30:Td96,{ const svg = d3.select(nuclear_v_mito); const links = svg.selectAll("path.link"); // datum = label const leftTips = svg.selectAll("circle.tip.left"); // datum has .thisLabel const rightTips = svg.selectAll("circle.tip.right"); // Capture baseline styles once (so we can restore them) links.each(function () { const s = d3.select(this); if (this.__w0 == null) this.__w0 = +s.attr("stroke-width") || 1; if (this.__op0 == null) this.__op0 = +s.attr("stroke-opacity") || 0.6; }); function cacheTipBase(sel) { sel.each(function () { const s = d3.select(this); if (this.__r0 == null) this.__r0 = +s.attr("r") || 2; }); } cacheTipBase(leftTips); cacheTipBase(rightTips); // Tooltip const tip = d3 .select(document.body) .append("div") .style("position", "fixed") .style("pointer-events", "none") .style("background", "rgba(255,255,255,0.96)") .style("border", "1px solid #ccc") .style("padding", "6px 8px") .style("border-radius", "6px") .style("font", "12px/1.3 system-ui, -apple-system, Segoe UI, sans-serif") .style("box-shadow", "0 2px 10px rgba(0,0,0,0.1)") .style("opacity", 0); // Precompute any info you want to show const Ltips = mito_data.data.filter((d) => d.isTip); const Rtips = plastid_data.data.filter((d) => d.isTip); const Lby = new Map(Ltips.map((d) => [d.thisLabel, d])); const Rby = new Map(Rtips.map((d) => [d.thisLabel, d])); function setTip(label, evt) { const L = Lby.get(label), R = Rby.get(label); if (!L || !R) return; const dRank = Math.abs(+L.y1 - +R.y1); tip .html( `

${label}

Δ rank: ${dRank}

${label}

Δ rank: ${dRank}

${label}

Δ rank: ${dRank}

` ) .style("opacity", 1) .style("left", evt.clientX + 12 + "px") .style("top", evt.clientY + 12 + "px"); } function highlight(label) { if (label == null) { // restore all originals links .attr("stroke-opacity", function () { return this.__op0; }) .attr("stroke-width", function () { return this.__w0; }); leftTips.attr("r", function () { return this.__r0; }); rightTips.attr("r", function () { return this.__r0; }); return; } // emphasize hovered label links .attr("stroke-opacity", (d) => (d === label ? 1 : 0.08)) .attr("stroke-width", function (d) { return d === label ? Math.max(2, this.__w0 * 1.8) : Math.max(0.5, this.__w0 * 0.5); }); leftTips.attr("r", function (d) { return d.thisLabel === label ? this.__r0 + 2 : this.__r0; }); rightTips.attr("r", function (d) { return d.thisLabel === label ? this.__r0 + 2 : this.__r0; }); } links .on("mouseenter", (evt, label) => { setTip(label, evt); highlight(label); }) .on("mousemove", (evt, label) => { setTip(label, evt); }) .on("mouseleave", () => { tip.style("opacity", 0); highlight(null); }); function wireTips(sel) { sel .on("mouseenter", (evt, d) => { setTip(d.thisLabel, evt); highlight(d.thisLabel); }) .on("mousemove", (evt, d) => { setTip(d.thisLabel, evt); }) .on("mouseleave", () => { tip.style("opacity", 0); highlight(null); }); } wireTips(leftTips); wireTips(rightTips); chart; // keep visible }33:T1b1e,function cophylo({ left, right, width = 960, height = 600, margin = { top: 20, right: 20, bottom: 20, left: 20 }, gap = 60, stroke = "#777", tipStroke = "black", tipFill = "black", linkStroke = "#999", linkOpacity = 0.5, tipRadius = 1, tipRadiusHighlight = 4, tipRadiusAccessor = null, // (label) => number | falsy linkStrokeWidth = 1, sortLinksByY = true, labelAccessor = (d) => d.thisLabel // customize if needed } = {}) { const EPS = 1e-9; const toHoriz = (d) => Math.abs((d.y1 ?? NaN) - (d.y0 ?? NaN)) < EPS; const toVert = (d) => Math.abs((d.x1 ?? NaN) - (d.x0 ?? NaN)) < EPS; const norm = (tree) => { const data = tree.data ?? []; const horizontal = data.filter(toHoriz); const vertical = tree.vertical_lines && tree.vertical_lines.length ? tree.vertical_lines : data.filter(toVert); // enrich labels/tip flags for (const d of horizontal) { if (d.thisLabel == null) d.thisLabel = labelAccessor(d); if (d.isTip == null) d.isTip = !!d.thisLabel && (d.children?.length ?? 0) === 0; } return { horizontal, vertical }; }; const L = norm(left); const R = norm(right); const innerW = width - margin.left - margin.right; const innerH = height - margin.top - margin.bottom; const leftW = (innerW - gap) / 2; const rightW = (innerW - gap) / 2; const extentX = (H) => d3.extent(H.flatMap((d) => [d.x0, d.x1])); const extentY = (H, V) => d3.extent([ ...H.flatMap((d) => [d.y0, d.y1]), ...V.flatMap((d) => [d.y0, d.y1]) ]); const [lxmin, lxmax] = extentX(L.horizontal); const [lymin, lymax] = extentY(L.horizontal, L.vertical); const [rxmin, rxmax] = extentX(R.horizontal); const [rymin, rymax] = extentY(R.horizontal, R.vertical); const xL = d3.scaleLinear().domain([lxmin, lxmax]).range([0, leftW]); const yL = d3.scaleLinear().domain([lymin, lymax]).range([0, innerH]); const xR = d3.scaleLinear().domain([rxmin, rxmax]).range([0, rightW]); const yR = d3.scaleLinear().domain([rymin, rymax]).range([0, innerH]); const leftTips = L.horizontal.filter( (d) => d.isTip && (d.x1 ?? 