,
+		"p25.3 23n,p25.2 421,p25.1 71n,p24.3 1062,p24.2 116n,p24.1 1341,p23 152n,p22.3 2523,p22.2 271n,p22.1 3052,p21.33 321n,p21.32 3351,p21.31 366n,p21.2 4051,p21.1 462n,p12.3 5184,p12.2 530n,p12.1 5724,p11.2 585n,p11.1 598a,q11.1 626a,q11.2 627n,q12 6924,q13 752n,q14.1 8322,q14.2 842n,q14.3 8732,q15 925n,q16.1 9894,q16.2 1000n,q16.3 10504,q21 1142n,q22.1 11793,q22.2 1181n,q22.31 12584,q22.32 1268n,q22.33 13003,q23.1 1309n,q23.2 13472,q23.3 1383n,q24.1 14223,q24.2 1451n,q24.3 14853,q25.1 1521n,q25.2 15522,q25.3 1606n,q26 16412,q27 n"
+	],
+	[
+		"7",
+		159345973,
+		"p22.3 28n,p22.2 451,p22.1 72n,p21.3 1374,p21.2 165n,p21.1 2094,p15.3 255n,p15.2 2792,p15.1 288n,p14.3 3493,p14.2 371n,p14.1 4333,p13 454n,p12.3 4903,p12.2 505n,p12.1 5393,p11.2 581n,p11.1 601a,q11.1 621a,q11.21 675n,q11.22 7272,q11.23 779n,q21.11 8674,q21.12 885n,q21.13 9153,q21.2 933n,q21.3 9843,q22.1 1042n,q22.2 10492,q22.3 1078n,q31.1 11503,q31.2 1177n,q31.31 12143,q31.32 1241n,q31.33 12753,q32.1 1296n,q32.2 13081,q32.3 1329n,q33 13852,q34 1434n,q35 14823,q36.1 1528n,q36.2 15521,q36.3 n"
+	],
+	[
+		"8",
+		145138636,
+		"p23.3 23n,p23.2 633,p23.1 128n,p22 1924,p21.3 235n,p21.2 2752,p21.1 290n,p12 3673,p11.23 385n,p11.22 3991,p11.21 432n,p11.1 452a,q11.1 472a,q11.21 513n,q11.22 5173,q11.23 546n,q12.1 6062,q12.2 613n,q12.3 6512,q13.1 671n,q13.2 6962,q13.3 720n,q21.11 7464,q21.12 747n,q21.13 8353,q21.2 859n,q21.3 9234,q22.1 979n,q22.2 10051,q22.3 1051n,q23.1 10953,q23.2 1111n,q23.3 11674,q24.11 1183n,q24.12 12152,q24.13 1263n,q24.21 13042,q24.22 1354n,q24.23 13893,q24.3 n"
+	],
+	[
+		"9",
+		138394717,
+		"p24.3 22n,p24.2 461,p24.1 90n,p23 1423,p22.3 166n,p22.2 1851,p22.1 199n,p21.3 2564,p21.2 280n,p21.1 3324,p13.3 363n,p13.2 3791,p13.1 390n,p12 4002,p11.2 422n,p11.1 430a,q11 455a,q12 615v,q13 650n,q21.11 6931,q21.12 713n,q21.13 7662,q21.2 785n,q21.31 8152,q21.32 843n,q21.33 8782,q22.1 892n,q22.2 9121,q22.31 939n,q22.32 9651,q22.33 998n,q31.1 10544,q31.2 1085n,q31.3 11211,q32 1149n,q33.1 11983,q33.2 1231n,q33.3 12751,q34.11 1306n,q34.12 13111,q34.13 1331n,q34.2 13451,q34.3 n"
+	],
+	[
+		"10",
+		133797422,
+		"p15.3 30n,p15.2 381,p15.1 66n,p14 1223,p13 173n,p12.33 1833,p12.32 184n,p12.31 2233,p12.2 243n,p12.1 2932,p11.23 311n,p11.22 3421,p11.21 380n,p11.1 398a,q11.1 416a,q11.21 455n,q11.22 4861,q11.23 511n,q21.1 5944,q21.2 628n,q21.3 6884,q22.1 731n,q22.2 7592,q22.3 803n,q23.1 8614,q23.2 877n,q23.31 9113,q23.32 923n,q23.33 9532,q24.1 975n,q24.2 10012,q24.31 1012n,q24.32 10311,q24.33 1040n,q25.1 11014,q25.2 1131n,q25.3 11733,q26.11 1199n,q26.12 12142,q26.13 1257n,q26.2 12882,q26.3 n"
+	],
+	[
+		"11",
+		135086622,
+		"p15.5 28n,p15.4 1172,p15.3 138n,p15.2 1692,p15.1 220n,p14.3 2624,p14.2 272n,p14.1 3103,p13 364n,p12 4344,p11.2 488n,p11.12 5103,p11.11 534a,q11 558a,q12.1 6013,q12.2 619n,q12.3 6361,q13.1 661n,q13.2 6871,q13.3 705n,q13.4 7552,q13.5 774n,q14.1 8594,q14.2 886n,q14.3 9304,q21 974n,q22.1 10234,q22.2 1030n,q22.3 11064,q23.1 1127n,q23.2 11462,q23.3 1213n,q24.1 12402,q24.2 1279n,q24.3 13092,q25 n"
+	],
+	[
+		"12",
+		133275309,
