@sjcrh/proteinpaint-client 2.35.1 → 2.36.0

package/dist/{2dmaf-217ef1f7.js → 2dmaf-af1dea59.js}

@@ -1 +1 @@
-import{M as t,bg as e,bh as s,o as a,E as n,bd as i,p as r,l,f as o,a as c,ay as p,aP as h,q as d,w as f,$ as u}from"./app-5ca65214.js";import{d as m,c as y,b as g}from"./axis-6cb4f314.js";import{s as x,b,e as k,a as v,f as _,d as D,c as w,S as T}from"./symbol-fc7cbd41.js";import"path";import"./math-2fb199c6.js";import"./constant-426a1483.js";class N{constructor(t){this.opts=t;this.anchorType=t.anchorType;this.shareheight=t.shareheight;this.sharewidth=t.sharewidth;const e="x"in t?t.x:0;const s="y"in t?t.y:0;this.settings={visible:true,opacity:.3,x:e,y:s,xOffset:t.axiswidth+t.sp+t.sample2height,yOffset:t.shareheight,currX:t.axiswidth+t.sp+t.sample2height+e,currY:t.shareheight-s,strokeWidth:"strokeWidth"in t?t.strokeWidth:5,stroke:"stroke"in t?t.stroke:"red",xarmlen:"xarmlen"in t?t.xarmlen:25};this.addControls(this.anchorType?null:this.opts.headerdiv)}setWrapper(t){this.opts.wrapper=t}addControls(e=null){if(e){e.append("button").text("Anchors").on("click",(t=>{this.anchormenu.showunder(t.target);this.xInput.property("value",(this.settings.x/this.sharewidth).toFixed(2));this.yInput.property("value",(this.settings.y/this.sharewidth).toFixed(2))}))}this.anchormenu=new t({border:"solid 1px black"});this.anchormenu.d.style("text-align","center");this.addCoordInput();this.addColorInput();this.addOpacityInput();if(!this.anchorType)this.addSubmitBtns();else this.addDeleteBtn()}addColorInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Color:&nbsp;");this.strokeInput=t.append("input");this.strokeInput.attr("this.anchorType","text").property("value",this.settings.stroke).style("width","50px")}addOpacityInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Opacity:&nbsp;");this.opacityInput=t.append("input");this.opacityInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",this.settings.opacity).style("width","50px")}addSubmitBtns(){if(this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("label").html("Add Anchor: ");t.append("button").html("R").on("click",(()=>{new R(this.getSettings("r"));this.anchormenu.hide()}));t.append("button").html("D").on("click",(()=>{new R(this.getSettings("d"));this.anchormenu.hide()}));t.append("button").html("X").on("click",(()=>{new R(this.getSettings("x"));this.anchormenu.hide()}));t.append("button").html("synced").on("click",(()=>{new R(this.getSettings("synced"));this.anchormenu.hide()}))}getSettings(t){return Object.assign({},this.opts,{anchorType:t,opacity:this.opacityInput.property("value"),x:this.xInput.property("value")*this.sharewidth,y:this.yInput.property("value")*this.shareheight,stroke:this.strokeInput.property("value")})}addCoordInput(){const t=this.anchormenu.d.append("div");t.append("label").html("X:&nbsp;");this.xInput=t.append("input");this.xInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px");const e=this.anchormenu.d.append("div");e.append("label").html("Y:&nbsp;");this.yInput=e.append("input");this.yInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px")}addDeleteBtn(){if(!this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("button").html("Delete").on("click",(()=>{this.g_anchor.remove();this.anchormenu.hide()}))}}class R extends N{constructor(t){super(t);this.render();this.strokeInput.on("change",(()=>{this.settings.stroke=this.strokeInput.property("value");this.g_anchor.style("stroke",this.settings.stroke);this.anchormenu.hide()}));this.opacityInput.on("change",(()=>{this.settings.opacity=input.property("value");this.g_anchor.style("opacity",this.settings.opacity);this.anchormenu.hide()}));this.xInput.on("change",(()=>{this.settings.x=+this.xInput.property("value")*this.sharewidth;this.settings.currX=this.settings.x+this.settings.xOffset;if(this.d_anchor){this.d_anchor.transition().duration(1e3).attr("x1",this.settings.currX).attr("x2",this.settings.currX)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}));this.yInput.on("change",(()=>{this.settings.y=+this.yInput.property("value")*this.shareheight;this.settings.currY=-this.settings.y+this.settings.yOffset;if(this.r_anchor){this.r_anchor.transition().duration(1e3).