@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (940) hide show
  1. package/dist/2dmaf-43QBND66.js +1367 -0
  2. package/dist/AggMatrixInput-X7NGFUHH.js +406 -0
  3. package/dist/AggregateMatrix-M4HRI4PX.js +41 -0
  4. package/dist/AppHeader-QBRQN6PM.js +830 -0
  5. package/dist/BoxPlot-V6SPSEQ2.js +1211 -0
  6. package/dist/CorrelationVolcano-UFPCYC77.js +617 -0
  7. package/dist/Cuminc-KXGXGLKZ.js +1219 -0
  8. package/dist/DE-K2YXHOOW.js +89 -0
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  12. package/dist/DifferentialAnalysis-A2BU4WB3.js +239 -0
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  23. package/dist/Geomap-UIIOLRFA.js +84 -0
  24. package/dist/HicApp-73ESVNBA.js +2245 -0
  25. package/dist/IDCViewer-RBYN5A4P.js +10812 -0
  26. package/dist/NumBinaryEditor-DJLSNSLE.js +279 -0
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  42. package/dist/ProteomeInput-TMZ3THRL.js +388 -0
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  55. package/dist/app-22JCSULA.js +42 -0
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  842. /package/dist/{matrix.layout-25HYKUF2.js.map → matrix.layout-MINLYQCA.js.map} +0 -0
  843. /package/dist/{matrix.legend-IMK7DH4V.js.map → matrix.legend-6GSDFZHS.js.map} +0 -0
  844. /package/dist/{matrix.renderers-3RZRN6HO.js.map → matrix.renderers-5BKOXDE3.js.map} +0 -0
  845. /package/dist/{matrix.serieses-ZTVHQ7QA.js.map → matrix.serieses-6FCFIFAQ.js.map} +0 -0
  846. /package/dist/{matrix.sort-EDXHT6NZ.js.map → matrix.sort-EHVVYDZ3.js.map} +0 -0
  847. /package/dist/{matrix.sort.unit.spec-LSNY7PHU.js.map → matrix.sort.unit.spec-BCWE4AFX.js.map} +0 -0
  848. /package/dist/{matrix.sorterUi-3DRNHG5Z.js.map → matrix.sorterUi-WL5I6S3K.js.map} +0 -0
  849. /package/dist/{matrix.sorterUi.unit.spec-GNIIWGRJ.js.map → matrix.sorterUi.unit.spec-XJR5KXRL.js.map} +0 -0
  850. /package/dist/{matrix.unit.spec-7A6ZFRXI.js.map → matrix.unit.spec-TUCKPE26.js.map} +0 -0
  851. /package/dist/{mavb-M5AXPLYX.js.map → mavb-GWSNRBLM.js.map} +0 -0
  852. /package/dist/{mds.fimo-QE5OFA22.js.map → mds.fimo-OMAQRSMW.js.map} +0 -0
  853. /package/dist/{mds.samplescatterplot-664EOHX2.js.map → mds.samplescatterplot-4UW3CC45.js.map} +0 -0
  854. /package/dist/{mds.survivalplot-H4TJD44D.js.map → mds.survivalplot-2CJYJBD2.js.map} +0 -0
  855. /package/dist/{multivalue-JD3CNQJR.js.map → multivalue-G44MHEYI.js.map} +0 -0
  856. /package/dist/{numericDictTermCluster-XPKEYXD7.js.map → numericDictTermCluster-5BDRGVQG.js.map} +0 -0
  857. /package/dist/{oncomatrix-TX5PZQ76.js.map → oncomatrix-ZTVO23ZH.js.map} +0 -0
  858. /package/dist/{oncomatrix.spec-6X2WAHL7.js.map → oncomatrix.spec-2QVK2A3Q.js.map} +0 -0
  859. /package/dist/{plot.2dvaf-5OHUFTMK.js.map → plot.2dvaf-CL5YUXKH.js.map} +0 -0
  860. /package/dist/{plot.app-XIVVJHWG.js.map → plot.app-4ANKPSNP.js.map} +0 -0
  861. /package/dist/{plot.barplot-PSODLAXD.js.map → plot.barplot-BMGDNZRA.js.map} +0 -0
  862. /package/dist/{plot.boxplot-W3ASYFOG.js.map → plot.boxplot-GMLQCDP6.js.map} +0 -0
  863. /package/dist/{plot.brainImaging-JGDLKLR7.js.map → plot.brainImaging-RZXX3NUZ.js.map} +0 -0
  864. /package/dist/{plot.disco-TPMXTTZK.js.map → plot.disco-3MD4J4C7.js.map} +0 -0
  865. /package/dist/{plot.ssgq-KIZIOZIF.js.map → plot.ssgq-ZC4UYKOT.js.map} +0 -0
  866. /package/dist/{plot.vaf2cov-MSMW72IY.js.map → plot.vaf2cov-4DHFMYQV.js.map} +0 -0
  867. /package/dist/{polar2-LA4MSRRN.js.map → polar2-TMB5EITR.js.map} +0 -0
  868. /package/dist/{profileForms-BJRNB2ZF.js.map → profileForms-GD7BIOOD.js.map} +0 -0
  869. /package/dist/{profilePlot-DDO53C4T.js.map → profilePlot-CZLK5E74.js.map} +0 -0
  870. /package/dist/{proteinView-NFUR42XQ.js.map → proteinView-FEEEXLKT.js.map} +0 -0
  871. /package/dist/{proteomeCohortCompare-OZVF3X66.js.map → proteomeCohortCompare-NVLJ2FXX.js.map} +0 -0
  872. /package/dist/{pseudbulk.unit.spec-RY72JF7A.js.map → pseudbulk.unit.spec-GHQZPNAH.js.map} +0 -0