+		"p13.33 32n,p13.32 531,p13.31 100n,p13.2 1263,p13.1 146n,p12.3 1984,p12.2 211n,p12.1 2634,p11.23 276n,p11.22 3052,p11.21 332n,p11.1 355a,q11 378a,q12 4604,q13.11 487n,q13.12 5111,q13.13 545n,q13.2 5621,q13.3 577n,q14.1 6273,q14.2 647n,q14.3 6732,q15 711n,q21.1 7533,q21.2 799n,q21.31 8634,q21.32 886n,q21.33 9224,q22 958n,q23.1 10123,q23.2 1035n,q23.3 10862,q24.11 1113n,q24.12 11191,q24.13 1139n,q24.21 11642,q24.22 1177n,q24.23 12032,q24.31 1254n,q24.32 12872,q24.33 n"
+	],
+	[
+		"13",
+		114364328,
+		"p13 46v,p12 101s,p11.2 165v,p11.1 177a,q11 189a,q12.11 226n,q12.12 2491,q12.13 272n,q12.2 2831,q12.3 316n,q13.1 3342,q13.2 349n,q13.3 3953,q14.11 446n,q14.12 4521,q14.13 467n,q14.2 5032,q14.3 547n,q21.1 5904,q21.2 618n,q21.31 6523,q21.32 681n,q21.33 7284,q22.1 749n,q22.2 7672,q22.3 785n,q31.1 8714,q31.2 894n,q31.3 9444,q32.1 975n,q32.2 9871,q32.3 1011n,q33.1 10424,q33.2 1064n,q33.3 10964,q34 n"
+	],
+	[
+		"14",
+		107043718,
+		"p13 36v,p12 80s,p11.2 161v,p11.1 172a,q11.1 182a,q11.2 241n,q12 3294,q13.1 348n,q13.2 3612,q13.3 374n,q21.1 4304,q21.2 467n,q21.3 5044,q22.1 536n,q22.2 5501,q22.3 576n,q23.1 6163,q23.2 643n,q23.3 6742,q24.1 698n,q24.2 7332,q24.3 788n,q31.1 8314,q31.2 844n,q31.3 8934,q32.11 914n,q32.12 9421,q32.13 958n,q32.2 10092,q32.31 1027n,q32.32 10352,q32.33 n"
+	],
+	[
+		"15",
+		101991189,
+		"p13 42v,p12 97s,p11.2 175v,p11.1 190a,q11.1 205a,q11.2 255n,q12 2782,q13.1 300n,q13.2 3092,q13.3 334n,q14 3983,q15.1 425n,q15.2 4331,q15.3 445n,q21.1 4923,q21.2 526n,q21.3 5883,q22.1 590n,q22.2 6341,q22.31 669n,q22.32 6701,q22.33 672n,q23 7241,q24.1 749n,q24.2 7631,q24.3 780n,q25.1 8142,q25.2 847n,q25.3 8852,q26.1 938n,q26.2 9802,q26.3 n"
+	],
+	[
+		"16",
+		90338345,
+		"p13.3 78n,p13.2 1042,p13.13 125n,p13.12 1472,p13.11 167n,p12.3 2122,p12.2 242n,p12.1 2852,p11.2 353n,p11.1 368a,q11.1 384a,q11.2 470v,q12.1 526n,q12.2 5602,q13 573n,q21 6664,q22.1 708n,q22.2 7282,q22.3 741n,q23.1 7923,q23.2 816n,q23.3 8412,q24.1 870n,q24.2 8871,q24.3 n"
+	],
+	[
+		"17",
+		83257441,
+		"p13.3 34n,p13.2 652,p13.1 108n,p12 1613,p11.2 227n,p11.1 251a,q11.1 274a,q11.2 335n,q12 3982,q21.1 402n,q21.2 4281,q21.31 468n,q21.32 4931,q21.33 521n,q22 5953,q23.1 602n,q23.2 6313,q23.3 646n,q24.1 6622,q24.2 691n,q24.3 7293,q25.1 768n,q25.2 7721,q25.3 n"
+	],
+	[
+		"18",
+		80373285,
+		"p11.32 29n,p11.31 722,p11.23 85n,p11.22 1091,p11.21 154n,p11.1 185a,q11.1 215a,q11.2 275n,q12.1 3514,q12.2 395n,q12.3 4593,q21.1 507n,q21.2 5623,q21.31 586n,q21.32 6132,q21.33 639n,q22.1 6914,q22.2 710n,q22.3 7541,q23 n"
+	],
+	[
+		"19",
+		58617616,
+		"p13.3 69n,p13.2 1261,p13.13 138n,p13.12 1611,p13.11 199n,p12 242v,p11 262a,q11 281a,q12 319v,q13.11 351n,q13.12 3781,q13.13 382n,q13.2 4291,q13.31 447n,q13.32 4751,q13.33 509n,q13.41 5311,q13.42 558n,q13.43 1"
+	],
+	[
+		"20",
+		64444167,
+		"p13 51n,p12.3 923,p12.2 120n,p12.1 1793,p11.23 213n,p11.22 2231,p11.21 257n,p11.1 281a,q11.1 304a,q11.21 335n,q11.22 3581,q11.23 390n,q12 4313,q13.11 435n,q13.12 4781,q13.13 512n,q13.2 5643,q13.31 578n,q13.32 5972,q13.33 n"
+	],
+	[
+		"21",
+		46709983,
+		"p13 31v,p12 70s,p11.2 109v,p11.1 120a,q11.1 130a,q11.2 150n,q21.1 2264,q21.2 255n,q21.3 3023,q22.11 344n,q22.12 3642,q22.13 383n,q22.2 4122,q22.3 n"