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}))}render(){this.g_anchor=this.opts.wrapper.append("g").style("stroke",this.settings.stroke).style("opacity",this.settings.opacity).style("display",this.settings.visible?"":"none").style("stroke-width",this.settings.strokeWidth).on("click",this.anchorType=="synced"?null:t=>{this.anchormenu.showunder(t.target)});this.renderD();this.renderR();this.renderX()}renderD(){if(!["synced","d"].includes(this.anchorType))return;this.d_anchor=this.g_anchor.append("line");const t=this.opts;this.updateD(t.shareheight+t.sp2,t.shareheight+t.sample1height)}updateD(t,e){if(!["synced","d"].includes(this.anchorType))return;this.settings.D={y1:t,y2:e};this.d_anchor.attr("x1",this.settings.currX).attr("x2",this.settings.currX).attr("y1",t).attr("y2",e)}renderR(){if(!["synced","r"].includes(this.anchorType))return;this.r_anchor=this.g_anchor.append("line");const t=this.opts;this.updateR(t.axiswidth+t.sp,t.sample2height+t.sp)}updateR(t,e){if(!["synced","r"].includes(this.anchorType))return;this.settings.R={x1:t,x2:e};this.r_anchor.attr("x1",t).attr("x2",e).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}renderX(){if(!["synced","x"].includes(this.anchorType))return;this.x_anchor=this.g_anchor.append("g").attr("transform","translate("+this.settings.currX+","+this.settings.currY+")");this.bindXDrag();this.x_anchor.append("circle").attr("cx",0).attr("cy",0).attr("r",this.settings.xarmlen).style("opacity",0);this.x_anchor.append("line").attr("x1",-this.settings.xarmlen).attr("x2",this.settings.xarmlen).attr("y1",0).attr("y2",0);this.x_anchor.append("line").attr("x1",0).attr("x2",0).attr("y1",this.settings.xarmlen).attr("y2",-this.settings.xarmlen)}bindXDrag(){if(!["synced"].includes(this.anchorType))return;this.x_anchor.on("mousedown",(t=>{const e=t.clientX;const s=t.clientY;let a=this.settings.currX,n=this.settings.currY;this.x_anchor.on("mousemove",(t=>{a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;this.r_anchor.attr("y1",n).attr("y2",n);this.d_anchor.attr("x1",a).attr("x2",a);this.x_anchor.attr("transform","translate("+a+","+n+")")})).on("mouseup",(t=>{this.x_anchor.on("mousemove",null);a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;if(a==this.settings.currX&&n==this.settings.currY){this.g_anchor.remove();return}this.settings.x=a<this.settings.xOffset?0:a-this.settings.xOffset;this.settings.y=n>this.settings.yOffset?0:-(n-this.settings.yOffset);this.settings.currX=this.settings.x+this.settings.xOffset;this.settings.currY=-this.settings.y+this.settings.yOffset;this.r_anchor.transition().duration(100).attr("y1",this.settings.currY).attr("y2",this.settings.currY);this.d_anchor.transition().duration(100).attr("x1",this.settings.currX).attr("x2",this.settings.currX);this.x_anchor.transition().duration(100).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")})).on("mouseleave",(()=>{this.x_anchor.on("mousemove",null)}))}))}}const I="#f9766c";const M="#609cff";const X="#01b937";const B={circle:x,cross:b,diamond:k,square:v,star:_,triangle:D,wye:w};const F={path:t=>t.symbol,circle:t=>!t.symbol};const Y={path:t=>t.symbol,ellipse:t=>!t.symbol};function A(t,a){let n,i,r,l,o,c;if(a!==undefined)[i,r,l,o,c]=e(a,t);else{[n,i,r,l,o,c]=s(100,100,t);n.header.text("2DMAF: mutant allele fraction plot between a pair of samples");n.body.style("margin","10px")}i.append("div").style("margin-top","20px").html("<ul>"+'<li><a href="https://docs.google.com/document/d/1anyEDMcW1lTSf8399Li2G9r57V-Fqp2591WvoODY7n4/edit#heading=h.mne2ecmp9m13" target=_blank>File format</a></li>'+'<li>To define samples differently than "Diagnosis/Relapse", <a href=https://plus.google.com/+XinZhou_s/posts/WqBVvmd3wYR target=_blank>see how</a>.