0) > (d.x0 ?? 0) ); const rightTips = R.horizontal.filter( (d) => d.isTip && (d.x1 ?? 0) > (d.x0 ?? 0) ); const leftByLabel = new Map(leftTips.map((d) => [d.thisLabel, d])); const rightByLabel = new Map(rightTips.map((d) => [d.thisLabel, d])); let shared = [...leftByLabel.keys()].filter((k) => rightByLabel.has(k)); if (sortLinksByY) { shared.sort((a, b) => { const la = leftByLabel.get(a), lb = leftByLabel.get(b); const ra = rightByLabel.get(a), rb = rightByLabel.get(b); const ya = (yL(la.y1) + yR(ra.y1)) / 2; const yb = (yL(lb.y1) + yR(rb.y1)) / 2; return ya - yb; }); } const leftOriginX = margin.left; const leftOriginY = margin.top; const rightOriginX = margin.left + leftW + gap + rightW; // mirror anchor const rightOriginY = margin.top; const svg = d3 .create("svg") .attr("viewBox", [0, 0, width, height]) // responsive .attr("preserveAspectRatio", "xMidYMid meet") .style("max-width", "100%") .style("height", "auto"); const gRoot = svg.append("g"); const strokeWidth = 1; // LINKS ---------------------------------------------------------------------- const leftPos = new Map( leftTips.map((d) => [ d.thisLabel, { x: leftOriginX + xL(d.x1), y: leftOriginY + yL(d.y1) } ]) ); const rightPos = new Map( rightTips.map((d) => [ d.thisLabel, { x: rightOriginX - xR(d.x1), y: rightOriginY + yR(d.y1) } // mirrored x ]) ); const linkPath = (L, R) => { const midX = (L.x + R.x) / 2; return `M${L.x},${L.y} C${midX},${L.y} ${midX},${R.y} ${R.x},${R.y}`; }; gRoot .append("g") .attr("class", "cophylo-links") .selectAll("path.link") .data(shared) .join("path") .attr("class", "link") .attr("d", (label) => { const Lp = leftPos.get(label), Rp = rightPos.get(label); return Lp && Rp ? linkPath(Lp, Rp) : null; }) .attr("fill", "none") .attr( "stroke", typeof linkStroke === "function" ? (d) => linkStroke(d) : linkStroke ) .attr("stroke-opacity", linkOpacity) .attr( "stroke-width", typeof linkStrokeWidth === "function" ? (d) => linkStrokeWidth(d) : linkStrokeWidth ); // LEFT ----------------------------------------------------------------------- const gLeft = gRoot .append("g") .attr("transform", `translate(${leftOriginX},${leftOriginY})`); gLeft .append("g") .selectAll("line.h") .data(L.horizontal) .join("line") .attr("x1", (d) => xL(d.x0) - strokeWidth / 2) .attr("y1", (d) => yL(d.y0)) .attr("x2", (d) => xL(d.x1) - strokeWidth / 2) .attr("y2", (d) => yL(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gLeft .append("g") .selectAll("line.v") .data(L.vertical) .join("line") .attr("x1", (d) => xL(d.x0)) .attr("y1", (d) => yL(d.y0)) .attr("x2", (d) => xL(d.x1)) .attr("y2", (d) => yL(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gLeft .append("g") .selectAll("circle.tip") .data(leftTips) .join("circle") .attr("class", "tip left") .attr("r", (d) => { const v = tipRadiusAccessor ? +tipRadiusAccessor(d.thisLabel) : 0; return v > 0 ? tipRadiusHighlight : tipRadius; }) .attr("cx", (d) => xL(d.x1)) .attr("cy", (d) => yL(d.y1)) .attr("fill", tipFill) .attr("stroke", tipStroke); // RIGHT (mirrored) ----------------------------------------------------------- const gRight = gRoot .append("g") .attr( "transform", `translate(${rightOriginX},${rightOriginY}) scale(-1,1)` ); gRight .append("g") .selectAll("line.h") .data(R.horizontal) .join("line") .attr("x1", (d) => xR(d.x0) - strokeWidth / 2) .attr("y1", (d) => yR(d.y0)) .attr("x2", (d) => xR(d.x1) - strokeWidth / 2) .attr("y2", (d) => yR(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gRight .append("g") .selectAll("line.v") .data(R.vertical) .join("line") .attr("x1", (d) => xR(d.x0)) .attr("y1", (d) => yR(d.y0)) .attr("x2", (d) => xR(d.x1)) .attr("y2", (d) => yR(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gRight .append("g") .selectAll("circle.tip") .data(rightTips) .join("circle") .attr("class", "tip right") .attr("r", (d) => { const v = tipRadiusAccessor ? +tipRadiusAccessor(d.thisLabel) : 0; return v > 0 ? tipRadiusHighlight : tipRadius; }) .attr("cx", (d) => xR(d.x1)) .attr("cy", (d) => yR(d.y1)) .attr("fill", tipFill) .attr("stroke", tipStroke); return Object.assign(svg.node(), { svg }); }34:T36a9,mito = 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`35:T36d9,plastid = 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`36:T3355,nuclear_mito = 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`37:T2d81,mito_nuclear = 