  873. /package/dist/{pseudobulk-UVT5G2VL.js.map → pseudobulk-G5UQIRKL.js.map} +0 -0
  874. /package/dist/{qualitative-X3VXNC7X.js.map → qualitative-EAUUCKU5.js.map} +0 -0
  875. /package/dist/{radar2-RTVUJ3AN.js.map → radar2-CJQ2L6KE.js.map} +0 -0
  876. /package/dist/{radarFacility2-ZGLZ5AKM.js.map → radarFacility2-BLVRZE4V.js.map} +0 -0
  877. /package/dist/{rememberedGvQ.unit.spec-RLLLWU5M.js.map → rememberedGvQ.unit.spec-DYRO2LO5.js.map} +0 -0
  878. /package/dist/{render-LR5BOYW6.js.map → render-KKAQPH6Y.js.map} +0 -0
  879. /package/dist/{report-37W5OXUM.js.map → report-OSOJHTSD.js.map} +0 -0
  880. /package/dist/{sampleView-BDC2WPH7.js.map → sampleView-WB74RLD7.js.map} +0 -0
  881. /package/dist/{samplelst-V2EIVZC5.js.map → samplelst-ZKXV5WOD.js.map} +0 -0
  882. /package/dist/{samplematrix-XOSKILUL.js.map → samplematrix-WJFYMWLT.js.map} +0 -0
  883. /package/dist/{sc-ZVZPWQY7.js.map → sc-RBRBUCLR.js.map} +0 -0
  884. /package/dist/{scatter-2ZE5MCYH.js.map → scatter-5K3QTIDK.js.map} +0 -0
  885. /package/dist/{scatter-ZOWFPGIS.js.map → scatter-SM7GQENM.js.map} +0 -0
  886. /package/dist/{selectGenomeWithTklst-EF7WYEAJ.js.map → selectGenomeWithTklst-ZZUJ7AQ7.js.map} +0 -0
  887. /package/dist/{singleCellCellType-TKCGC3G3.js.map → singleCellCellType-LCF2JNZ2.js.map} +0 -0
  888. /package/dist/{singleCellCellType.unit.spec-JZ6UHC5F.js.map → singleCellCellType.unit.spec-T6DYH4BC.js.map} +0 -0
  889. /package/dist/{singleCellGeneExpression-I2INGXGI.js.map → singleCellGeneExpression-2XUYTH4C.js.map} +0 -0
  890. /package/dist/{singleCellGeneExpression.unit.spec-KL77FSHZ.js.map → singleCellGeneExpression.unit.spec-SMRCLOF4.js.map} +0 -0
  891. /package/dist/{singleCellNumericValue-2X5NCEHL.js.map → singleCellNumericValue-57I33FZT.js.map} +0 -0
  892. /package/dist/{singleCellNumericValue.unit.spec-OUDBX5MY.js.map → singleCellNumericValue.unit.spec-4YNB4OEV.js.map} +0 -0
  893. /package/dist/{singleCellPlot-Q6INE54V.js.map → singleCellPlot-L6TKQHGD.js.map} +0 -0
  894. /package/dist/{singlecell-5N2P5ZAT.js.map → singlecell-LZKR3UDV.js.map} +0 -0
  895. /package/dist/{singlecell-NPSWMNI3.js.map → singlecell-UKN2VCXQ.js.map} +0 -0
  896. /package/dist/{snp-2WPJYPDE.js.map → snp-3LJITU5B.js.map} +0 -0
  897. /package/dist/{snp.unit.spec-PPWIIOX6.js.map → snp.unit.spec-ZQNU6XRM.js.map} +0 -0
  898. /package/dist/{snplocus-T3HZFZWA.js.map → snplocus-OME7UQBW.js.map} +0 -0
  899. /package/dist/{spliceevent.a53ss.diagram-APCF4LV5.js.map → spliceevent.a53ss.diagram-C32IEFMU.js.map} +0 -0
  900. /package/dist/{spliceevent.exonskip.diagram-TT5JGBSC.js.map → spliceevent.exonskip.diagram-CZ7MVRLK.js.map} +0 -0
  901. /package/dist/{spliceevent.noeventdiagram-CPXQSX3Z.js.map → spliceevent.noeventdiagram-ZO6R3776.js.map} +0 -0
  902. /package/dist/{ssGSEA-FSX6P7HA.js.map → ssGSEA-BGPQ2PFY.js.map} +0 -0
  903. /package/dist/{ssGSEA.unit.spec-TXYT665R.js.map → ssGSEA.unit.spec-U7TBUSSK.js.map} +0 -0
  904. /package/dist/{stattable-BD64SFYV.js.map → stattable-FISGQCED.js.map} +0 -0
  905. /package/dist/{studyCatalog-6BOWO4PO.js.map → studyCatalog-UHFUT2CJ.js.map} +0 -0
  906. /package/dist/{summarizeCnvGeneexp-AMLYJIPU.js.map → summarizeCnvGeneexp-OVZO6KIB.js.map} +0 -0
  907. /package/dist/{summarizeGeneexpSurvival-IDM7T333.js.map → summarizeGeneexpSurvival-KVQ4JGWK.js.map} +0 -0
  908. /package/dist/{summarizeMutationCnv-R6SYSJQC.js.map → summarizeMutationCnv-RAKGHNLE.js.map} +0 -0
  909. /package/dist/{summarizeMutationDiagnosis-XZJ4JLW2.js.map → summarizeMutationDiagnosis-LGCINAGG.js.map} +0 -0
  910. /package/dist/{summarizeMutationSurvival-ABJ5RL4L.js.map → summarizeMutationSurvival-J7H7L4FX.js.map} +0 -0
  911. /package/dist/{summary-NVYCTE6P.js.map → summary-2632JZXH.js.map} +0 -0
  912. /package/dist/{summary.integration.spec-SSLTLVNW.js.map → summary.integration.spec-5WBS2ZRP.js.map} +0 -0