+	],
+	[
+		"22",
+		50818468,
+		"p13 43v,p12 94s,p11.2 137v,p11.1 150a,q11.1 174a,q11.21 217n,q11.22 2311,q11.23 255n,q12.1 2922,q12.2 318n,q12.3 3722,q13.1 406n,q13.2 4382,q13.31 481n,q13.32 4912,q13.33 n"
+	],
+	[
+		"X",
+		156040895,
+		"p22.33 44n,p22.32 612,p22.31 96n,p22.2 1742,p22.13 192n,p22.12 2192,p22.11 249n,p21.3 2934,p21.2 315n,p21.1 3784,p11.4 425n,p11.3 4763,p11.23 501n,p11.22 5481,p11.21 581n,p11.1 610a,q11.1 638a,q11.2 654n,q12 6852,q13.1 730n,q13.2 7472,q13.3 768n,q21.1 8544,q21.2 870n,q21.31 9274,q21.32 943n,q21.33 9913,q22.1 1033n,q22.2 10452,q22.3 1094n,q23 11743,q24 1218n,q25 12954,q26.1 1313n,q26.2 13451,q26.3 1389n,q27.1 14123,q27.2 1430n,q27.3 14804,q28 n"
+	],
+	[
+		"Y",
+		57227415,
+		"p11.32 3n,p11.31 62,p11.2 103n,p11.1 104a,q11.1 106a,q11.21 124n,q11.221 1712,q11.222 196n,q11.223 2382,q11.23 266n,q12 v"
+	]
+];
+var STAINS = {
+	n: "gneg",
+	1: "gpos25",
+	2: "gpos50",
+	3: "gpos75",
+	4: "gpos100",
+	a: "acen",
+	v: "gvar",
+	s: "stalk"
+};
+/** The published human banding (GRCh38, UCSC cytoBand), as rows. Reference coordinates, not measurements. */
+var GenomeCytobands = class {
+	static #rows = null;
+	static get rows() {
+		return this.#rows ??= GRCH38.flatMap(([chrom, length, packed]) => {
+			let start = 0;
+			return packed.split(",").map((item) => {
+				const [band, tail] = item.split(" ");
+				const end = tail.length > 1 ? +tail.slice(0, -1) * 1e5 : length;
+				const row = {
+					chrom,
+					start,
+					end,
+					band,
+					stain: STAINS[tail.at(-1)]
+				};
+				start = end;
+				return row;
+			});
+		});
+	}
+};
+export { GenomeCytobands };

package/dist/charts/genomics/GenomeIdeogram.js

@@ -0,0 +1,422 @@
+import { Chart2D } from "../../core/Chart2D.js";
+import { ChartFamily, DataShape, Dimension } from "../../core/enums.js";
+import { GenomeAssembly } from "./GenomeAssembly.js";
+import { GenomeSamples } from "./GenomeSamples.js";
+import { GenomeStainScale } from "./GenomeStainScale.js";
+import { GenomeAlign, GenomeAnnotationMark, GenomeBandLevel, GenomeIdeogramLayout, GenomeOutline } from "./genomicsEnums.js";
+import { max, scaleLinear, ticks } from "d3";
+// src/charts/genomics/GenomeIdeogram.ts
+var CHAR = 6.2;
+var WAIST = .32;
+var STALK = .45;
+var NAME_ROOM = 14;
+/** ISCN karyogram rows. */
+var KARYOGRAM_ROWS = [
+	[
+		"1",
+		"2",
+		"3",
+		"4",
+		"5"
+	],
+	[
+		"6",
+		"7",
+		"8",
+		"9",
+		"10",
+		"11",
+		"12"
+	],
+	[
+		"13",
+		"14",
+		"15",
+		"16",
+		"17",
+		"18"
+	],
+	[
+		"19",
+		"20",
+		"21",
+		"22",
+		"X",
+		"Y"
+	]
+];
+/** Show a genome's chromosomes as stained bands around their centromeres, and where features fall on them. */
+var GenomeIdeogram = class GenomeIdeogram extends Chart2D {
+	static meta = {
+		id: "genome-ideogram",
+		name: "Genome ideogram",
+		family: ChartFamily.Scientific,
+		dimension: Dimension.Two,
+		shape: DataShape.Genome,
+		description: "Draws chromosomes as Giemsa bands around their centromeres and maps annotated loci onto genomic position.",
+		tags: [
+			"genomics",
+			"chromosome",
+			"cytoband",