</li>'+"</ul>");i.append("p").html("<a href=https://proteinpaint.stjude.org/ppdemo/hg19/2dmaf/2dmaf.txt target=_blank>Example file</a>");function p(t,e){o.style("color",e?"red":"black").html(t)}const h=()=>{l.selectAll("*").remove();const e=l.append("input").attr("type","file").on("change",(e=>{const s=e.target.files[0];if(!s){h();return}if(!s.size){p("Invalid file "+s.name);h();return}const a=new FileReader;a.onload=e=>{const a=r.options[r.selectedIndex].innerHTML;const n=C(e.target.result.trim().split(/\r?\n/),t[a],s.name,c);if(n){p(n,1);h();return}i.remove();l.remove();o.remove()};a.onerror=function(){p("Error reading file "+s.name,1);h();return};a.readAsText(s,"utf8")}));setTimeout((()=>e.node().focus()),1100)};h()}function z(t,e){if(!t.genome){a(e,".genome missing for 2dmaf");return}if(!t.input){a(e,".input missing for 2dmaf");return}const s=C(t.input.trim().split(/\r?\n/),t.genome,t.datasetname||"unnamed dataset",e);if(s){a(e,"2DMAF data error: "+s)}}function C(t,e,s,a){const[r,l,o]=O(t[0].trim());if(r){return r}const c={};const p={};const h={};const d={good:0,purity1set:false,purity2set:false,pairsetname:{}};const f=[];const u={};for(const t in n){u[n[t].label.toUpperCase()]=t}for(let e=1;e<t.length;e++){if(t[e]=="")continue;if(t[e][0]=="#"){if(t[e].startsWith("##samplename")){const s=t[e].trim().split(/[\s\t]+/);if(s.length==4){d.pairsetname[s[1]]={1:s[2],2:s[3]}}else{return"Line "+(e+1)+': invalid samplename line: must be "##samplename [patient] [sample1] [sample2]"'}}continue}const s=t[e].trim().split("\t");const a={};for(let t=0;t<l.length;t++){if(s[t]!=undefined&&s[t]!=""){a[l[t]]=s[t]}}if(!a.sample){return"Line "+(e+1)+": missing sample"}if(a.chr){if(a.chr.indexOf("chr")!=0){a.chr="chr"+a.chr}}if(a.chrstart){a.chrstart=Number.parseInt(a.chrstart);if(Number.isNaN(a.chrstart)){return"Line "+(e+1)+": invalid chromosome position"}}if(a.Dcnvloh){a.Dcnvlohraw=a.Dcnvloh;const t=a.Dcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Dcnvloh=true}else{a.Dcnvloh=false}}if(a.Rcnvloh){a.Rcnvlohraw=a.Rcnvloh;const t=a.Rcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Rcnvloh=true}else{a.Rcnvloh=false}}if(!a.call_d){f.push([e,"missing call_d",s]);continue}if(a.call_d!="somatic"&&a.call_d!="wildtype"){f.push([e,"call_d is neither somatic nor wildtype",s]);continue}if(!a.call_r){f.push([e,"missing call_r",s]);continue}if(a.call_r!="somatic"&&a.call_r!="wildtype"){f.push([e,"call_r is neither somatic nor wildtype",s]);continue}if(a.call_d=="somatic"){if(a.call_r=="somatic"){a.set_share=true}else{a.set_1=true}}else{if(a.call_r=="somatic"){a.set_2=true}}if(!a.type){f.push([e,"missing type",s]);continue}const i=a.type.toLowerCase();if(i=="snv"||i=="snp"||i=="mnv"||i=="complex"){a.issnv=true}else if(i=="indel"||i=="ins"||i=="del"){a.isindel=true}else{f.push([e,"type must be either SNV or INDEL",s]);continue}let r="MinD.D";let o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.D";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.D"]<a["MinD.D"]){f.push([e,"TinD.D value lower than MinD.D",s]);continue}r="MinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="MinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.R"]<a["MinD.R"]){f.push([e,"TinD.R value lower than MinD.R",s]);continue}r="MinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}if(a.symbol){if(!B[a.symbol]){f.push([e,"Invalid symbol value='"+a.symbol+"'",s]);continue}}if(a.class){const t=a.class.toUpperCase();if(t in u){a.class=u[t]}else{f.push([e,"invalid mutation class "+a.class,s]);continue}}a.style={fill:a.issnv?"white":"black",fillhl:a.class?n[a.class].color:"#ccc",stroke:a.chr=="chrX"?"black":a.issnv?"black":"none",strokehl:a.class?n[a.class].color:"black",fillopacity:a.issnv?0:.2,strokeopacity:.2};if(a["TinD.D"]>0){a.maf1=a["MinD.D"]/a["TinD.D"]}if(a["TinD.R"]>0){a.maf2=a["MinD.R"]/a["TinD.R"]}p[a.sample]=1;if(a.gene){h[a.gene]=1}if(!(a.sample in c)){c[a.sample]={name:a.sample,shown:false,header:l,mlst:[]}}const m=c[a.sample];m.mlst.push(a);if(a.purity1){let t=Number.parseFloat(a.purity1);if(Number.isNaN(t)){f.push([e,"diagnosis tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity1==undefined){m.purity1=t;d.purity1set=true}else if(m.purity1!