@euphrasiologist/lwphylo 1.3.0 → 1.4.0

package/dist/drawPhylogeny.umd.js

@@ -1,2 +1,2 @@
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Use 'rect', 'radial', or 'unrooted'.")}});
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function(t,{layout:e="rect",width:a=800,height:i=800,margin:l={top:20,right:300,bottom:20,left:50},radialMargin:o=80,strokeWidth:c=1,radialMode:h="outer",tipLabels:d=!0,labelFontSize:f=10,tipRadius:g,internalNodeCircles:m=!1,internalNodeRadius:M=3,nodeLabels:b=!1,nodeLabelFontSize:w,scaleBar:k=!1,alignTipLabels:_=!1,showTooltips:v=!0,tooltipFormatter:A=(t,e)=>`${t.thisLabel??"(unnamed)"}\nroot→tip: ${(+e).toFixed(4)}`,hoverStroke:L="#1f77b4",hoverWidth:T=3,highlightTips:$=[],highlightStroke:j="#e63946",highlightWidth:z=2.5}={}){const P=t=>"number"==typeof t&&Number.isFinite(t),S=w??f;function E(t,{prefer:e="auto"}={}){return function(n){let a=t.get(n);if(!a)return 0;if("r"===e||"auto"===e&&"r"in a)return Number(a.r??0);if("x1"===e||"auto"===e&&"x1"in a)return Number(a.x1??0);let r=0;for(;a&&null!=a.parentId;)r+=Number(a.branchLength||0),a=t.get(a.parentId);return r}}if("rect"===e){const X=u(x(t)),Y=X.horizontal_lines,F=X.vertical_lines,B=Y.filter(t=>t.isTip),D=new Map(X.data.map(t=>[t.thisId,t])),N=new Map(B.map(t=>[t.thisId,t])),O=new Map(B.map(t=>[t.thisLabel,t])),W=E(D,{prefer:"x1"}),U=g??2,R=n.max(Y,t=>t.y1),q=n.min(Y,t=>t.y1),C=n.max(Y,t=>t.x1),G=n.scaleLinear().domain([q-1,R+1]).range([l.top,i-l.bottom]),H=n.scaleLinear().domain([0,C]).range([l.left,a-l.right]),J=n.create("svg").attr("width",a).attr("height",i).attr("font-family","sans-serif").attr("font-size",10),K=J.append("g"),Q=J.append("g").attr("class","phylo_static_highlight"),V=J.append("g").attr("class","phylo_hover_highlight");K.selectAll(".hline").data(Y).join("line").attr("x1",t=>H(t.x0)).attr("y1",t=>G(t.y0)).attr("x2",t=>H(t.x1)).attr("y2",t=>G(t.y1)).attr("stroke","#555").attr("stroke-width",c),K.selectAll(".vline").data(F).join("line").attr("x1",t=>H(t.x0)).attr("y1",t=>G(t.y0)).attr("x2",t=>H(t.x1)).attr("y2",t=>G(t.y1)).attr("stroke","#555").attr("stroke-width",c);const Z=K.selectAll(".tip-dot").data(B).join("circle").attr("cx",t=>H(t.x1)).attr("cy",t=>G(t.y1)).attr("r",U).attr("fill","black");if(v&&Z.append("title").text(t=>A(t,W(t.thisId))),Z.on("mouseenter",function(t,e){V.selectAll("*").remove(),et(e.thisId,V,L,T),n.select(this).attr("r",U+2)}).on("mouseleave",function(){V.selectAll("*").remove(),n.select(this).attr("r",U)}),m){const nt=X.data.filter(t=>!t.isTip),at=K.append("g").attr("class","phylo_internal_dots").selectAll("circle").data(nt).join("circle").attr("cx",t=>H(t.x1)).attr("cy",t=>G(t.y1)).attr("r",M).attr("fill","white").attr("stroke","#555").attr("stroke-width",1);v&&at.append("title").text(t=>A(t,W(t.thisId)))}if(b){const