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,Prunella_vulgaris:27.82)100/100:2.837992,((Euphrasia_confusa:5.575948,Rhinanthus_minor:5.575948)87.7/100:2.299295,Melampyrum_sylvaticum:7.875243)100/100:22.782749)99.1/100:0.925666,(Verbena_officinalis:15.120211,(Verbascum_nigrum:0.053499,Verbascum_thapsus:0.053499)100/100:15.066712)100/100:16.463447)99.8/100:1.55925,((Callitriche_obtusangula:29.70762,((Veronica_serpyllifolia:5.446113,Veronica_scutellata:5.446113)91.7/100:1.071835,((Veronica_arvensis:2.7782,Veronica_verna:2.7782)97.9/100:1.627799,Veronica_triphyllos:4.405999)99.4/100:2.111948)100/100:23.189672)99.9/100:2.100654,((Linaria_vulgaris:8.589782,Misopates_orontium:8.589782)99/100:3.176866,Cymbalaria_muralis:11.766648)99.7/100:20.041626)98.8/100:1.334634)100/100:6.1832,(Ligustrum_vulgare:2.75075,Syringa_vulgaris:2.75075)100/100:36.575359)100/100:13.190292,((Quercus_cerris:38.60298,((Cruciata_laevipes:1.760754,(Galium_aparine:1.124346,Galium_uliginosum:1.124346)96.7/100:0.636408)99.9/100:1.394333,Sherardia_arvensis:3.155087)100/100:35.447893)100/100:11.316074,Pentaglottis_sempervirens:49.919054)61.8/75:2.597347)49.7/74:2.368458,((Calystegia_soldanella:1.940441,Convolvulus_arvensis:1.940441)100/100:45.896215,(Solanum_dulcamara:33.9,Solanum_nigrum:33.9)100/100:13.936656)100/100:7.048203)100/100:9.336966,(Ilex_aquifolium:60.998765,((Sambucus_nigra:19.03286,Succisa_pratensis:19.03286)100/100:40.536853,((Torilis_japonica:53.311535,(Hedera_helix:21.509465,Hydrocotyle_vulgaris:21.509465)99.8/100:31.802071)100/100:5.62796,(((Arctium_minus:1.595348,Carduus_nutans:1.595348)100/100:46.179006,(Carlina_vulgaris:47.647875,(((((((Jacobaea_maritima:0.000611,Jacobaea_vulgaris:0.000611)99.1/100:1.022296,Senecio_sylvaticus:1.022907)91.8/99:0.50755,((Petasites_albus:0.274754,Petasites_hybridus:0.274754)60.2/100:0.081725,Tussilago_farfara:0.356479)91.2/100:1.173977)100/100:3.929565,Calendula_officinalis:5.460022)3.6/57:0.695487,((Tripolium_pannonicum:0.669932,Galatella_linosyris:0.669932)100/100:5.074378,((Filago_lutescens:0.320685,Logfia_minima:0.320685)99.5/100:1.609844,(Gnaphalium_uliginosum:1.602163,Pseudognaphalium_luteoalbum:1.602163)88.7/100:0.328366)100/100:3.813782)78.7/99:0.411199)83.5/98:3.366774,((((Matricaria_chamomilla:0.293511,Matricaria_discoidea:0.293511)99.8/100:0.65852,Tanacetum_vulgare:0.952031)99.8/100:1.265379,Tanacetum_parthenium:2.21741)100/100:6.491948,Pulicaria_dysenterica:8.709359)92.2/100:0.812925)86.9/100:37.937717,(Lapsana_communis:12.048601,Tragopogon_pratensis:12.048601)99.9/100:35.411399)95.5/100:0.187875)61.3/99:0.126479)100/100:7.507457,(Jasione_montana:26.002716,(Lobelia_dortmanna:7.943033,Lobelia_urens:7.943033)100/100:18.059683)100/100:29.279095)100/100:3.657685)62.4/96:0.630218)98/100:1.429052)86.9/99:3.22306)95.4/98:49.752368,(((Calluna_vulgaris:66,Vaccinium_vitis_idaea:66)100/100:45.001211,((Primula_veris:0.246904,Primula_vulgaris:0.246904)100/100:28.096421,Samolus_valerandi:28.343326)100/100:82.657886)39.8/37:0.66459,(Impatiens_glandulifera:0.687649,Impatiens_parviflora:0.687649)100/100:110.978152)100/100:2.308391)20.3/45:0.433102,Cornus_suecica:114.407295)100/100:6.640673)64.8/77:3.784541)99.8/91:0.017408)37.3/76:0.359493,Buxus_sempervirens:124.455608)100/100:0.265133,(((Adonis_annua:34.405434,(Ranunculus_sardous:4.634709,Ranunculus_sceleratus:4.634709)100/100:29.770725)99.9/100:21.594566,(Aquilegia_vulgaris:14.326715,Thalictrum_minus:14.326715)100/100:41.673285)100/100:9.562751,Berberis_vulgaris:65.562751)100/100:58.627725)100/100:0.191776,(((Aponogeton_distachyos:43.141987,(Potamogeton_natans:29.952021,(Triglochin_maritima:1.319346,Triglochin_palustris:1.319346)100/100:28.632675)100/100:13.189966)100/100:61.715154,Lemna_minuta:104.857141)97.8/100:8.142859,(((((((Bromus_sterilis:10.87137,(Poa_chaixii:7.223609,Polypogon_viridis:7.223609)99.8/100:3.64776)100/100:18.262838,Leersia_oryzoides:29.134207)17.1/100:1.305793,(Digitaria_sanguinalis:10.916558,Phragmites_australis:10.916558)99.2/100:19.523442)100/100:44.280313,(((((((Carex_hirta:0.68274,Carex_riparia:0.68274)83.8/96:0.543448,Carex_rostrata:1.226188)99.4/100:2.894136,(((Carex_depauperata:3.36326,Carex_caryophyllea:3.36326)75.5/99:0.08509,(Carex_nigra:1.210612,Carex_acutiformis:1.210612)97.2/100:2.237738)93.8/100:0.572049,(((Carex_extensa:2.645698,Carex_distans:2.645698)61/100:0.294382,Carex_laevigata:2.94008)100/100:0.900661,(Carex_pendula:2.871951,Carex_sylvatica:2.871951)96.5/100:0.96879)88.8/99:0.179658)41.9/98:0.099925)100/100:4.315327,(Carex_arenaria:2.106747,Carex_divulsa:2.106747)100/100:6.328904)100/100:9.609864,((Eriophorum_vaginatum:6.488387,Scirpus_sylvaticus:6.488387)100/100:8.405196,Trichophorum_cespitosum:14.893583)50.9/98:3.151932)100/100:13.438233,((Cyperus_fuscus:20.74179,(Schoenoplectus_triqueter:1.386569,Schoenoplectus_lacustris:1.386569