=t){f.push([e,"diagnosis tumor purity value "+t+" is different from existing value "+m.purity1+" in "+a.sample,s])}}}if(a.purity2){let t=Number.parseFloat(a.purity2);if(Number.isNaN(t)){f.push([e,"relapse tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity2==undefined){m.purity2=t;d.purity2set=true}else if(m.purity2!=t){f.push([e,"relapse tumor purity value "+t+" is different from existing value "+m.purity2+" in "+a.sample,s])}}}d.good++}if(f.length>0){i(l,f)}if(d.good==0){return"No valid data."}a.append("p").text("File: "+s);let m=0;for(const t in h)m++;const y=16;const g=a.append("table");const x=g.append("tr");const b=x.append("td").attr("valign","top");b.append("div").html('<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+I+'"></div> Diagnosis only '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+X+'"></div> Shared '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+M+'"></div> Relapse only');const k=b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");const v=x.append("td").style("vertical-align","top");for(const t in c){const e=d.pairsetname[t];if(e){c[t].setname=e}else{c[t].setname={1:"Diagnosis",2:"Relapse"}}}const _={genome:e,pairs:c,color1:I,color2:M,colorshare:X,rowh:y,peoplewidth:150,genewidth:150,showholder:v,genelimit:Math.min(20,m),purity1set:d.purity1set,purity2set:d.purity2set};E(_,k)}function O(t){const e=t.toLowerCase().split("\t");const s=t.split("\t");if(s.length<=1){return["invalid file header"]}const a=(...t)=>{for(const s of t){const t=e.indexOf(s);if(t!=-1)return t}return-1};let i=a("person","sample","samplename","patient");if(i==-1)return["sample missing from header"];s[i]="sample";i=a("type");if(i==-1)return["type missing from header"];s[i]="type";i=a("mind.d1_g1","mind.d","mind");if(i==-1)return["MinD.D missing from header"];s[i]="MinD.D";i=a("tind.d1_g1","tind.d","tind");if(i==-1)return["TinD.D missing from header"];s[i]="TinD.D";i=a("mind.r1_g1","mind.r","minr");if(i==-1)return["MinD.R missing from header"];s[i]="MinD.R";i=a("tind.r1_g1","tind.r","tinr");if(i==-1)return["TinD.R missing from header"];s[i]="TinD.R";i=a("call_d1_g1","call_d");if(i==-1)return["call_d missing from header"];s[i]="call_d";i=a("call_r1_g1","call_r");if(i==-1)return["call_r missing from header"];s[i]="call_r";i=a("genename","gene");if(i==-1)return["gene missing from header"];s[i]="gene";i=a("amino_acid_change","annovar_sj_aachange","aachange","protein_change");if(i==-1)return["amino_acid_change missing from header"];s[i]="mname";i=a("class","mclass","variant_class","variant_classification","annovar_sj_class");if(i==-1)return["variant_class missing from header"];s[i]="class";i=a("chromosome","chr");if(i==-1)return["chromosome missing from header"];s[i]="chr";i=a("start","start_position","wu_hg19_pos","chr_position");if(i==-1)return["start missing from header"];s[i]="chrstart";i=a("minn.d1_g1","minn.d");if(i!=-1)s[i]="MinN.D";i=a("tinn.d1_g1","tinn.d");if(i!=-1)s[i]="TinN.D";i=a("minn.r1_g1","minn.r");if(i!=-1)s[i]="MinN.R";i=a("tinn.r1_g1","tinn.r");if(i!=-1)s[i]="TinN.R";i=a("mrna_accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq");if(i!=-1)s[i]="isoform";i=a("primary_purity","purity_d");if(i!=-1)s[i]="purity1";i=a("relapse_purity","purity_r");if(i!=-1)s[i]="purity2";i=a("tag_d_cnvloh","cnvloh_d");if(i!=-1)s[i]="Dcnvloh";i=a("tag_r_cnvloh","cnvloh_r");if(i!=-1)s[i]="Rcnvloh";const r=[];for(const t of s){switch(t){case"Dcnvloh":r.push({label:"D. CNV/LOH",get:t=>t.Dcnvlohraw});break;case"Rcnvloh":r.push({label:"R. CNV/LOH",get:t=>t.Rcnvlohraw});break;case"type":r.push({label:"Type",get:t=>t.type});break;case"chr":break;case"chrstart":r.push({label:"Genome Loc.",get:t=>t.chr+":"+(t.chrstart+1)});break;case"class":r.push({label:"Class",get:t=>{if(t.class==p){return t.originalclasslabel?t.originalclasslabel:n[t.class].label}return n[t.class].label}});break;case"mname":r.push({label:"Mutation",get:t=>{let e=t.mname;if(!e)e=t.cdna_change;return e}});break;case"MinD.