rt=X.data.filter(t=>!t.isTip&&t.thisLabel);J.append("g").attr("class","phylo_node_labels").selectAll("text").data(rt).join("text").attr("x",t=>H(t.x1)-4).attr("y",t=>G(t.y1)-4).attr("text-anchor","end").attr("font-size",S).text(t=>t.thisLabel)}const tt=H(C);if(d&&_&&K.append("g").attr("class","phylo_align_guides").selectAll("line").data(B).join("line").attr("x1",t=>H(t.x1)).attr("x2",tt).attr("y1",t=>G(t.y1)).attr("y2",t=>G(t.y1)).attr("stroke","#999").attr("stroke-width",1).attr("stroke-dasharray","2,2"),d){const st=J.append("g").attr("class","phylo_labels").selectAll("text").data(B).join("text").attr("x",t=>(_?tt:H(t.x1))+4).attr("y",t=>G(t.y1)).attr("dy","0.32em").attr("font-size",f).text(t=>t.thisLabel?.replace(/_/g," ")??"");v&&st.append("title").text(t=>A(t,W(t.thisId))),st.on("mouseenter",function(t,e){V.selectAll("*").remove(),et(e.thisId,V,L,T),n.select(this).attr("font-weight",600)}).on("mouseleave",function(){V.selectAll("*").remove(),n.select(this).attr("font-weight",null)})}if($&&$.length){new Set([...$.filter(P).map(t=>N.get(t)),...$.filter(t=>!P(t)).map(t=>O.get(t))].filter(Boolean)).forEach(t=>{et(t.thisId,Q,j,z)})}function et(t,e,n,a){let r=D.get(t);for(;r&&null!=r.parentId;){const t=D.get(r.parentId);if(!t)break;e.append("line").attr("x1",H(r.x0)).attr("x2",H(r.x0)).attr("y1",G(t.y0)).attr("y2",G(r.y0)).attr("stroke",n).attr("stroke-width",a).attr("stroke-linecap","round"),e.append("line").attr("x1",H(r.x0)).attr("x2",H(r.x1)).attr("y1",G(r.y0)).attr("y2",G(r.y1)).attr("stroke",n).attr("stroke-width",a).attr("stroke-linecap","round"),r=t}}return k&&I(J,{scale:H,basis:C,defaultX:l.left,defaultY:i-l.bottom/2,scaleBar:k,fontSize:f}),J.node()}if("radial"===e){if(a!==i)throw new Error("width and height must be the same for radial layout");const it=p(x(t),{angleStrategy:"fan",arcsStyle:"fan"}),lt="outer"===h;if("phylo"!==h&&"outer"!==h)throw new Error("radialMode must be either 'phylo' or 'outer'");const ot=g??3,ct=0,ht=a,dt=i,pt=n.max(it.data,t=>t.r)??0,ft=pt>0?pt*(ht/2)/(ht/2-o):1,ut=ht/2,gt=dt/2,yt=n.scaleLinear().domain([-ft,ft]).range([0,ht]),xt=n.scaleLinear().domain([-ft,ft]).range([dt,0]),It=t=>t*(ht/(2*ft)),mt=new Map(it.data.map(t=>[t.thisId,t])),Mt=it.data.filter(t=>t.isTip),bt=Mt.length?n.max(Mt,t=>t.r):0,wt=E(mt,{prefer:"r"}),kt=new Map(Mt.map(t=>[t.thisId,t])),_t=new Map(Mt.map(t=>[t.thisLabel,t]));function vt(t,e,n,a){const r=yt(t),s=xt(e),i=yt(n)-r,l=xt(a)-s,o=Math.hypot(i,l)||1,c=Math.max(0,(o-ct)/o);return{X0:r,Y0:s,X1s:r+i*c,Y1s:s+l*c,len:o}}const