  913. /package/dist/{summaryInput-SJOZETRP.js.map → summaryInput-BH6C3ATV.js.map} +0 -0
  914. /package/dist/{sunburst-RU5ZPJKW.js.map → sunburst-AMRR2IHM.js.map} +0 -0
  915. /package/dist/{survival-DVG6Y2FV.js.map → survival-2RNJQVFS.js.map} +0 -0
  916. /package/dist/{survival-BHJQMXKI.js.map → survival-WYCH4QOQ.js.map} +0 -0
  917. /package/dist/{survival.integration.spec-OJUPTY5N.js.map → survival.integration.spec-7IFPY4I4.js.map} +0 -0
  918. /package/dist/{svgraph-ETFA4GRX.js.map → svgraph-YQWS52ZJ.js.map} +0 -0
  919. /package/dist/{svmr-AI3RU4JK.js.map → svmr-NRN6LGKK.js.map} +0 -0
  920. /package/dist/{table-YCTSMLQL.js.map → table-3QOMV2NN.js.map} +0 -0
  921. /package/dist/{termCollection-VEVKKJZD.js.map → termCollection-2ZJ7TJGO.js.map} +0 -0
  922. /package/dist/{termCollection-GMKEZR6D.js.map → termCollection-3MCVR7BA.js.map} +0 -0
  923. /package/dist/{termCollection.unit.spec-EU6YCEPX.js.map → termCollection.unit.spec-QYOEA3X6.js.map} +0 -0
  924. /package/dist/{termCollectionFractionSelection-UBS74X36.js.map → termCollectionFractionSelection-5AH6EF4L.js.map} +0 -0
  925. /package/dist/{termCollectionFractionSelection.unit.spec-Y5OJFGDD.js.map → termCollectionFractionSelection.unit.spec-WPGW4WJN.js.map} +0 -0
  926. /package/dist/{tk-W6Z4FJMW.js.map → tk-DQ7D5UEO.js.map} +0 -0
  927. /package/dist/{tk-HMF4HCNV.js.map → tk-ONKYBG6R.js.map} +0 -0
  928. /package/dist/{tp.ui-NECRDJCS.js.map → tp.ui-C7BTMHEI.js.map} +0 -0
  929. /package/dist/{tvs.dt-2JEH3F35.js.map → tvs.dt-PLRMK7OT.js.map} +0 -0
  930. /package/dist/{tvs.dtcnv.categorical-YBXKEBR2.js.map → tvs.dtcnv.categorical-IZUY2AQO.js.map} +0 -0
  931. /package/dist/{tvs.dtcnv.continuous-AD3SJ6BY.js.map → tvs.dtcnv.continuous-ENV3RHHA.js.map} +0 -0
  932. /package/dist/{tvs.dtfusion-ODI3CLQS.js.map → tvs.dtfusion-2DVCV6AM.js.map} +0 -0
  933. /package/dist/{tvs.dtitd-V3LYLPJY.js.map → tvs.dtitd-XNDIRQYU.js.map} +0 -0
  934. /package/dist/{tvs.dtsnvindel-R3V5LTNL.js.map → tvs.dtsnvindel-4D3G7XSF.js.map} +0 -0
  935. /package/dist/{tvs.dtsv-ZQLKEDLJ.js.map → tvs.dtsv-QYMIMC4Z.js.map} +0 -0
  936. /package/dist/{tvs.numeric-22AHXO5K.js.map → tvs.numeric-M5LH3PRH.js.map} +0 -0
  937. /package/dist/{tvs.samplelst-G25A7HM6.js.map → tvs.samplelst-2KEU2ZWB.js.map} +0 -0
  938. /package/dist/{tvs.termCollection-WLVCWDEJ.js.map → tvs.termCollection-FEY746V5.js.map} +0 -0
  939. /package/dist/{vocabulary-6K537FJM.js.map → vocabulary-BR4NJDPS.js.map} +0 -0
  940. /package/dist/{wsi.direct-SNPPQPVO.js.map → wsi.direct-JWDUNHIO.js.map} +0 -0
@@ -0,0 +1,237 @@
1
+ import {
2
+ DataPointInteractions,
3
+ axisstyle,
4
+ createLollipopFromGene,
5
+ drawHoverShapes,
6
+ showResultsTable,
7
+ table2col,
8
+ to_svg
9
+ } from "./chunk-55FABQU2.js";
10
+ import {
11
+ Menu
12
+ } from "./chunk-ELJX3QIQ.js";
13
+ import {
14
+ icons
15
+ } from "./chunk-6RRZRISL.js";
16
+ import {
17
+ axisLeft
18
+ } from "./chunk-Z2ZITHT4.js";
19
+ import {
20
+ linear
21
+ } from "./chunk-4OLM3KSB.js";
22
+ import {
23
+ select_default
24
+ } from "./chunk-I6Y4O3RR.js";
25
+
26
+ // plots/manhattan/manhattan.ts
27
+ var manhattanLayoutDefaults = {
28
+ plotWidth: 1e3,
29
+ plotHeight: 400,
30
+ pngDotRadius: 2,
31
+ yAxisX: 70,
32
+ yAxisY: 40,
33
+ yAxisSpace: 20,
34
+ xAxisLabelPad: 30,
35
+ yAxisPad: 5,
36
+ axisColor: "#545454",
37
+ showYAxisLine: true,
38
+ fontSize: 12,
39
+ showLegend: true,
40
+ legendItemWidth: 80,
41
+ legendDotRadius: 3,
42
+ legendRightOffset: 15,
43
+ legendTextOffset: 12,
44
+ legendVerticalOffset: 4,
45
+ legendFontSize: 12,
46
+ showInteractiveDots: true,
47
+ interactiveDotRadius: 2,
48
+ interactiveDotStrokeWidth: 1,
49
+ showDownload: true,
50
+ interactiveDotsCap: 5e3,
51
+ maxTooltipGenes: 5
52
+ };
53
+ function plotManhattan(div, data, settings, app, custom = {}) {
54
+ const handle = { points: [], highlight: () => {
55
+ } };
56
+ settings = {
57
+ ...settings
58
+ };
59