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis,label:"D. tumor MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinD.D":break;case"MinD.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse,label:"R. tumor MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinD.R":break;case"MinN.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis_normal,label:"D. normal MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinN.D":break;case"MinN.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse_normal,label:"R. normal MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinN.R":break;case"call_d":r.push({label:"D. call",get:t=>t.call_d});break;case"call_r":r.push({label:"R. call",get:t=>t.call_r});break;case"purity1":r.push({label:"D. purity",get:t=>t.purity1});break;case"purity2":r.push({label:"R. purity",get:t=>t.purity2});break;default:r.push({label:t,get:e=>e[t]})}}return[null,s,r]}function S(e,s){const a=new t({border:"solid 1px black"});const i=[];const o=[];const p=[];const f=s.mlst;const u=f[0].sample;const m=T();let x=0;let b={};const k={};for(const t of f){if(t["TinD.D"]>0){x=Math.max(x,t["TinD.D"])}if(t["TinD.R"]>0){x=Math.max(x,t["TinD.R"])}if(t.set_share){p.push(t)}else if(t.set_1){i.push(t)}else if(t.set_2){o.push(t)}if(!(t.class in 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F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.D"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ft=$.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const 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e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,dt)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(i.length){for(const t of i){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,at)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}}function Nt(t,e,s){if(e.selected){t.style.border="";e.selected=false}else{t.style.border="solid 1px black";e.selected=true}const a=s.filter((t=>t.gene==e.gene&&t.class==e.class&&t.mname==e.mname));a.selectAll("rect").attr("fill-opacity",e.selected?.5:e.style.fillopacity).attr("fill",e.selected?e.style.fillhl:e.style.fill);a.selectAll("circle,ellipse,line").attr("stroke-opacity",e.selected?1:e.style.strokeopacity).attr("stroke",e.selected?e.style.strokehl:e.style.stroke).attr("stroke-width",e.selected?2:1);if(e.selected){let t=Math.max(20,e.radius),s=0;if((e.set_1||e.set_share)&&e.maf1>=.8){t=-e.radius;s=e.radius*2}const n=a.append("g").attr("class","sja_2dmaf_mlabel").attr("transform","translate("+t+","+s+")");let i;n.append("text").text(e.labelAs?e.labelAs:e.gene+" "+e.mname).attr("fill",e.style.fillhl).attr("dominant-baseline","middle").attr("text-anchor","start").attr("font-size",e.radius).each((function(){i=this.getBBox().width}));n.append("rect").attr("y",-e.radius/2).attr("width",i).attr("height",e.radius).attr("fill","black").attr("fill-opacity",0).on("mouseover",(t=>d(t.target).attr("fill-opacity",.2))).on("mouseout",(t=>d(t.target).attr("fill-opacity",0))).on("mousedown",(e=>{const a=t,i=s,r=e.clientX,l=e.clientY,o=d(document.body);o.on("mousemove",(e=>{e.preventDefault();t=a+e.clientX-r;s=i+e.clientY-l;n.attr("transform","translate("+t+","+s+")")}));o.on("mouseup",(()=>{o.on("mousemove",null).on("mouseup",null)}))}))}else{a.select(".sja_2dmaf_mlabel").remove()}}return E}function j(t,e,s){if(!e.selected){d(t.target).attr("fill",e.style.fillhl).attr("fill-opacity",.2)}s.clear();s.show(t.clientX,t.clientY);s.d.append("div").html((e.gene||"no gene")+' <span style="color:'+e.style.fillhl+'">'+(e.mname||"")+"</span>"+(e.class?' <span style="font-size:70%">'+n[e.class].label+"</span>":""))}function L(t,e,s){if(!e.selected){d(t.ele).attr("fill",e.style.fill).attr("fill-opacity",e.style.fillopacity).attr("stroke",e.style.stroke)}s.hide()}function V(t,e,s){const a=f({x:t.clientX+30,y:t.clientY-30});a.header.text((s.gene?s.gene:"No gene")+" "+(s.mname?s.mname:""));var n=[];for(let t=0;t<e.length;t++){n.push({k:e[t],v:s[e[t]]})}u(a.body,n)}function W(t,e){const