+			"karyotype",
+			"iscn"
+		],
+		sample: (seed) => GenomeSamples.cancerGenome(seed),
+		variants: {
+			layout: [
+				GenomeIdeogramLayout.Columns,
+				GenomeIdeogramLayout.Rows,
+				GenomeIdeogramLayout.Karyogram,
+				GenomeIdeogramLayout.Single
+			],
+			align: [GenomeAlign.Centromere, GenomeAlign.Telomere],
+			level: [
+				GenomeBandLevel.Published,
+				GenomeBandLevel.SubBand,
+				GenomeBandLevel.Band
+			],
+			annotationMark: [
+				GenomeAnnotationMark.Triangle,
+				GenomeAnnotationMark.Tick,
+				GenomeAnnotationMark.Lollipop,
+				GenomeAnnotationMark.None
+			],
+			outline: [GenomeOutline.Constricted, GenomeOutline.Block]
+		},
+		valid: (v) => {
+			return (v.layout === GenomeIdeogramLayout.Columns || v.layout === GenomeIdeogramLayout.Rows || v.outline === GenomeOutline.Constricted) && (v.layout !== GenomeIdeogramLayout.Single || v.align === GenomeAlign.Centromere);
+		}
+	};
+	defaults() {
+		return {
+			layout: GenomeIdeogramLayout.Columns,
+			align: GenomeAlign.Centromere,
+			level: GenomeBandLevel.Published,
+			annotationMark: GenomeAnnotationMark.Triangle,
+			outline: GenomeOutline.Constricted
+		};
+	}
+	plotMargin() {
+		return {
+			top: 10,
+			right: 12,
+			bottom: 8,
+			left: 12
+		};
+	}
+	#assembly() {
+		return new GenomeAssembly(this.options.data, this.options.bandFields, this.options.level);
+	}
+	table() {
+		return this.#assembly().table(["annotations", "bands"]);
+	}
+	/** Bp above and below the shared alignment line, so one bp is the same length on every chromosome. */
+	static #extent(list, align) {
+		const above = (c) => align === GenomeAlign.Centromere ? c.centromere ?? c.length / 2 : 0;
+		return [max(list, above) ?? 0, max(list, (c) => c.length - above(c)) ?? 1];
+	}
+	#placeLine(list, box, horizontal, scale, slotCap) {
+		const align = this.options.align;
+		const [before, after] = GenomeIdeogram.#extent(list, align);
+		const bp = scale ?? (horizontal ? box.width : box.height) / (before + after || 1);
+		const slot = Math.min(slotCap ?? Infinity, (horizontal ? box.height : box.width) / (list.length || 1));
+		const half = Math.max(1.5, Math.min(horizontal ? 5 : 7, slot * (horizontal ? .27 : .21)));
+		return list.map((chromosome, i) => {
+			const anchor = align === GenomeAlign.Centromere ? chromosome.centromere ?? chromosome.length / 2 : 0;
+			const base = (horizontal ? box.x : box.y) + (before - anchor) * bp;
+			const middle = (horizontal ? box.y : box.x) + slot * i + (horizontal ? slot / 2 : half + 2);
+			return {
+				chromosome,
+				half,
+				horizontal,
+				room: slot - half * 2 - 3,
+				along: (position) => base + position * bp,
+				point: (along, across) => horizontal ? [along, middle + across] : [middle + across, along],
+				name: horizontal ? {
+					x: box.x - 4,
+					y: middle,
+					anchor: "end"
+				} : {
+					x: middle,
+					y: box.y + box.height + 11,
+					anchor: "middle"
+				}
+			};
+		});
+	}
+	#placements(list, focus, width, height) {
+		const { layout } = this.options;
+		if (layout === GenomeIdeogramLayout.Rows) return this.#placeLine(list, {
+			x: 20,
+			y: 0,
+			width: width - 20,
+			height
+		}, true);
+		if (layout === GenomeIdeogramLayout.Columns) return this.#placeLine(list, {
+			x: 0,
+			y: 0,
+			width,
+			height: height - NAME_ROOM
+		}, false);
+		if (layout === GenomeIdeogramLayout.Single) return focus ? this.#placeSingle(focus, width, height) : [];
+		const known = KARYOGRAM_ROWS.flat();
+		const rows = KARYOGRAM_ROWS.map((names) => list.filter((c) => names.includes(c.name)));
+		rows.at(-1).push(...list.filter((c) => !known.includes(c.name)));
+		const live = rows.filter((row) => row.length);
+		const spans = live.map((row) => GenomeIdeogram.#extent(row, this.options.align));
+		const bp = (height - live.length * 18) / (spans.reduce((sum, [a, b]) => sum + a + b, 0) || 1);
+		const widest = Math.max(...live.map((row) => row.length), 1);
+		let y = 0;
+		return live.flatMap((row, i) => {
+			const rise = (spans[i][0] + spans[i][1]) * bp;
+			const placed = this.#placeLine(row, {
+				x: 0,
+				y,
+				width,
+				height: rise
+			}, false, bp, Math.max(width / widest, width / row.length * .8));
+			y += rise + NAME_ROOM + 4;
+			return placed;
+		});
+	}
+	#placeSingle(chromosome, width, height) {
+		const half = Math.min(14, Math.max(8, width * .025)), middle = width * .36;
+		const bp = (height - NAME_ROOM) / chromosome.length;
+		return [{
+			chromosome,
+			half,
+			horizontal: false,
+			room: width - middle - half - 2,
+			along: (position) => position * bp,
+			point: (along, across) => [middle + across, along],
+			name: {
+				x: middle,
+				y: height - 1,
+				anchor: "middle"
+			}
+		}];
+	}
+	#profile(band, chromosome, place) {
+		const from = place.along(band.start), to = place.along(band.end);
+		if (this.options.outline === GenomeOutline.Block) return {
+			from,
+			to,
+			h0: 1,
+			h1: 1
+		};
+		if (band.stain === "stalk") return {
+			from,
+			to,
+			h0: STALK,
+			h1: STALK
+		};
+		if (band.stain !== "acen" || chromosome.bands.filter((item) => item.stain === "acen").length < 2) return {
+			from,
+			to,
+			h0: 1,
+			h1: 1
+		};
+		return band.end === chromosome.centromere ? {
+			from,
+			to,
+			h0: 1,
+			h1: WAIST
+		} : {
+			from,
+			to,
+			h0: WAIST,
+			h1: 1
+		};
+	}
+	/** Closed shape over runs of varying half-width, with an optional rounded telomere at each end. */
+	#silhouette(runs, place, capStart, capEnd) {
+		const rounded = this.options.outline !== GenomeOutline.Block;
+		const first = runs[0], last = runs.at(-1), width = place.half;
+		const start = rounded && capStart ? Math.min(width, first.to - first.from) : 0;
+		const end = rounded && capEnd ? Math.min(width, last.to - last.from) : 0;
+		const at = (along, h) => place.point(along, h * width).map((n) => +n.toFixed(2)).join(" ");
+		const side = (sign) => runs.flatMap((run) => [[run.from, run.h0 * sign], [run.to, run.h1 * sign]]);
+		const left = side(-1), right = side(1).reverse();
+		if (start) left[0] = [first.from + start, -first.h0];
+		if (end) left[left.length - 1] = [last.to - end, -last.h1];
+		if (end) right[0] = [last.to - end, last.h1];
+		if (start) right[right.length - 1] = [first.from + start, first.h0];