At=n.create("svg").attr("width",ht).attr("height",dt).attr("font-family","sans-serif").attr("font-size",10),Lt=At.append("g"),Tt=At.append("g").attr("class","phylo_static_lines"),$t=At.append("g").attr("class","phylo_static_arcs"),jt=At.append("g").attr("class","phylo_hover_lines"),zt=At.append("g").attr("class","phylo_hover_arcs");Lt.append("g").attr("class","phylo_arcs").selectAll("path").data(it.arcs).join("path").attr("d",t=>null==t.sweep?r(ut,gt,It(t.radius),t.start,t.end):s(ut,gt,It(t.radius),t.start,t.end,t.sweep??"ccw",t.largeArc??0)).attr("fill","none").attr("stroke","#777").attr("stroke-width",c),Lt.append("g").attr("class","phylo_radii").selectAll("line").data(it.radii).join("line").each(function(t,e){const a=t.x0,r=t.y0,s=(i=t).childId??i.thisId??i.id1??null;var i;const l=null!=s?mt.get(s):void 0,o=!(!l||!l.isTip);let h=t.x1,d=t.y1;lt&&o&&(h=bt*Math.cos(l.angle),d=bt*Math.sin(l.angle));const{X0:p,Y0:f,X1s:u,Y1s:g}=vt(a,r,h,d);n.select(this).attr("x1",p).attr("y1",f).attr("x2",u).attr("y2",g).attr("stroke","#777").attr("stroke-width",c)}),d&&_&&!lt&&Lt.append("g").attr("class","phylo_align_guides").selectAll("line").data(Mt).join("line").attr("x1",t=>yt(t.x)).attr("y1",t=>xt(t.y)).attr("x2",t=>yt(bt*Math.cos(t.angle))).attr("y2",t=>xt(bt*Math.sin(t.angle))).attr("stroke","#999").attr("stroke-width",1).attr("stroke-dasharray","2,2");const Pt=Lt.append("g").attr("class","phylo_tip_dots").selectAll("circle").data(Mt).join("circle").each(function(t,e){const a=lt?bt*Math.cos(t.angle):t.x,r=lt?bt*Math.sin(t.angle):t.y;n.select(this).attr("cx",yt(a)).attr("cy",xt(r)).attr("r",ot).attr("fill","black").attr("stroke","black").attr("stroke-width",1.5)});if(v&&Pt.append("title").text(t=>A(t,wt(t.thisId))),m){const Ft=it.data.filter(t=>!t.isTip),Bt=Lt.append("g").attr("class","phylo_internal_dots").selectAll("circle").data(Ft).join("circle").attr("cx",t=>yt(t.x)).attr("cy",t=>xt(t.y)).attr("r",M).attr("fill","white").attr("stroke","#555").attr("stroke-width",1);v&&Bt.append("title").text(t=>A(t,wt(t.thisId)))}if(b){const Dt=it.data.filter(t=>!t.isTip&&t.thisLabel);Lt.append("g").attr("class","phylo_node_labels").selectAll("text").data(Dt).join("text").attr("x",t=>yt(t.x)+4).attr("y",t=>xt(t.y)-4).attr("font-size",S).attr("fill","black").text(t=>t.thisLabel)}const St=t=>"string"==typeof t?+t:t,Et=new Map(it.radii.map(t=>[St(t.childId??t.thisId??t.id1),t])),Xt=new Map(it.child_arcs.map(t=>[St(t.childId),t]));if(d){const Nt=Lt.append("g").attr("class","phylo_labels").selectAll("g.label").data(Mt).join("g").attr("class","label").attr("transform",t=>{const e=lt||_?bt:t.r,n=e*Math.cos(t.angle),a=e*Math.sin(t.angle);return`translate(${yt(n)},${xt(a)})`}).each(function(t){let e=180*-t.angle/Math.PI,a=10,r="start";t.angle>Math.PI/2&&t.angle<3*Math.PI/2&&(e+=180,a*=-1,r="end"),n.select(this).append("g").attr("transform",`rotate(${e})`).append("text").attr("x",a).attr("alignment-baseline","middle").attr("text-anchor",r).attr("font-size",f).attr("fill","black").text(t=>t.thisLabel?.replace(/_/g," ")??"")