+ let interactivePoints = data.plotData.points;
60
+ if (data.plotData.points.length > settings.interactiveDotsCap) {
61
+ interactivePoints = data.plotData.points.sort((a, b) => Math.abs(b.y) - Math.abs(a.y)).slice(0, settings.interactiveDotsCap);
62
+ }
63
+ const signed = data.plotData.y_min < 0;
64
+ div.style("position", "relative");
65
+ const geneTip = new Menu({ padding: "" });
66
+ const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
67
+ const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
68
+ const yPad = data.plotData.y_pad ?? settings.pngDotRadius;
69
+ const yAxisLow = signed ? data.plotData.y_min + yPad : 0;
70
+ const yAxisScale = linear().domain([yAxisLow, data.plotData.y_max - yPad]).range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)]);
71
+ const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
72
+ axisG.call(
73
+ axisLeft(yAxisScale).tickSizeOuter(0)
74
+ // removes top/bottom cap lines for clean look
75
+ );
76
+ axisstyle({
77
+ axis: axisG,
78
+ color: settings.axisColor,
79
+ fontsize: settings.fontSize + 2,
80
+ showline: settings.showYAxisLine
81
+ });
82
+ svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text((custom.yAxisLabel ?? "-log\u2081\u2080(q-value)") + (data.plotData.has_capped_points ? " [capped]" : ""));
83
+ svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
84
+ const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
85
+ if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
86
+ const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
87
+ const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
88
+ const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
89
+ const linkedLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
90
+ handle.points = interactivePoints;
91
+ handle.highlight = (dots) => drawHoverShapes(
92
+ linkedLayer,
93
+ dots.map((d) => ({
94
+ path: circlePath(settings.pngDotRadius + 2),
95
+ transform: `translate(${d.pixel_x},${d.pixel_y})`,
96
+ stroke: "black",
97
+ strokeWidth: 2
98
+ }))
99
+ );
100
+ const grin2Hover = (d, container) => {
101
+ const table = table2col({ holder: container.append("div"), margin: "10px" });
102
+ table.addRow("Gene", d.gene);
103
+ table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
104
+ const [t1, t2] = table.addRow();
105
+ t1.text("Type");
106
+ t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
107
+ table.addRow("Q-value", d.q_value.toPrecision(3));
108
+ table.addRow("Subject count", d.nsubj);
109
+ };
110
+ const grin2Table = (dots) => ({
111
+ columns: [
112
+ { label: "Gene" },
113
+ { label: "Position" },
114
+ { label: "Type" },
115
+ { label: "Q-value", sortable: true },
116
+ { label: "Subject count", sortable: true }
117
+ ],
118
+ rows: dots.map((d) => [
119
+ { value: d.gene },
120
+ { value: `${d.chrom}:${d.start}-${d.end}` },
121
+ {
122
+ html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
123
+ },
124
+ { value: d.q_value.toPrecision(3) },
125
+ { value: d.nsubj }
126
+ ])
127
+ });
128
+ const interactions = new DataPointInteractions({
129
+ cover,
130
+ hoverLayer,
131
+ hoverTip: geneTip,
132
+ points: interactivePoints,
133
+ getX: (d) => d.pixel_x,
134
+ getY: (d) => d.pixel_y,
135
+ hitRadius: settings.pngDotRadius + 3,
136
+ toHoverSpec: (d) => ({
137
+ path: circlePath(settings.pngDotRadius),
138
+ transform: `translate(${d.pixel_x},${d.pixel_y})`,
139
+ fill: "none",
140
+ stroke: "black",
141
+ strokeWidth: settings.interactiveDotStrokeWidth
142
+ }),
143
+ maxTooltipRows: settings.maxTooltipGenes,
144
+ onHover: custom.onHover,
145
+ itemNoun: custom.itemNoun ?? "gene",
146
+ renderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,
147
+ buildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,
148
+ // A caller with actions gets the module's standard click flow: an action menu for one
149
+ // dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.