)100/100:19.355221)100/100:7.532122,Eleocharis_quinqueflora:28.273912)99.9/100:3.209836)100/100:22.218485,((Juncus_effusus:8.143771,Juncus_squarrosus:8.143771)100/100:7.694315,(Luzula_pallescens:1.056958,Luzula_sylvatica:1.056958)100/100:14.781128)100/100:37.864147)100/100:21.01808)99.7/100:3.845595,Sparganium_emersum:78.565908)100/100:7.732204,Narthecium_ossifragum:86.298112)17.2/89:1.777351,Iris_foetidissima:88.075462)100/100:24.924538)100/100:10.9987)97.8/100:54.733876,((((((((((Antitrichia_curtipendula:2.447692,Climacium_dendroides:2.447692)97.1/100:1.826342,(Cratoneuron_filicinum:3.358389,Thuidium_tamariscinum:3.358389)89.5/100:0.915644)0/96:0.001477,Rhytidiadelphus_loreus:4.27551)60.7/97:0.481593,(((Calliergon_cordifolium:0.707883,Straminergon_stramineum:0.707883)99.4/100:3.20307,(Hyocomium_armoricum:3.363665,((Pseudoscleropodium_purum:0.812044,Rhynchostegium_megapolitanum:0.812044)91/100:1.186123,Rhynchostegiella_tenella:1.998168)100/100:1.365497)90.2/99:0.547288)79/100:0.544168,(Hypnum_cupressiforme:4.205286,(Heterocladium_heteropterum:2.859549,Neckera_pumila:2.859549)91.4/100:1.345737)86.5/58:0.249835)86.7/58:0.301982)95.4/100:0.729419,((Orthothecium_rufescens:4.199263,Plagiothecium_denticulatum:4.199263)92.3/100:0.923685,Pseudotaxiphyllum_elegans:5.122948)86.8/84:0.363574)78.2/100:0.672876,Isopterygiella_pulchella:6.159398)100/100:9.81889,Ulota_crispa:15.978288)100/100:7.481866,Bryoerythrophyllum_caledonicum:23.460154)100/100:10.35984,(Polytrichastrum_sexangulare:2.650781,(Polytrichum_commune:1.884972,Polytrichum_formosum:1.884972)94.5/100:0.765808)100/100:31.169213)100/100:12.376562,((Sphagnum_tenellum:1.37586,Sphagnum_contortum:1.37586)91.4/100:0.468597,Sphagnum_girgensohnii:1.844457)100/100:44.352098)100/100:23.068268)100/100:49.658814,Lunularia_cruciata:19.60601)100/100:0,Herbertus_hutchinsiae:19.60601)Root; `38:T3358,plastid_nuclear = `((((((((((((((((Acaena_ovalifolia:0.0316725818,(((Comarum_palustre:0.0278555239,(Fragaria_moschata:0.0045369199,Fragaria_vesca:0.0008259303)1/100:0.0153109437)1/100:0.009006198,(Potentilla_anserina:0.0263510559,(Potentilla_indica:0.0156712197,Potentilla_sterilis:0.0073213962)1/100:0.0074712357)1/100:0.0066001599)1/100:0.0070637131,((Rosa_canina:0.0116979478,Rosa_rugosa:0.004872724)1/96.3:0.0012901881,(Rosa_agrestis:0.0061704014,Rosa_spinosissima:0.0039598706)0.98/99.7:0.0024524785)1/100:0.0086507061)1/17:0.0017856362):0.007626304,(Geum_rivale:0.0065393494,Geum_urbanum:0.0062498708)1/100:0.0455302451)1/100:0.0052750647,(Rubus_caesius:0.0087365516,Rubus_idaeus:0.004721101)1/100:0.0132950087)1/35.5:0.0112418211,Filipendula_ulmaria:0.0557198418)1/100:0.0326232083,(Dryas_octopetala:0.0383467483,((Crataegus_laevigata:0.0097147274,((Malus_x_robusta:0.005405998,(Malus_domestica:0.0027335493,Malus_sylvestris:0.0027882784)1/100:0.0025487844)1/100:0.0033012356,Pyrus_communis:0.0125681431)1/100:0.0027849149)1/100:0.031850871,Prunus_padus:0.0333862948)1/100:0.0171861891)1/45.5:0.0059130579)1/100:0.0345012284,(Frangula_alnus:0.0636732319,((Humulus_lupulus:0.0597227992,(Parietaria_judaica:0.0838256473,(Urtica_dioica:0.0266674476,Urtica_urens:0.0272688875)1/100:0.0792178879)1/100:0.0320030912)1/100:0.0151036412,(Ulmus_glabra:0.0049639931,Ulmus_minor:0.0087411984)1/100:0.0600595019)1/100:0.0159033732)1/100:0.0108357141)1/100:0.0110713542,(((((Alnus_glutinosa:0.0027115088,Alnus_incana:0.0132208527)1/100:0.0187048051,Corylus_avellana:0.0221749668)1/100:0.0325378081,Myrica_gale:0.0534655307)1/100:0.0076566263,(Fagus_sylvatica:0.0355751414,((Quercus_ilex:0.0052245736,Quercus_cerris:0.0134341476)1/74.5:0.0013569606,(Quercus_petraea:0.0085118474,Quercus_robur:0.0040642636)1/100:0.0046472326)1/100:0.0300946493)1/100:0.0185094695)1/100:0.0211591804,(((Astragalus_alpinus:0.0108085097,Astragalus_glycyphyllos:0.0154869329)1/100:0.0364482389,(((Lathyrus_linifolius:0.0163906541,Vicia_sativa:0.0196573539)1/100:0.0251940453,((Trifolium_dubium:0.0255484131,((Trifolium_fragiferum:0.0102375987,(Trifolium_occidentale:0.0082144358,Trifolium_subterraneum:0.0238667493)1/83.7:0.003229104)1/95.6:0.0022077588,Trifolium_striatum:0.0130732754)1/100:0.011389909)1/100:0.008666013,(Medicago_arabica:0.0079465839,Medicago_lupulina:0.0076967947)1/100:0.0238634755)1/99.7:0.0044683743)1/100:0.0075334167,Ononis_reclinata:0.0353369353)1/100:0.025991395)1/100:0.026961374,Laburnum_anagyroides:0.0502586908)1/100:0.0638929681)1/74.8:0.0054063675)1/100:0.0080156581,(((Euonymus_europaeus:0.0992037475,(((Hypericum_androsaemum:0.018926985,(Hypericum_hirsutum:0.0139251311,Hypericum_pulchrum:0.0098470547)1/100:0.0171086188)1/100:0.1044078309,(((Euphorbia_lathyris:0.0267580315,Euphorbia_peplus:0.0369512968)1/100:0.0197247049,Euphorbia