});v&&Nt.append("title").text(t=>A(t,wt(t.thisId))),Nt.on("mouseenter",function(t,e){jt.selectAll("*").remove(),zt.selectAll("*").remove(),Yt(e,jt,zt,L,T),n.select(this).select("text").attr("font-weight",600)}).on("mouseleave",function(){jt.selectAll("*").remove(),zt.selectAll("*").remove(),n.select(this).select("text").attr("font-weight",null)})}function Yt(t,e,n,a="#1f77b4",i=3){let l="number"==typeof t||"string"==typeof t?mt.get(t):t;if(!l)return;let o=!0;for(;l&&null!=l.parentId;){const c=Et.get(St(l.thisId));if(c){const p=c.x0,f=c.y0;let u=c.x1,g=c.y1;if(lt&&o&&l.isTip){const M=bt;u=M*Math.cos(l.angle),g=M*Math.sin(l.angle)}const{X0:y,Y0:x,X1s:I,Y1s:m}=vt(p,f,u,g);e.append("line").attr("x1",y).attr("y1",x).attr("x2",I).attr("y2",m).attr("stroke",a).attr("stroke-width",i).attr("stroke-linecap","round")}const h=Xt.get(St(l.thisId));function d(t){const e=It(t.radius);return null==t.sweep?r(ut,gt,e,t.start,t.end):s(ut,gt,e,t.start,t.end,t.sweep??"ccw",t.largeArc??0)}h&&n.append("path").attr("d",d(h)).attr("fill","none").attr("stroke",a).attr("stroke-width",i),o=!1,l=mt.get(l.parentId)}}if(Pt.on("mouseenter",function(t,e){jt.selectAll("*").remove(),zt.selectAll("*").remove(),Yt(e,jt,zt,L,T),n.select(this).attr("r",ot+2)}).on("mouseleave",function(){jt.selectAll("*").remove(),zt.selectAll("*").remove(),n.select(this).attr("r",ot)}),$&&$.length){new Set([...$.filter(P).map(t=>kt.get(t)),...$.filter(t=>!P(t)).map(t=>_t.get(t))].filter(Boolean)).forEach(t=>{Yt(t.thisId,Tt,$t,j,z)})}return k&&I(At,{scale:yt,basis:pt,defaultX:20,defaultY:dt-20,scaleBar:k,fontSize:f}),At.node()}if("unrooted"===e){const Ot=y(x(t)),Wt=a,Ut=i,Rt=n.extent(Ot.data,t=>t.x),qt=n.extent(Ot.data,t=>t.y),Ct=Math.max(Math.abs(Rt[0]),Math.abs(Rt[1])),Gt=Math.max(Math.abs(qt[0]),Math.abs(qt[1])),Ht=Math.max(Ct,Gt),Jt=Ht+2*o,Kt=n.scaleLinear().domain([-Jt,Jt]).range([0,Wt]),Qt=n.scaleLinear().domain([-Jt,Jt]).range([Ut,0]),Vt=n.create("svg").attr("width",Wt).attr("height",Ut).attr("font-family","sans-serif").attr("font-size",10),Zt=Vt.append("g"),te=Vt.append("g").attr("class","phylo_static_highlight"),ee=Vt.append("g").attr("class","phylo_hover_highlight");Zt.append("g").attr("class","phylo_lines").selectAll("line").data(Ot.edges).join("line").attr("x1",t=>Kt(t.x1)).attr("y1",t=>Qt(t.y1)).attr("x2",t=>Kt(t.x2)).attr("y2",t=>Qt(t.y2)).attr("stroke-width",c).attr("stroke","#777");const