150
+ ...custom.getActions ? {
151
+ getActions: custom.getActions,
152
+ renderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,
153
+ getRowKey: custom.getRowKey
154
+ } : {
155
+ // Manhattan single-click goes straight to a lollipop launch — no menu.
156
+ // Release hover-suppression immediately so the cursor's next move re-engages.
157
+ onSingleClick: (d, _event, ctx) => {
158
+ ctx.dismiss();
159
+ if (app && d.gene) createLollipopFromGene(d.gene, app);
160
+ },
161
+ // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
162
+ // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
163
+ // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
164
+ // Content is built BEFORE show2 so Menu can measure the populated rect for
165
+ // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
166
+ // and extends off the right edge of the viewport.
167
+ onMultiClick: (dots, event, ctx) => {
168
+ if (!app) {
169
+ ctx.dismiss();
170
+ return;
171
+ }
172
+ ctx.clickMenu.clear();
173
+ const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
174
+ showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
175
+ ctx.clickMenu.show2(event.clientX, event.clientY);
176
+ }
177
+ }
178
+ });
179
+ interactions.attach();
180
+ }
181
+ if (data.plotData.chrom_data) {
182
+ const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
183
+ Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
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+ const chromLabel = chrom.replace("chr", "");
185
+ if (chromLabel === "M") return;
186
+ const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
187
+ svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
188
+ });
189
+ }
190
+ svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr("y", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text("Chromosomes");
191
+ const title = svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text(custom.title ?? "Manhattan Plot");
192
+ const titleWidth = title.node().getBBox?.().width || 100;
193
+ if (settings.showDownload) {
194
+ const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + titleWidth + 8}px`);
195
+ icons["download"](downloadDiv, {
196
+ width: 16,
197
+ height: 16,
198
+ title: "Download Manhattan plot",
199
+ handler: () => {
200
+ const svgNode = svg.node();
201
+ const clone = svgNode.cloneNode(true);
202
+ const bbox = svgNode.getBBox();
203
+ clone.setAttribute("width", bbox.width.toString());
204
+ clone.setAttribute("height", bbox.height.toString());
205
+ clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
206
+ to_svg(clone, `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`, {
207
+ apply_dom_styles: true
208
+ });
209
+ }
210
+ });
211
+ }
212
+ const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type).filter(Boolean))];
213
+ const legendData = custom.legend?.map((l) => ({ type: l.label, color: l.color, hollow: l.hollow })) ?? mutationTypes.map((type) => {
214
+ const point = data.plotData.points.find((p) => p.type === type);
215
+ return {
216
+ type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
217
+ color: point?.color
218
+ };
219
+ });
220
+ if (settings.showLegend && legendData.length > 0) {
221
+ const legendY = settings.yAxisY / 2;
222
+ const totalWidth = legendData.length * settings.legendItemWidth;
223
+ const legendX = settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) - totalWidth - settings.legendRightOffset;
224
+ legendData.forEach((item, i) => {
225
+ const x = legendX + i * settings.legendItemWidth;
226
+ svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.hollow ? "none" : item.color).attr("stroke", item.hollow ? item.color : "none");
227
+ svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
228
+ });
229
+ }
230
+ return handle;
231
+ }
232
+
233
+ export {
234
+ manhattanLayoutDefaults,
235
+ plotManhattan
236
+ };
237
+ //# sourceMappingURL=chunk-XXPUZVS4.js.map
@@ -0,0 +1,7 @@
1
+ {
2
+ "version": 3,
3
+ "sources": ["../plots/manhattan/manhattan.ts"],
4
+ "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport { select } from 'd3-selection'\nimport {\n\tMenu,\n\ticons,\n\taxisstyle,\n\ttable2col,\n\tshowResultsTable,\n\tcreateLollipopFromGene,\n\tDataPointInteractions,\n\tdrawHoverShapes,\n\ttype ActionMenuItem\n} from '#dom'\nimport { to_svg } from '#src/client'\nimport type { ManhattanPoint } from './manhattanTypes'\n\n/**\n * Creates an interactive Manhattan plot on top of a PNG background plot image.