s=t.pairs[e];if(s.shown){s.shown=false;s.holder.remove();if(s.handle){s.handle.attr("font-weight","normal")}}else{s.shown=true;if(s.holder){t.showholder.node().appendChild(s.holder.node())}else{s.holder=S(t.showholder,s)}if(s.handle){s.handle.attr("font-weight","bold")}}}function E(t,e){const s=[];for(const e in t.pairs){s.push([e,t.pairs[e].mlst.length])}e.selectAll("*").remove();const a=e.append("div").style("margin-bottom","5px");a.append("span").text(s.length+" individual"+(s.length>1?"s":""));const n=e.append("svg");const i=5,p=20,h=t.rowh;let d=0;for(const t of s){n.append("text").text(t[0]).attr("font-size",h).attr("font-family",r).each((function(){d=Math.max(d,this.getBBox().width)})).remove()}n.attr("width",d+i+t.peoplewidth+30).attr("height",p+i+h*s.length);s.sort(((t,e)=>e[1]-t[1]));let f=0;for(const e in t.pairs){f=Math.max(f,t.pairs[e].mlst.length)}const u=n.append("g").attr("transform","translate("+(d+i)+","+p+")").call(m().scale(l().domain([0,f]).range([0,t.peoplewidth])).tickFormat(o("d")).ticks(3));c({axis:u,showline:true,color:"black"});const y=t.peoplewidth/f;let g=p+i;for(const e of s){const s=e[0];t.pairs[s].handle=n.append("text").text(s).attr("class","sja_svgtext2").attr("font-size",h-2).attr("font-family",r).attr("x",d).attr("y",g+i+h/2).attr("text-anchor","end").on("click",(()=>{W(t,s)}));let a=0,l=0,o=0;for(const e of t.pairs[s].mlst){if(e.set_1)a++;else if(e.set_2)l++;else if(e.set_share)o++}const c=n.append("g").attr("transform","translate("+(d+i)+","+g+")");if(a>0){c.append("rect").attr("width",y*a).attr("height",h-1).attr("fill",t.color1)}if(o>0){c.append("rect").attr("x",y*a).attr("width",y*o).attr("height",h-1).attr("fill",t.colorshare)}if(l>0){c.append("rect").attr("x",y*(a+o)).attr("width",y*l).attr("height",h-1).attr("fill",t.color2)}g+=h}}export{z as d2mafparseinput,A as d2mafui};
+import{M as t,bg as e,bh as s,o as a,E as n,bd as i,p as r,l,f as o,a as c,ay as p,aP as h,q as d,w as f,$ as u}from"./app-172cc04d.js";import{d as m,c as y,b as g}from"./axis-6cb4f314.js";import{s as x,b,e as k,a as v,f as _,d as D,c as w,S as T}from"./symbol-fc7cbd41.js";import"path";import"./math-2fb199c6.js";import"./constant-426a1483.js";class N{constructor(t){this.opts=t;this.anchorType=t.anchorType;this.shareheight=t.shareheight;this.sharewidth=t.sharewidth;const e="x"in t?t.x:0;const s="y"in t?t.y:0;this.settings={visible:true,opacity:.3,x:e,y:s,xOffset:t.axiswidth+t.sp+t.sample2height,yOffset:t.shareheight,currX:t.axiswidth+t.sp+t.sample2height+e,currY:t.shareheight-s,strokeWidth:"strokeWidth"in t?t.strokeWidth:5,stroke:"stroke"in t?t.stroke:"red",xarmlen:"xarmlen"in t?t.xarmlen:25};this.addControls(this.anchorType?null:this.opts.headerdiv)}setWrapper(t){this.opts.wrapper=t}addControls(e=null){if(e){e.append("button").text("Anchors").on("click",(t=>{this.anchormenu.showunder(t.target);this.xInput.property("value",(this.settings.x/this.sharewidth).toFixed(2));this.yInput.property("value",(this.settings.y/this.sharewidth).toFixed(2))}))}this.anchormenu=new t({border:"solid 1px black"});this.anchormenu.d.style("text-align","center");this.addCoordInput();this.addColorInput();this.addOpacityInput();if(!this.anchorType)this.addSubmitBtns();else this.addDeleteBtn()}addColorInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Color:&nbsp;");this.strokeInput=t.append("input");this.strokeInput.attr("this.anchorType","text").property("value",this.settings.stroke).style("width","50px")}addOpacityInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Opacity:&nbsp;");this.opacityInput=t.append("input");this.opacityInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",this.settings.opacity).style("width","50px")}addSubmitBtns(){if(this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("label").html("Add Anchor: ");t.append("button").html("R").on("click",(()=>{new R(this.getSettings("r"));this.anchormenu.hide()}));t.append("button").html("D").on("click",(()=>{new R(this.getSettings("d"));this.anchormenu.hide()}));t.append("button").html("X").on("click",(()=>{new