ne=g??4,ae=Zt.append("g").attr("class","phylo_points").selectAll("circle").data(Ot.data).join("circle").attr("class","dot").attr("r",t=>t.isTip?ne:m?M:0).attr("cx",t=>Kt(t.x)).attr("cy",t=>Qt(t.y)).attr("stroke","black").attr("stroke-width",2).attr("fill",t=>t.isTip?"black":"white");if(b){const de=Ot.data.filter(t=>!t.isTip&&t.thisLabel);Zt.append("g").attr("class","phylo_node_labels").selectAll("text").data(de).join("text").attr("x",t=>Kt(t.x)+4).attr("y",t=>Qt(t.y)-4).attr("font-size",S).attr("fill","black").text(t=>t.thisLabel)}const re=new Map(Ot.data.map(t=>[t.thisId,t])),se=new Map(Ot.data.filter(t=>t.isTip).map(t=>[t.thisId,t])),ie=new Map(Ot.data.filter(t=>t.isTip).map(t=>[t.thisLabel,t])),le=E(re);v&&ae.filter(t=>t.isTip).append("title").text(t=>A(t,le(t.thisId)));const oe=new Map,ce=new Map(Ot.data.map(t=>[t.thisId,t]));if(Ot.edges.forEach(t=>{const e=ce.get(t.id1);e?.isTip&&oe.set(t.id1,t)}),d){const pe=Zt.append("g").attr("class","phylo_labels").selectAll("g").data(Ot.data.filter(t=>t.isTip)).join("g").attr("transform",t=>`translate(${Kt(t.x)},${Qt(t.y)})`).each(function(t){const e=oe.get(t.thisId);if(!e)return;const a=Kt(e.x1),r=Qt(e.y1),s=Kt(e.x2)-a,i=Qt(e.y2)-r;let l=180*Math.atan2(i,s)/Math.PI,o=-10,c="end";(l>90||l<-90)&&(l+=180,c="start",o=10),n.select(this).append("g").attr("transform",`rotate(${l})`).append("text").attr("x",o).attr("alignment-baseline","middle").attr("text-anchor",c).attr("font-size",f).attr("fill","black").text(t.thisLabel?.replace(/_/g," ")??"")});v&&pe.append("title").text(t=>A(t,le(t.thisId))),pe.on("mouseenter",function(t,e){he(e.thisId,ee,L,T),n.select(this).select("text").attr("font-weight",600)}).on("mouseleave",function(){ee.selectAll("*").remove(),n.select(this).select("text").attr("font-weight",null)})}if(ae.filter(t=>t.isTip).on("mouseenter",function(t,e){he(e.thisId,ee,L,T),n.select(this).attr("r",ne+2)}).on("mouseleave",function(){ee.selectAll("*").remove(),n.select(this).attr("r",ne)}),$&&$.length){new Set([...$.filter(P).map(t=>se.get(t)),...$.filter(t=>!P(t)).map(t=>ie.get(t))].filter(Boolean)).forEach(t=>{he(t.thisId,te,j,z)})}function he(t,e,n,a){const r=new Map(Ot.edges.map(t=>[t.id1,t]));e.selectAll("*").remove();let s=re.get(t);for(;s&&null!=s.parentId;){const t=r.get(s.thisId);t&&e.append("line").attr("x1",Kt(t.x1)).attr("y1",Qt(t.y1)).attr("x2",Kt(t.x2)).attr("y2",Qt(t.y2)).attr("stroke",n).attr("stroke-width",a).attr("stroke-linecap","round"),s=re.get(s.parentId)}}return k&&I(Vt,{scale:Kt,basis:Ht,defaultX:20,defaultY:Ut-20,scaleBar:k,fontSize:f}),Vt.node()}throw new Error("Unsupported layout type. Use 'rect', 'radial', or 'unrooted'.")}});
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