_maculata:0.049183394)1/100:0.0301857295,Mercurialis_annua:0.0779757653)1/100:0.0170855954)1/65.9:0.0056578124,(((Populus_nigra:0.0075656006,Populus_tremula:0.0190357885)1/100:0.008781568,((Salix_caprea:0.0071549182,Salix_repens:0.0049823525)1/100:0.0090540992,Salix_cinerea:0.0073664106)1/100:0.0190939369)0.75/100:0.0481699285,Viola_odorata:0.0821608958)1/100:0.0106551698)1/100:0.0163970283)0.77/95:0.0055564162,((Acer_campestre:0.0402856984,Aesculus_hippocastanum:0.0323358155)1/100:0.0528931816,Malva_neglecta:0.1073026091)1/99.7:0.0077496455)0.55/100:0.0065517175,((((((Arabidopsis_thaliana:0.0248914063,Lepidium_didymum:0.0263477348)1/94.5:0.0041979634,(Barbarea_vulgaris:0.0131642065,((Cardamine_flexuosa:0.0004478841,Cardamine_hirsuta:0.003604817)1/100:0.0163311051,Nasturtium_officinale:0.0181198605)1/99.6:0.0039309645)1/100:0.0099146203)0.99/100:0.0098173017,((Arabis_hirsuta:0.0146591601,(Draba_incana:0.0189451179,Draba_verna:0.0351510757)1/100:0.0116750202)1/100:0.0127555158,Brassica_nigra:0.0416486442)0.68/86:0.0041851785)1/100:0.007590541,Matthiola_sinuata:0.0312257846)1/100:0.1243651964,(Chamaenerion_angustifolium:0.0279354887,Epilobium_hirsutum:0.0279320515)1/100:0.1034642479)0.76/99.8:0.0148342173,((Geranium_molle:0.0337027395,Geranium_rotundifolium:0.0249984379)1/100:0.0303878447,(Erodium_maritimum:0.0177590306,Erodium_moschatum:0.0190451179)1/100:0.0225176977)1/100:0.0702489283)1/100:0.0093265812)0.92/53.1:0.004394489)1/100:0.0108803982,((Myriophyllum_alterniflorum:0.1036735345,Umbilicus_rupestris:0.1306843326)1/100:0.0209221795,(Ribes_rubrum:0.0526062736,Saxifraga_aizoides:0.1044484911)1/100:0.0229298558)1/100:0.0163192381)0.63/100:0.0040271036,(((((Agrostemma_githago:0.056342681,(Arenaria_serpyllifolia:0.0286278236,Moehringia_trinervia:0.0219753545)1/100:0.0294180799)1/100:0.0128573232,(Spergula_arvensis:0.0292606473,(Spergularia_bocconei:0.0053071483,Spergularia_marina:0.0041479147)1/100:0.0292507703)1/100:0.0225025225)1/100:0.0395325931,((Blitum_bonus_henricus:0.0348698069,Chenopodium_album:0.0341306049)1/100:0.0172417181,Salicornia_ramosissima:0.0680061633)1/100:0.0279411059)1/100:0.0450503436,((((Fallopia_convolvulus:0.0245167956,(Polygonum_aviculare:0.0082030963,Polygonum_maritimum:0.0095347005)1/100:0.0279262988)1/100:0.0179655059,Oxyria_digyna:0.0595752864)1/100:0.0190144536,Persicaria_maculosa:0.0537920664)1/100:0.0585332703,Tamarix_gallica:0.1025703586)1/99.8:0.013366558)1/100:0.0422688924,(((((((((((Ajuga_chamaepitys:0.0473581597,((((Ballota_nigra:0.0222631316,(Lamium_amplexicaule:0.0140188979,Lamium_purpureum:0.0077512995)1/100:0.0192860089)0.99/100:0.0101497649,Melittis_melissophyllum:0.0226950564)1/79.6:0.0056910664,Galeopsis_tetrahit:0.0342787123)1/100:0.0333820871,(Scutellaria_galericulata:0.0057456862,Scutellaria_minor:0.0080133249)1/100:0.0392603931)0.56/96.7:0.0069156036)1/100:0.0086163012,Prunella_vulgaris:0.0781517701)1/100:0.0125043011,(((Euphrasia_confusa:0.0293744641,Rhinanthus_minor:0.022893934)1/100:0.0070835149,Melampyrum_sylvaticum:0.0361398505)1/100:0.0501060251,Verbena_officinalis:0.056044834)0.85/99.6:0.0077150413)1/99.4:0.0061744069,(Verbascum_nigrum:0.0073877036,Verbascum_thapsus:0.0070587542)1/100:0.0547391103)1/100:0.0072338284,((Callitriche_obtusangula:0.0926653321,(Veronica_serpyllifolia:0.0233157621,(((Veronica_arvensis:0.0123016703,Veronica_verna:0.0160293789)1/100:0.0119677806,Veronica_triphyllos:0.0318595915)1/100:0.007410464,Veronica_scutellata:0.0253581757)1/100:0.0111578676)0.87/100:0.0595027884)1/100:0.0157019123,(Cymbalaria_muralis:0.0337329359,(Linaria_vulgaris:0.0451523941,Misopates_orontium:0.0273076833)1/100:0.0100989444)1/100:0.0228797275)1/100:0.0133302794)1/100:0.0241250774,(Ligustrum_vulgare:0.0178885142,Syringa_vulgaris:0.0146875202)1/100:0.0653241293)1/100:0.0236920945,(((Calystegia_soldanella:0.0131052315,Convolvulus_arvensis:0.0077663709)1/100:0.0741632562,(Solanum_dulcamara:0.0119079979,Solanum_nigrum:0.0088862261)1/100:0.0742434688)1/100:0.0208998227,((Sherardia_arvensis:0.0334901957,(Cruciata_laevipes:0.0344171131,(Galium_aparine:0.0140166907,Galium_uliginosum:0.0096258265)1/100:0.0116435607)1/99.9:0.0075743114)1/100:0.1054664853,Pentaglottis_sempervirens:0.1227964455)0.97/79.9:0.0137035686)0.71/100:0.0084386336)1/100:0.0163697179,Ilex_aquifolium:0.0714388079)0.85/99.5:0.0057030985,(((Sambucus_nigra:0.0616171131,Succisa_pratensis:0.0851314342)1/100:0.012643044,((Hedera_helix:0.0375313438,Hydrocotyle_vulgaris:0.0570126124)1/100:0.0124733686,Torilis_japonica:0.0795458001)1/100:0.0357345557)1/96.8:0.0058084497,(((((((((Tanacetum_parthenium:0.0144315848,Tanacetum_vulgare:0.0071433843)1/99.5:0.0023913511,(Matricaria_chamomilla:0.0070215782,Matricaria_discoidea:0.0075619804)1/100:0.0098844391)1/100:0.0439192659,((Filago_lutescens:0.0110858967,Logfia_minima:0.0092055109)1/100:0.0049641171,(Pseudognaphalium_luteoalbum:0.0127637995,Gnaphalium_uliginosum:0.0116536982)0.64/99.9:0.0026364766)1/100:0.022158159)1/44.5:0.004770583,((Galatella_linosyris:0.0130139086,Tripolium_pannonicum:0.0162544399)0.96/100:0.0269757361,Calendula_officinalis:0.0463065825)1/95.7:0.0044325903)0.91/100:0.0058118593,(((Jacobaea_maritima:0.0053503597,Jacobaea_vulgaris:0.0077216275)1/100:0.015794205,Senecio_sylvaticus:0.0208961216)1/100:0.0086584883,(Petasites_albus:0.0091125889,(Petasites_hybridus:0.0109396863,Tussilago_farfara:0.0149602356)1/11.4:0.0042486198)1/100:0.0132109669)1/100:0.0263191152)1/99.2:0.0061047813,Pulicaria_dysenterica:0.0385464693)1/100:0.0083013704,(Lapsana_communis:0.0489700778,Tragopogon_pratensis:0.0329309422)1/100:0.0156782316)1/99.8:0.0051182961,(Carlina_vulgaris:0.033189443,(Carduus_nutans:0.0231108738,Arctium_minus:0.012348675)1/100:0.0142388926)1/100:0.0072069529)0.84/100:0.0601638506,(Jasione_montana:0.0635169317,(Lobelia_dortmanna:0.0242090523,Lobelia_urens:0.0127569671)1/100:0.0326459109)1/100:0.0275770494)1/100:0.0240363773)1/100:0.0123666373)1/100:0.0055481564,Cornus_suecica:0.0855200724)0.9/63.9:0.0042853035,(((Calluna_vulgaris:0.0435234173,Vaccinium_vitis_idaea:0.0325915714)1/100:0.0493392276,((Primula_veris:0.0037580855,Primula_vulgaris:0.0033073434)1/100:0.0789475487,Samolus_valerandi:0.0617470653)1/100:0.0406059531)1/99.7:0.010316622,(Impatiens_glandulifera:0.0248854288,Impatiens_parviflora:0.0142980611)1/100:0.1221906068)0.99/100:0.0139152055)1/100:0.0115205606)1/87.5:0.00500731)1/83:0.025172306,Buxus_sempervirens:0.0860669817)1/100:0.0087918853,(((Aquilegia_vulgaris:0.0189382686,Thalictrum_minus:0.0184096205)1/100:0.0353028679,(Adonis_annua:0.0606043345,(Ranunculus_sardous:0.0261135225,Ranunculus_sceleratus:0.0195023057)1/100:0.0629060944)1/100:0.0127096628)1/100:0.0367502013,Berberis_vulgaris:0.086041256)1/100:0.0254285091)1/99.4:0.0250998192,((Lemna_minuta:0.1858686671,(Aponogeton_distachyos:0.123709765,(Potamogeton_natans:0.0940984613,(Triglochin_maritima:0.0162881064,Triglochin_palustris:0.013847866)1/100:0.0898388592)1/100:0.0209462803)1/91.9:0.0347689422)0.99/99.9:0.0132659333,((((((((((((Carex_sylvatica:0.0046152289,Carex_pendula:0.0031346681)1/95.7:0.000579064,((Carex_laevigata:0.0060878146,Carex_distans:0.0047007828)1/99.9:0.0015077611,Carex_extensa:0.0069963236)1/100:0.0021717297)1/100:0.002540853,((Carex_acutiformis:0.0053815013,Carex_caryophyllea:0.0077819927)0.84/99.7:0.0015770095,(Carex_nigra:0.0108594846,((Carex_hirta:0.0041162312,Carex_riparia:0.0053236642)0.81/64.9:0.0006817449,Carex_rostrata:0.0040189566)1/100:0.002802626)1/92.6:0.000602554)0.34/99.2:0.0011412899)0.96/96.3:0.0018281901,Carex_depauperata:0.0108145312)1/100:0.0028300249,(Carex_arenaria:0.0082923727,Carex_divulsa:0.0072543223)1/100:0.0057303462)1/100:0.0123405529,(Trichophorum_cespitosum:0.016128415,(Eriophorum_vaginatum:0.0138784394,Scirpus_sylvaticus:0.00781236)1/100:0.0079202953)1/99.7:0.0040565966)1/100:0.0193211325,((Cyperus_fuscus:0.0337976802,(Schoenoplectus_lacustris:0.0047732325,Schoenoplectus_triqueter:0.0043020762)1/100:0.0278529782)1/100:0.0087123099,Eleocharis_quinqueflora:0.0469998668)0.87/99.8:0.0052768437)1/100:0.0478905168,((Juncus_effusus:0.0367371863,Juncus_squarrosus:0.0599390586)1/100:0.0340929864,(Luzula_pallescens:0.0083570977,Luzula_sylvatica:0.0056872096)1/100:0.0686926534)1/100:0.0527651442)1/100:0.050137189,((Leersia_oryzoides:0.0468276275,(Bromus_sterilis:0.0403435227,(Poa_chaixii:0.0310973637,Polypogon_viridis:0.0194739177)1/100:0.0131502463)1/100:0.0432082887)0.98/100:0.0146637418,(Digitaria_sanguinalis:0.0438025649,Phragmites_australis:0.029997093)1/100:0.0169198483)1/100:0.1066146111)1/100:0.0288744483,Sparganium_emersum:0.0794758278)1/100:0.0231672135,Narthecium_ossifragum:0.1356874504)1/26.2:0.0075378297,Iris_foetidissima:0.1115480109)1/100:0.019912853)1/100:0.0256972665)1/100:0.256700998,(((((((Calliergon_cordifolium:0.006546612,Straminergon_stramineum:0.0110803598)1/100:0.0065128871,((Antitrichia_curtipendula:0.0254042546,(Climacium_dendroides:0.0175890876,Rhytidiadelphus_loreus:0.0175710202)11.5:0.0009810618)0.76/96.2:0.0011758219,((Cratoneuron_filicinum:0.0283509736,(Thuidium_tamariscinum:0.0169749593,Hypnum_cupressiforme:0.0189194246)1/100:0.0071826712)0.83/98.4:0.001592049,((Hyocomium_armoricum:0.0115092153,((Pseudoscleropodium_purum:0.006184379,Rhynchostegium_megapolitanum:0.0169104254)1/67.9:0.0020980344,Rhynchostegiella_tenella:0.0194634571)1/100:0.0025297148)1/100:0.0024073312,(Heterocladium_heteropterum:0.0218499152,Neckera_pumila:0.0146143484)0.81/100:0.0033644759)1/93.7:0.0010618761)1/65.4:0.0011807401)0.54/66.7:0.0010945075)0.51/98:0.0019999236,(Orthothecium_rufescens:0.0208572046,((Pseudotaxiphyllum_elegans:0.0122632082,Plagiothecium_denticulatum:0.0164348978)1/100:0.005640108,Isopterygiella_pulchella:0.0106924919)0.62/96.6:0.0011428395)0.86/85.7:0.0010667835)0.99/100:0.0240863371,Ulota_crispa:0.0506602287)1/100:0.0232018461,Bryoerythrophyllum_caledonicum:0.067207731)1/100:0.0603714581,(Polytrichastrum_sexangulare:0.0097975325,(Polytrichum_commune:0.0171465602,Polytrichum_formosum:0.011973801)1/100:0.0087522349)1/100:0.0691988475)1/100:0.0519917317,(Sphagnum_tenellum:0.0052496232,(Sphagnum_contortum:0.0073849901,Sphagnum_girgensohnii:0.0089878759)1/43:0.0021989511)0.99/100:0.1094168668)1/100:0.0655828661)1/100:0.0764077878,Lunularia_cruciata:0.1196796628)1/100:0,Herbertus_hutchinsiae:0.1554659938)Root; `39:T2da0,nuclear_plastid = 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7076,Phragmites_australis:14.387076)100/100:16.052924)100/100:49.471701)100/100:3.393692,Sparganium_emersum:83.305393)100/100:4.448853,Iris_foetidissima:87.754246)99.5/100:1.447792,Narthecium_ossifragum:89.202038)100/100:6.951044)100/100:15.573983)100/100:20.288928,((((((((((((Antitrichia_curtipendula:12.682685,Climacium_dendroides:12.682685)100/100:2.577706,Rhytidiadelphus_loreus:15.260391)99.2/69:0.575963,((Calliergon_cordifolium:4.966922,Straminergon_stramineum:4.966922)100/100:10.797725,(Cratoneuron_filicinum:13.840649,Thuidium_tamariscinum:13.840649)100/100:1.923997)23.3/69:0.071708)96.1/98:0.300961,(Hyocomium_armoricum:15.444711,((Pseudoscleropodium_purum:6.425543,Rhynchostegium_megapolitanum:6.425543)100/100:5.620511,Rhynchostegiella_tenella:12.046053)100/100:3.398658)100/98:0.692604)100/100:0.283842,(Hypnum_cupressiforme:14.945529,(Heterocladium_heteropterum:11.836218,Neckera_pumila:11.836218)100/100:3.109311)100/100:1.475628)100/100:1.125399,(Orthothecium_rufescens:14.389996,Pseudotaxiphyllum_elegans:14.389996)55.8/85:3.15656)99.9/90:2.457589,Plagiothecium_denticulatum:20.004145)99.4/90:5.772654,Isopterygiella_pulchella:25.776799)100/100:11.337191,Ulota_crispa:37.11399)100/100:10.146432,Bryoerythrophyllum_caledonicum:47.260422)100/100:20.306921,(Polytrichastrum_sexangulare:10.587015,(Polytrichum_commune:4.690111,Polytrichum_formosum:4.690111)100/100:5.896905)100/100:56.980328)100/100:14.642959,((Sphagnum_tenellum:2.113979,Sphagnum_contortum:2.113979)81.5/98:0.902369,Sphagnum_girgensohnii:3.016348)100/100:79.193953)100/100:9.227835)100/100:28.994936,Lunularia_cruciata:62.443201)100/100:0,Herbertus_hutchinsiae:62.443201)Root; `3a:[] 2e:{"title":"lwCoPhylo","cells":[{"id":0,"value":"# lwCoPhylo","pinned":false,"hidden":false,"mode":"md"},{"id":5,"value":"Attempt to plot two trees against eachother. Tips have already been optimally rotated using `R::phytools::cophylo()` function.","pinned":false,"hidden":false,"mode":"md"},{"id":165,"value":"## Cophylo plot including ferns","pinned":false,"hidden":false,"mode":"md"},{"id":197,"value":"### Nuclear vs mitochondria","pinned":false,"hidden":false,"mode":"md"},{"id":207,"value":"Broadly very congruent!","pinned":false,"hidden":false,"mode":"md"},{"id":199,"value":"nuclear_v_mito = cophylo({\n left: lw.rectangleLayout(lw.readTree(nuclear_mito)),\n right: lw.rectangleLayout(lw.readTree(mito_nuclear)),\n width: 600,\n height: 800,\n gap: 120,\n stroke: \"#666\",\n tipRadius: 0.5,\n linkStrokeWidth: (label) =>\n 0.5 + (movedByLabel_nuc_mito.get(label)?.norm ?? 0) * 4,\n linkStroke: (label) =>\n (movedByLabel_nuc_mito.get(label)?.diff ?? 0) >= thresh\n ? \"#d62728\"\n : \"#bbb\",\n linkOpacity: 0.5\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":204,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":229,"value":"### Nuclear vs plastid","pinned":false,"hidden":false,"mode":"md"},{"id":241,"value":"nuclear_v_plastid = cophylo({\n left: lw.rectangleLayout(lw.readTree(nuclear_plastid)),\n right: lw.rectangleLayout(lw.readTree(plastid_nuclear)),\n width: 600,\n height: 800,\n gap: 120,\n stroke: \"#666\",\n tipRadius: 0.5,\n linkStrokeWidth: (label) =>\n 0.5 + (movedByLabel_nuc_plastid.get(label)?.norm ?? 0) * 4,\n linkStroke: (label) =>\n (movedByLabel_nuc_plastid.get(label)?.diff ?? 0) >= thresh\n ? \"#d62728\"\n : \"#bbb\",\n linkOpacity: 0.5\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":259,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":179,"value":"### Plastid vs mitochondria","pinned":false,"hidden":false,"mode":"md"},{"id":47,"value":"chart = cophylo({\n left: mito_data,\n right: plastid_data,\n width: 600,\n height: 800,\n gap: 120,\n stroke: \"#666\",\n tipRadius: 0.5,\n linkStrokeWidth: (label) => 0.5 + (movedByLabel.get(label)?.norm ?? 