+		const line = (list) => list.map(([along, h]) => `L${at(along, h)}`).join("");
+		const capEndPath = end ? `Q${at(last.to, -last.h1)} ${at(last.to, 0)}Q${at(last.to, last.h1)} ${at(last.to - end, last.h1)}` : "";
+		const capStartPath = start ? `Q${at(first.from, first.h0)} ${at(first.from, 0)}Q${at(first.from, -first.h0)} ${at(first.from + start, -first.h0)}` : "";
+		return `M${at(left[0][0], left[0][1])}${line(left.slice(1))}${capEndPath}${line(right)}${capStartPath}Z`;
+	}
+	#drawChromosomes(ctx, places) {
+		const stain = new GenomeStainScale(ctx.theme);
+		const items = places.flatMap((place) => place.chromosome.bands.map((band, i, all) => {
+			const run = this.#profile(band, place.chromosome, place);
+			return {
+				band,
+				d: this.#silhouette([run], place, i === 0, i === all.length - 1)
+			};
+		}));
+		const bands = ctx.marks("bands", "path", items, (d) => d.band.key).attr("fill", (d) => stain.fill(d.band));
+		ctx.set(bands, {
+			d: (d) => d.d,
+			"fill-opacity": 1
+		}, { "fill-opacity": 0 });
+		ctx.hover(bands, ({ band }) => ({
+			title: `${band.chrom}${band.name}`,
+			rows: [["Stain", band.stain], ["Position", GenomeAssembly.span(band.start, band.end)]]
+		}));
+		const shells = ctx.marks("outlines", "path", places, (d) => d.chromosome.name).attr("fill", "none").attr("stroke", ctx.theme.inkMuted).attr("stroke-width", .75).attr("pointer-events", "none");
+		ctx.set(shells, { d: (place) => this.#silhouette(place.chromosome.bands.map((band) => this.#profile(band, place.chromosome, place)), place, true, true) });
+		const legible = places.filter((_, i) => places.length < 3 || i % this.#nameStride(places) === 0);
+		const names = ctx.marks("chromosome-names", "text", legible, (d) => d.chromosome.name);
+		ctx.text(names, 9.5).attr("text-anchor", (d) => d.name.anchor).attr("dy", (d) => d.horizontal ? "0.33em" : null).attr("pointer-events", "none").attr("x", (d) => d.name.x).attr("y", (d) => d.name.y).text((d) => d.chromosome.name);
+	}
+	/** Every name fits at 11px of slot; below that, every other one is shown. */
+	#nameStride(places) {
+		const [a, b] = places;
+		if (!a || !b) return 1;
+		return (a.horizontal ? Math.abs(a.point(0, 0)[1] - b.point(0, 0)[1]) : Math.abs(a.point(0, 0)[0] - b.point(0, 0)[0])) >= 10.5 ? 1 : 2;
+	}
+	static #markerSize(d) {
+		return Math.max(3, Math.min(8, d.place.room));
+	}
+	/** Lollipop height, from the chromosome's edge: value over the tallest one, within the slot. */
+	#stem(d, marks) {
+		const peak = max(marks, (mark) => mark.item.value ?? 0) || 1;
+		return d.place.half + 3 + (d.item.value ?? 0) / peak * Math.max(0, Math.min(26, d.place.room) - GenomeIdeogram.#markerSize(d));
+	}
+	/** Distance from the axis to clear space past a mark. */
+	#clearance(d, marks) {
+		const size = GenomeIdeogram.#markerSize(d);
+		if (this.options.annotationMark === GenomeAnnotationMark.Lollipop) return this.#stem(d, marks) + size / 2 + 3;
+		return d.place.half + (this.options.annotationMark === GenomeAnnotationMark.Tick ? 6 : size + 3);
+	}
+	#drawAnnotations(ctx, marks, assembly) {
+		const mode = this.options.annotationMark;