\n *\n * @param {Object} div - div element to contain the plot\n * @param {Object} data - Plot data\n * @param {Object} settings - Display configuration options:\n * @param {number} [settings.plotWidth=500] - Plot area width\n * @param {number} [settings.plotHeight=200] - Plot area height\n * @param {boolean} [settings.showLegend=true] - Whether to display legend\n * @param {boolean} [settings.showDownload=true] - Whether to show download button\n * @param {boolean} [settings.showInteractiveDots=true] - Whether to show hoverable data points\n * @param {number} [settings.yAxisX=70] - Y-axis positioning\n * @param {number} [settings.yAxisSpace=40] - Space between Y-axis and plot\n * @param {number} [settings.yAxisY=40] - Top margin\n * @param {number} [settings.fontSize=12] - Base font size\n * @param {number} [settings.pngDotRadius=2] - Radius of dots in PNG plot\n * @param {number} [settings.legendItemWidth=80] - Horizontal space per legend item\n * @param {number} [settings.legendDotRadius=3] - Size of legend dots\n * @param {number} [settings.legendRightOffset=15] - Offset from right edge\n * @param {number} [settings.legendTextOffset=12] - Distance between dot and text\n * @param {number} [settings.legendVerticalOffset=4] - Vertical offset for legend items\n * @param {number} [settings.legendFontSize=12] - Font size for legend text\n * @param {number} [settings.interactiveDotRadius=2] - Radius of interactive dots\n * @param {number} [settings.xAxisLabelPad=20] - Amount of padding we give for x-axis title padding\n * @param {number} [settings.interactiveDotStrokeWidth=1] - Stroke width for interactive dots\n * @param {string} [settings.axisColor='#545454'] - Color for y-axis\n * @param {boolean} [settings.showYAxisLine=true] - Whether to show y-axis line\n * @param {number} [settings.interactiveDotsCap=5000] - Interactive dots cap\n * @param {number} [settings.maxTooltipGenes=5] - Maximum number of genes to show in tooltip\n * @param {Object} [app] - Optional app context for dispatching events\n *\n *\n * @description\n * Renders a genomic Manhattan plot by overlaying interactive elements on the base PNG plot image.\n * Features include chromosome labels, legend, hoverable data points with tooltips,\n * and proper axis scaling. The plot combines a static PNG plot image of all points with dynamic SVG elements\n * including axes, labels, legend, and top genes (represented as interactive dots) for detailed information on hover.\n */\n\n/** What a caller other than GRIN2 supplies: the plot is drawn the same way, but what a dot IS --\n * what its tooltip says, what clicking it offers, what the axis is called -- belongs to the caller.\n * Every field is optional and defaults to the GRIN2 behaviour, so GRIN2 passes nothing. */\nexport type ManhattanCustom<T = any> = {\n\ttitle?: string\n\tyAxisLabel?: string\n\t/** legend entries; default derives one per point `type` from the data. `hollow` draws the\n\t * swatch as an open circle, for a plot whose dots are drawn that way */\n\tlegend?: { label: string; color: string; hollow?: boolean }[]\n\titemNoun?: string\n\trenderSingleHoverTooltip?: (d: T, container: any) => void\n\tbuildMultiHitTableData?: (dots: T[]) => { columns: any[]; rows: any[] }\n\t/** Given, clicking a dot opens the standard action menu (buttons over the info table) rather\n\t * than GRIN2's lollipop launch; multi-hit clicks open the standard pick-a-row menu. */\n\tgetActions?: (d: T) => ActionMenuItem[]\n\trenderSingleHitInfo?: (d: T, container: any) => void\n\tgetRowKey?: (d: T) => string\n\t/** see DataPointInteractionsOpts.onHover */\n\tonHover?: (dots: T[]) => void\n}\n\n/** Returned by plotManhattan: the live points, and a way to ring some of them from outside -- for a\n * hover on another plot showing the same items. Separate from the plot's own hover layer, so the two\n * never erase each other. */\nexport type ManhattanHandle = { points: any[]; highlight: (dots: any[]) => void }\n\n/** Layout settings shared by every caller. GRIN2 keeps its own copy in its settings (they are\n * part of its persisted state); a caller without such state spreads these. */\nexport const manhattanLayoutDefaults = {\n\tplotWidth: 1000,\n\tplotHeight: 400,\n\tpngDotRadius: 2,\n\tyAxisX: 70,\n\tyAxisY: 40,\n\tyAxisSpace: 20,\n\txAxisLabelPad: 30,\n\tyAxisPad: 5,\n\taxisColor: '#545454',\n\tshowYAxisLine: true,\n\tfontSize: 12,\n\tshowLegend: true,\n\tlegendItemWidth: 80,\n\tlegendDotRadius: 3,\n\tlegendRightOffset: 15,\n\tlegendTextOffset: 12,\n\tlegendVerticalOffset: 4,\n\tlegendFontSize: 12,\n\tshowInteractiveDots: true,\n\tinteractiveDotRadius: 2,\n\tinteractiveDotStrokeWidth: 1,\n\tshowDownload: true,\n\tinteractiveDotsCap: 5000,\n\tmaxTooltipGenes: 5\n}\n\nexport function plotManhattan(\n\tdiv: any,\n\tdata: any,\n\tsettings: any,\n\tapp?: any,\n\tcustom: ManhattanCustom = {}\n): ManhattanHandle {\n\tconst handle: ManhattanHandle = { points: [], highlight: () => {} }\n\t// Get our settings\n\tsettings = {\n\t\t...settings\n\t}\n\n\t// Check size of interactive data. Ranked by |y| so a signed plot (hypomethylation below the\n\t// line) keeps its strongest dots on both sides rather than only the positive ones.