R(this.getSettings("x"));this.anchormenu.hide()}));t.append("button").html("synced").on("click",(()=>{new R(this.getSettings("synced"));this.anchormenu.hide()}))}getSettings(t){return Object.assign({},this.opts,{anchorType:t,opacity:this.opacityInput.property("value"),x:this.xInput.property("value")*this.sharewidth,y:this.yInput.property("value")*this.shareheight,stroke:this.strokeInput.property("value")})}addCoordInput(){const t=this.anchormenu.d.append("div");t.append("label").html("X:&nbsp;");this.xInput=t.append("input");this.xInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px");const e=this.anchormenu.d.append("div");e.append("label").html("Y:&nbsp;");this.yInput=e.append("input");this.yInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px")}addDeleteBtn(){if(!this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("button").html("Delete").on("click",(()=>{this.g_anchor.remove();this.anchormenu.hide()}))}}class R extends N{constructor(t){super(t);this.render();this.strokeInput.on("change",(()=>{this.settings.stroke=this.strokeInput.property("value");this.g_anchor.style("stroke",this.settings.stroke);this.anchormenu.hide()}));this.opacityInput.on("change",(()=>{this.settings.opacity=input.property("value");this.g_anchor.style("opacity",this.settings.opacity);this.anchormenu.hide()}));this.xInput.on("change",(()=>{this.settings.x=+this.xInput.property("value")*this.sharewidth;this.settings.currX=this.settings.x+this.settings.xOffset;if(this.d_anchor){this.d_anchor.transition().duration(1e3).attr("x1",this.settings.currX).attr("x2",this.settings.currX)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}));this.yInput.on("change",(()=>{this.settings.y=+this.yInput.property("value")*this.shareheight;this.settings.currY=-this.settings.y+this.settings.yOffset;if(this.r_anchor){this.r_anchor.transition().duration(1e3).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}))}render(){this.g_anchor=this.opts.wrapper.append("g").style("stroke",this.settings.stroke).style("opacity",this.settings.opacity).style("display",this.settings.visible?"":"none").style("stroke-width",this.settings.strokeWidth).on("click",this.anchorType=="synced"?null:t=>{this.anchormenu.showunder(t.target)});this.renderD();this.renderR();this.renderX()}renderD(){if(!["synced","d"].includes(this.anchorType))return;this.d_anchor=this.g_anchor.append("line");const t=this.opts;this.updateD(t.shareheight+t.sp2,t.shareheight+t.sample1height)}updateD(t,e){if(!["synced","d"].includes(this.anchorType))return;this.settings.D={y1:t,y2:e};this.d_anchor.attr("x1",this.settings.currX).attr("x2",this.settings.currX).attr("y1",t).attr("y2",e)}renderR(){if(!["synced","r"].includes(this.anchorType))return;this.r_anchor=this.g_anchor.append("line");const t=this.opts;this.updateR(t.axiswidth+t.sp,t.sample2height+t.sp)}updateR(t,e){if(!["synced","r"].includes(this.anchorType))return;this.settings.R={x1:t,x2:e};this.r_anchor.attr("x1",t).attr("x2",e).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}renderX(){if(!["synced","x"].includes(this.anchorType))return;this.x_anchor=this.g_anchor.append("g").attr("transform","translate("+this.settings.currX+","+this.settings.currY+")");this.bindXDrag();this.x_anchor.append("circle").attr("cx",0).attr("cy",0).attr("r",this.settings.xarmlen).style("opacity",0);this.x_anchor.append("line").attr("x1",-this.settings.xarmlen).attr("x2",this.settings.xarmlen).attr("y1",0).attr("y2",0);this.x_anchor.append("line").attr("x1",0).attr("x2",0).attr("y1",this.settings.xarmlen).attr("y2",-this.settings.xarmlen)}bindXDrag(){if(!