+		const edge = (d) => d.place.half + 1;
+		const size = GenomeIdeogram.#markerSize;
+		const stem = (d) => this.#stem(d, marks);
+		const tip = (d) => ({
+			title: d.item.label || "Annotation",
+			color: d.color,
+			rows: [
+				["Locus", assembly.locus(d.item.chrom, d.item.start)],
+				["Position", GenomeAssembly.span(d.item.start, d.item.end)],
+				...d.item.value == null ? [] : [["Value", d.item.value]]
+			]
+		});
+		const paintColor = (d) => d.color;
+		if (mode === GenomeAnnotationMark.Triangle) {
+			const triangle = (d) => {
+				const near = d.place.point(d.at, edge(d)), s = size(d);
+				const a = d.place.point(d.at - s / 2, edge(d) + s), b = d.place.point(d.at + s / 2, edge(d) + s);
+				return `M${near.join(" ")}L${a.join(" ")}L${b.join(" ")}Z`;
+			};
+			const marksSel = ctx.marks("triangles", "path", marks, (d) => d.key).attr("fill", paintColor);
+			ctx.set(marksSel, {
+				d: triangle,
+				"fill-opacity": 1
+			}, { "fill-opacity": 0 });
+			ctx.hover(marksSel, tip);
+		}
+		if (mode === GenomeAnnotationMark.Tick) {
+			const ticksSel = ctx.marks("ticks", "line", marks, (d) => d.key).attr("stroke", paintColor).attr("stroke-width", 2);
+			ctx.set(ticksSel, {
+				x1: (d) => d.place.point(d.at, -d.place.half - 1)[0],
+				y1: (d) => d.place.point(d.at, -d.place.half - 1)[1],
+				x2: (d) => d.place.point(d.at, d.place.half + 3)[0],
+				y2: (d) => d.place.point(d.at, d.place.half + 3)[1]
+			});
+			ctx.hover(ticksSel, tip);
+		}
+		if (mode === GenomeAnnotationMark.Lollipop) {
+			const stems = ctx.marks("stems", "line", marks, (d) => d.key).attr("stroke", paintColor).attr("stroke-width", 1.5);
+			ctx.set(stems, {
+				x1: (d) => d.place.point(d.at, edge(d))[0],
+				y1: (d) => d.place.point(d.at, edge(d))[1],
+				x2: (d) => d.place.point(d.at, stem(d))[0],
+				y2: (d) => d.place.point(d.at, stem(d))[1]
+			});
+			const heads = ctx.marks("heads", "circle", marks, (d) => d.key).attr("fill", paintColor).attr("stroke", ctx.theme.surface).attr("stroke-width", (d) => size(d) >= 8 ? 2 : 1);
+			ctx.set(heads, {
+				cx: (d) => d.place.point(d.at, stem(d))[0],
+				cy: (d) => d.place.point(d.at, stem(d))[1],
+				r: (d) => size(d) / 2
+			}, { r: 0 });
+			ctx.hover(heads, tip);
+		}
+	}
+	/** Greedy by value: a label needs room beside its chromosome and clear space along it. */
+	#labels(ctx, marks) {
+		const taken = /* @__PURE__ */ new Map();
+		const kept = [...marks].sort((a, b) => (b.item.value ?? 0) - (a.item.value ?? 0)).filter((mark) => {
+			const wide = mark.item.label.length * CHAR;
+			const need = this.#clearance(mark, marks) - mark.place.half + (mark.place.horizontal ? 12 : wide);
+			const clear = mark.place.horizontal ? wide + 6 : 11;
+			const used = taken.get(mark.place.chromosome.name) ?? [];
+			if (need > mark.place.room || used.some((at) => Math.abs(at - mark.at) < clear)) return false;
+			taken.set(mark.place.chromosome.name, [...used, mark.at]);
+			return true;
+		});
+		const point = (d) => d.place.point(d.at, this.#clearance(d, marks) + (d.place.horizontal ? 4 : 0));
+		const labels = ctx.marks("labels", "text", kept, (d) => d.key);