\n\tlet interactivePoints = data.plotData.points\n\tif (data.plotData.points.length > settings.interactiveDotsCap) {\n\t\tinteractivePoints = data.plotData.points\n\t\t\t.sort((a: any, b: any) => Math.abs(b.y) - Math.abs(a.y))\n\t\t\t.slice(0, settings.interactiveDotsCap)\n\t}\n\t// A signed plot has y_min below zero; its axis is symmetric and its zero line sits mid-plot.\n\tconst signed = data.plotData.y_min < 0\n\n\t// Set the positioning up for download button to work properly\n\tdiv.style('position', 'relative')\n\n\t// Hover tooltip menu \u2014 DataPointInteractions writes into this on hover.\n\tconst geneTip = new Menu({ padding: '' })\n\n\tconst svg = div\n\t\t.append('svg')\n\t\t.attr('data-testid', 'sjpp-manhattan')\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4) // Extra space for x-axis labels, legend, and title\n\n\t// Add y-axis\n\t// yPlot \u2192 full padded scale, aligns exactly with PNG coordinates\n\t// yAxisScale \u2192 trimmed scale for axis labels, ignores PNG padding\n\t// --- Y-Axis Setup ---\n\t// This section builds two linked scales:\n\t//\n\t// 1) yPlot \u2192 full PNG-aligned scale (includes padding added by Rust)\n\t// 2) yAxisScale \u2192 visual axis scale (no padding; shows only real data values)\n\t//\n\t// The reason for two scales is that the PNG image itself was rendered\n\t// with top/bottom padding for dot radius. We need one scale to stay\n\t// pixel-perfect with the PNG (for dots, overlays, etc.), and another\n\t// scale to make the visible y-axis line up only with the *real* data region.\n\n\t// 1) yPlot: true positioning scale used for all pixel-aligned elements\n\t// - Domain = padded range from Rust (includes buffer above/below real data)\n\t// - Range = full PNG pixel height (0 is top, png_height is bottom)\n\tconst yPlot = scaleLinear()\n\t\t.domain([data.plotData.y_min, data.plotData.y_max]) // padded domain from Rust\n\t\t.range([settings.plotHeight + 2 * settings.pngDotRadius, 0]) // full PNG height\n\n\t// 2) yAxisScale: used only for the visible axis labels/ticks\n\t// - Domain = true data values (no padding)\n\t// - Range = subset of pixel space between yPlot(0) and yPlot(realMax [data.plotData.y_max - data.plotData.png_dot_radius])\n\t// so the axis sits entirely within the real data area\n\t// the PNG pads its y range by the dot radius; older renders had that padding equal the radius\n\t// in y units, newer ones state it\n\tconst yPad = data.plotData.y_pad ?? settings.pngDotRadius\n\tconst yAxisLow = signed ? data.plotData.y_min + yPad : 0\n\tconst yAxisScale = scaleLinear()\n\t\t.domain([yAxisLow, data.plotData.y_max - yPad])\n\t\t.range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)])\n\n\t// Axis group\n\tconst axisG = svg\n\t\t.append('g')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`)\n\n\taxisG.call(\n\t\td3axis.axisLeft(yAxisScale).tickSizeOuter(0) // removes top/bottom cap lines for clean look\n\t)\n\n\taxisstyle({\n\t\taxis: axisG,\n\t\tcolor: settings.axisColor,\n\t\tfontsize: settings.fontSize + 2,\n\t\tshowline: settings.showYAxisLine\n\t})\n\n\t// Add y-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY)\n\t\t.attr('y', settings.yAxisX / 2)\n\t\t.attr('transform', 'rotate(-90)')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text((custom.yAxisLabel ?? '-log\u2081\u2080(q-value)') + (data.plotData.has_capped_points ? ' [capped]' : ''))\n\n\t// Add png image\n\tsvg\n\t\t.append('image')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius)\n\t\t.attr('href', `data:image/png;base64,${data.pngImg || data.png}`)\n\n\t// Create scales for positioning elements\n\tconst xScale = scaleLinear()\n\t\t.domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer])\n\t\t.range([0, settings.plotWidth + 2 * settings.pngDotRadius])\n\n\t// Add interactive dots layer\n\tif (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {\n\t\t// Hover-ring layer \u2014 `pointer-events: none` so rings never intercept clicks.\n\t\tconst hoverLayer = svg\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t\t.style('pointer-events', 'none')\n\n\t\t// Cover as a sibling HTML div positioned over the plot area \u2014 avoids\n\t\t// the mouse-event quirks of nesting inside SVG.\n\t\tconst cover = select(svg.node().parentNode as HTMLElement)\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('left', `${settings.yAxisX + settings.yAxisSpace}px`)\n\t\t\t.style('top', `${settings.yAxisY}px`)\n\t\t\t.style('width', `${settings.plotWidth + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('height', `${settings.plotHeight + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('pointer-events', 'all')\n\n\t\t// Circle as an SVG path so it flows through the generic `drawHoverShapes`.