0) * 4,\n linkStroke: (label) =>\n (movedByLabel.get(label)?.diff ?? 0) >= thresh ? \"#d62728\" : \"#bbb\",\n linkOpacity: 0.5\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":127,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":168,"value":"## Cophylo plot excluding ferns","pinned":false,"hidden":false,"mode":"md"},{"id":183,"value":"### Plastid vs mitochondria","pinned":false,"hidden":false,"mode":"md"},{"id":114,"value":"## Correlation in tip rank","pinned":false,"hidden":false,"mode":"md"},{"id":116,"value":"// Spearman correlation of tip ranks\nfunction spearmanRankCorr(left, right) {\n const Ly = new Map(left.data.filter(d => d.isTip).map(d => [d.thisLabel, +d.y1]));\n const Ry = new Map(right.data.filter(d => d.isTip).map(d => [d.thisLabel, +d.y1]));\n const shared = [...Ly.keys()].filter(k => Ry.has(k));\n const x = shared.map(k => Ly.get(k));\n const y = shared.map(k => Ry.get(k));\n const mean = a => d3.mean(a);\n const sd = a => Math.sqrt(d3.variance(a));\n const cov = (a,b) => d3.mean(a.map((v,i) => (v-mean(a))*(b[i]-mean(b))));\n return cov(x,y) / (sd(x)*sd(y));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":117,"value":"spearmanRankCorr(mito_data, plastid_data)","pinned":false,"hidden":false,"mode":"ojs"},{"id":85,"value":"## The `cophylo` function","pinned":false,"hidden":false,"mode":"md"},{"id":86,"value":"This takes two trees. I'd personally use `R::phytools::cophylo()` to compute these trees first.","pinned":false,"hidden":false,"mode":"md"},{"id":9,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":94,"value":"Optionally add tip movement.","pinned":false,"hidden":false,"mode":"md"},{"id":121,"value":"viewof moved_table = Inputs.table(moved, {\n columns: [\"label\", \"y_left\", \"y_right\", \"diff\", \"signed\", \"norm\"],\n rows: 10\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":105,"value":"movedByLabel = new Map(moved.map(d => [d.label, d]));","pinned":false,"hidden":false,"mode":"ojs"},{"id":250,"value":"movedByLabel_nuc_mito = new Map(moved_nuc_mito.map(d => [d.label, d]));","pinned":false,"hidden":false,"mode":"ojs"},{"id":253,"value":"movedByLabel_nuc_plastid = new Map(moved_nuc_plastid.map((d) => [d.label, d]))","pinned":false,"hidden":false,"mode":"ojs"},{"id":108,"value":"thresh = d3.quantile(moved.map((d) => d.diff).sort(d3.ascending), 0.9) ?? 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":96,"value":"moved = tipMovementByRank(mito_data, plastid_data)","pinned":false,"hidden":false,"mode":"ojs"},{"id":244,"value":"moved_nuc_mito = tipMovementByRank(\n lw.rectangleLayout(lw.readTree(nuclear_mito)),\n lw.rectangleLayout(lw.readTree(mito_nuclear))\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":247,"value":"moved_nuc_plastid = tipMovementByRank(\n lw.rectangleLayout(lw.readTree(nuclear_plastid)),\n lw.rectangleLayout(lw.readTree(plastid_nuclear))\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":88,"value":"function tipMovementByRank(left, right) {\n const Ly = new Map(\n left.data.filter((d) => d.isTip).map((d) => [d.thisLabel, +d.y1])\n );\n const Ry = new Map(\n right.data.filter((d) => d.isTip).map((d) => [d.thisLabel, +d.y1])\n );\n const shared = [...Ly.keys()].filter((k) => Ry.has(k));\n\n const rows = shared\n .map((label) => {\n const ly = Ly.get(label),\n ry = Ry.get(label);\n return {\n label,\n y_left: ly,\n y_right: ry,\n diff: Math.abs(ly - ry),\n signed: ly - ry\n };\n })\n .sort((a, b) => d3.descending(a.diff, b.diff));\n\n // add a normalized difference in [0,1]\n const n = rows.length || 1;\n for (const r of rows) r.norm = r.diff / (n - 1);\n return rows;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":99,"value":"## Data","pinned":false,"hidden":false,"mode":"md"},{"id":25,"value":"mito_data = lw.rectangleLayout(lw.readTree(mito))","pinned":false,"hidden":false,"mode":"ojs"},{"id":12,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":21,"value":"plastid_data = lw.rectangleLayout(lw.readTree(plastid))","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":189,"value":"### The others","pinned":false,"hidden":false,"mode":"md"},{"id":191,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":194,"value":"$37","pinned":false,"hidden":false,"mode":"ojs"},{"id":231,"value":"$38","pinned":false,"hidden":false,"mode":"ojs"},{"id":238,"value":"$39","pinned":false,"hidden":false,"mode":"ojs"},{"id":103,"value":"## Imports","pinned":false,"hidden":false,"mode":"md"},{"id":18,"value":"lw = import(\n \"https://unpkg.com/@euphrasiologist/lwphylo@1.1.5/src/index.js?module\"\n)","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W3a","stdlib":"1","titling":"auto"}