+		ctx.text(labels, 9.5).attr("pointer-events", "none").attr("text-anchor", (d) => d.place.horizontal ? "middle" : "start").attr("dy", "0.33em").attr("x", (d) => point(d)[0]).attr("y", (d) => point(d)[1]).text((d) => d.item.label);
+	}
+	/** Band names on the left, as ISCN ideograms carry them, and a Mb ruler beyond. */
+	#drawSingleAxis(ctx, place) {
+		const { chromosome } = place;
+		let last = -Infinity;
+		const named = chromosome.bands.filter((band) => {
+			if (place.along(band.end) - place.along(band.start) < 2) return false;
+			const at = place.along((band.start + band.end) / 2);
+			if (at - last < 11) return false;
+			last = at;
+			return true;
+		});
+		const textAt = (band) => place.point(place.along((band.start + band.end) / 2), -place.half - 6);
+		const names = ctx.marks("band-names", "text", named, (d) => d.key);
+		ctx.text(names, 9.5).attr("text-anchor", "end").attr("dy", "0.33em").attr("pointer-events", "none").attr("x", (d) => textAt(d)[0]).attr("y", (d) => textAt(d)[1]).text((d) => d.name);
+		const axisAcross = place.point(0, 0)[0] - place.half - 60;
+		const scale = scaleLinear([0, chromosome.length / 1e6], [place.along(0), place.along(chromosome.length)]);
+		const rule = ctx.marks("ruler-ticks", "line", ticks(0, chromosome.length / 1e6, 6), (d) => d).attr("stroke", ctx.theme.axis);
+		ctx.set(rule, {
+			x1: axisAcross - 4,
+			x2: axisAcross,
+			y1: (d) => scale(d),
+			y2: (d) => scale(d)
+		});
+		const line = ctx.marks("ruler", "line", [0]).attr("stroke", ctx.theme.axis);
+		ctx.set(line, {
+			x1: axisAcross,
+			x2: axisAcross,
+			y1: scale(0),
+			y2: scale(chromosome.length / 1e6)
+		});
+		const labels = ctx.marks("ruler-labels", "text", ticks(0, chromosome.length / 1e6, 6), (d) => d);
+		ctx.text(labels, 9.5, "muted").attr("text-anchor", "end").attr("dy", "0.33em").attr("x", axisAcross - 6).attr("y", (d) => scale(d)).text((d) => `${d}${d ? "" : " Mb"}`);
+	}
+	draw(ctx) {
+		const { layout, annotationMark, annotationFields, focus } = this.options;
+		const assembly = this.#assembly();
+		const notes = assembly.annotations(annotationFields);
+		const single = layout === GenomeIdeogramLayout.Single;
+		const target = single ? assembly.busiest(notes.map((note) => note.chrom), focus) : void 0;
+		const places = this.#placements(assembly.chromosomes, target, ctx.plot.width, ctx.plot.height);
+		this.#drawChromosomes(ctx, places);
+		const byName = new Map(places.map((place) => [place.chromosome.name, place]));
+		if (annotationMark !== GenomeAnnotationMark.None) for (const note of notes) ctx.palette.color(note.group);
+		const marks = annotationMark === GenomeAnnotationMark.None ? [] : notes.flatMap((item) => {
+			const place = byName.get(item.chrom);
+			return place ? [{
+				key: item.key,
+				item,
+				place,
+				at: place.along((item.start + item.end) / 2),
+				color: ctx.palette.color(item.group)
+			}] : [];
+		});
+		this.#drawAnnotations(ctx, marks, assembly);
+		this.#labels(ctx, marks);
+		if (single && places[0]) this.#drawSingleAxis(ctx, places[0]);
+	}
+};
+export { GenomeIdeogram };