\n\t\tconst circlePath = (r: number) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`\n\n\t\tconst linkedLayer = svg\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t\t.style('pointer-events', 'none')\n\t\thandle.points = interactivePoints\n\t\thandle.highlight = dots =>\n\t\t\tdrawHoverShapes(\n\t\t\t\tlinkedLayer,\n\t\t\t\tdots.map(d => ({\n\t\t\t\t\tpath: circlePath(settings.pngDotRadius + 2),\n\t\t\t\t\ttransform: `translate(${d.pixel_x},${d.pixel_y})`,\n\t\t\t\t\tstroke: 'black',\n\t\t\t\t\tstrokeWidth: 2\n\t\t\t\t}))\n\t\t\t)\n\n\t\tconst grin2Hover = (d: ManhattanPoint, container: any) => {\n\t\t\tconst table = table2col({ holder: container.append('div'), margin: '10px' })\n\t\t\ttable.addRow('Gene', d.gene)\n\t\t\ttable.addRow('Position', `${d.chrom}:${d.start}-${d.end}`)\n\t\t\tconst [t1, t2] = table.addRow()\n\t\t\tt1.text('Type')\n\t\t\tt2.html(`<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`)\n\t\t\ttable.addRow('Q-value', d.q_value.toPrecision(3))\n\t\t\ttable.addRow('Subject count', d.nsubj)\n\t\t}\n\t\tconst grin2Table = (dots: ManhattanPoint[]) => ({\n\t\t\tcolumns: [\n\t\t\t\t{ label: 'Gene' },\n\t\t\t\t{ label: 'Position' },\n\t\t\t\t{ label: 'Type' },\n\t\t\t\t{ label: 'Q-value', sortable: true },\n\t\t\t\t{ label: 'Subject count', sortable: true }\n\t\t\t],\n\t\t\trows: dots.map(d => [\n\t\t\t\t{ value: d.gene },\n\t\t\t\t{ value: `${d.chrom}:${d.start}-${d.end}` },\n\t\t\t\t{\n\t\t\t\t\thtml: `<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`\n\t\t\t\t},\n\t\t\t\t{ value: d.q_value.toPrecision(3) },\n\t\t\t\t{ value: d.nsubj }\n\t\t\t])\n\t\t})\n\n\t\tconst interactions = new DataPointInteractions<ManhattanPoint>({\n\t\t\tcover,\n\t\t\thoverLayer,\n\t\t\thoverTip: geneTip,\n\t\t\tpoints: interactivePoints,\n\t\t\tgetX: d => d.pixel_x,\n\t\t\tgetY: d => d.pixel_y,\n\t\t\thitRadius: settings.pngDotRadius + 3,\n\t\t\ttoHoverSpec: d => ({\n\t\t\t\tpath: circlePath(settings.pngDotRadius),\n\t\t\t\ttransform: `translate(${d.pixel_x},${d.pixel_y})`,\n\t\t\t\tfill: 'none',\n\t\t\t\tstroke: 'black',\n\t\t\t\tstrokeWidth: settings.interactiveDotStrokeWidth\n\t\t\t}),\n\t\t\tmaxTooltipRows: settings.maxTooltipGenes,\n\t\t\tonHover: custom.onHover,\n\t\t\titemNoun: custom.itemNoun ?? 'gene',\n\t\t\trenderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,\n\t\t\tbuildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,\n\t\t\t// A caller with actions gets the module's standard click flow: an action menu for one\n\t\t\t// dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.\n\t\t\t...(custom.getActions\n\t\t\t\t? {\n\t\t\t\t\t\tgetActions: custom.getActions,\n\t\t\t\t\t\trenderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,\n\t\t\t\t\t\tgetRowKey: custom.getRowKey\n\t\t\t\t }\n\t\t\t\t: {\n\t\t\t\t\t\t// Manhattan single-click goes straight to a lollipop launch \u2014 no menu.\n\t\t\t\t\t\t// Release hover-suppression immediately so the cursor's next move re-engages.\n\t\t\t\t\t\tonSingleClick: (d, _event, ctx) => {\n\t\t\t\t\t\t\tctx.dismiss()\n\t\t\t\t\t\t\tif (app && d.gene) createLollipopFromGene(d.gene, app)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t// Manhattan multi-click shows showResultsTable directly with `app + clickMenu`\n\t\t\t\t\t\t// so the table renders inline Matrix/Lollipop buttons. Reuses the module's\n\t\t\t\t\t\t// clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.\n\t\t\t\t\t\t// Content is built BEFORE show2 so Menu can measure the populated rect for\n\t\t\t\t\t\t// its right-edge clamp \u2014 otherwise the wide table is placed at cursor+offsetX\n\t\t\t\t\t\t// and extends off the right edge of the viewport.\n\t\t\t\t\t\tonMultiClick: (dots, event, ctx) => {\n\t\t\t\t\t\t\tif (!app) {\n\t\t\t\t\t\t\t\tctx.dismiss()\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tctx.clickMenu.clear()\n\t\t\t\t\t\t\tconst holder = ctx.clickMenu.d.append('div').style('margin', '10px')\n\t\t\t\t\t\t\tshowResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu })\n\t\t\t\t\t\t\tctx.clickMenu.show2(event.clientX, event.clientY)\n\t\t\t\t\t\t}\n\t\t\t\t })\n\t\t})\n\n\t\tinteractions.attach()\n\t}\n\n\t// Add chromosome labels\n\tif (data.plotData.chrom_data) {\n\t\tconst chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10\n\n\t\tObject.entries(data.plotData.chrom_data).forEach(([chrom, chromData]: [string, any]) => {\n\t\t\tconst chromLabel = chrom.replace('chr', '')\n\n\t\t\t// Skip chrM\n\t\t\tif (chromLabel === 'M') return\n\n\t\t\t// Calculate center position for label\n\t\t\tconst centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center)\n\n\t\t\t// Append chromosome label\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', centerPos)\n\t\t\t\t.attr('y', chromLabelY)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t\t\t.text(chromLabel)\n\t\t})\n\t}\n\n\t// Add x-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2)\n\t\t.attr('y', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text('Chromosomes')\n\n\t// Add title\n\tconst title = svg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('y', settings.yAxisY / 2)\n\t\t.attr('font-weight', 'bold')\n\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t.text(custom.title ?? 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+ "names": []
7
+ }