["synced"].includes(this.anchorType))return;this.x_anchor.on("mousedown",(t=>{const e=t.clientX;const s=t.clientY;let a=this.settings.currX,n=this.settings.currY;this.x_anchor.on("mousemove",(t=>{a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;this.r_anchor.attr("y1",n).attr("y2",n);this.d_anchor.attr("x1",a).attr("x2",a);this.x_anchor.attr("transform","translate("+a+","+n+")")})).on("mouseup",(t=>{this.x_anchor.on("mousemove",null);a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;if(a==this.settings.currX&&n==this.settings.currY){this.g_anchor.remove();return}this.settings.x=a<this.settings.xOffset?0:a-this.settings.xOffset;this.settings.y=n>this.settings.yOffset?0:-(n-this.settings.yOffset);this.settings.currX=this.settings.x+this.settings.xOffset;this.settings.currY=-this.settings.y+this.settings.yOffset;this.r_anchor.transition().duration(100).attr("y1",this.settings.currY).attr("y2",this.settings.currY);this.d_anchor.transition().duration(100).attr("x1",this.settings.currX).attr("x2",this.settings.currX);this.x_anchor.transition().duration(100).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")})).on("mouseleave",(()=>{this.x_anchor.on("mousemove",null)}))}))}}const I="#f9766c";const M="#609cff";const X="#01b937";const B={circle:x,cross:b,diamond:k,square:v,star:_,triangle:D,wye:w};const F={path:t=>t.symbol,circle:t=>!t.symbol};const Y={path:t=>t.symbol,ellipse:t=>!t.symbol};function A(t,a){let n,i,r,l,o,c;if(a!==undefined)[i,r,l,o,c]=e(a,t);else{[n,i,r,l,o,c]=s(100,100,t);n.header.text("2DMAF: mutant allele fraction plot between a pair of samples");n.body.style("margin","10px")}i.append("div").style("margin-top","20px").html("<ul>"+'<li><a href="https://docs.google.com/document/d/1anyEDMcW1lTSf8399Li2G9r57V-Fqp2591WvoODY7n4/edit#heading=h.mne2ecmp9m13" target=_blank>File format</a></li>'+'<li>To define samples differently than "Diagnosis/Relapse", <a href=https://plus.google.com/+XinZhou_s/posts/WqBVvmd3wYR target=_blank>see how</a>.</li>'+"</ul>");i.append("p").html("<a href=https://proteinpaint.stjude.org/ppdemo/hg19/2dmaf/2dmaf.txt target=_blank>Example file</a>");function p(t,e){o.style("color",e?"red":"black").html(t)}const h=()=>{l.selectAll("*").remove();const e=l.append("input").attr("type","file").on("change",(e=>{const s=e.target.files[0];if(!s){h();return}if(!s.size){p("Invalid file "+s.name);h();return}const a=new FileReader;a.onload=e=>{const a=r.options[r.selectedIndex].innerHTML;const n=C(e.target.result.trim().split(/\r?\n/),t[a],s.name,c);if(n){p(n,1);h();return}i.remove();l.remove();o.remove()};a.onerror=function(){p("Error reading file "+s.name,1);h();return};a.readAsText(s,"utf8")}));setTimeout((()=>e.node().focus()),1100)};h()}function z(t,e){if(!t.genome){a(e,".genome missing for 2dmaf");return}if(!t.input){a(e,".input missing for 2dmaf");return}const s=C(t.input.trim().split(/\r?\n/),t.genome,t.datasetname||"unnamed dataset",e);if(s){a(e,"2DMAF data error: "+s)}}function C(t,e,s,a){const[r,l,o]=O(t[0].trim());if(r){return r}const c={};const p={};const h={};const d={good:0,purity1set:false,purity2set:false,pairsetname:{}};const f=[];const u={};for(const t in n){u[n[t].label.toUpperCase()]=t}for(let e=1;e<t.length;e++){if(t[e]=="")continue;if(t[e][0]=="#"){if(t[e].startsWith("##samplename")){const s=t[e].trim().split(/[\s\t]+/);if(s.length==4){d.pairsetname[s[1]]={1:s[2],2:s[3]}}else{return"Line "+(e+1)+': invalid samplename line: must be "##samplename [patient] [sample1] [sample2]"'}}continue}const s=t[e].trim().split("\t");const a={};for(let t=0;t<l.length;t++){if(s[t]!=undefined&&s[t]!=""){a[l[t]]=s[t]}}if(!a.sample){return"Line "+(e+1)+": missing sample"}if(a.chr){if(a.chr.indexOf("chr")!=0){a.chr="chr"+a.chr}}if(a.chrstart){a.chrstart=Number.parseInt(a.chrstart);if(Number.isNaN(a.chrstart)){return"Line "+(e+1)+": invalid chromosome position"}}if(a.Dcnvloh){a.Dcnvlohraw=a.Dcnvloh;const t=a.Dcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Dcnvloh=true}else{a.Dcnvloh=false}}if(a.Rcnvloh){a.Rcnvlohraw=a.Rcnvloh;const t=a.Rcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Rcnvloh=true}else{a.Rcnvloh=false}}if(!a.call_d){f.push([e,"missing call_d",s]);continue}if(a.call_d!="somatic"&&a.call_d!="wildtype"){f.push([e,"call_d is neither somatic nor wildtype",s]);continue}if(!a.call_r){f.push([e,"missing call_r",s]);continue}if(a.call_r!="somatic"&&a.call_r!="wildtype"){f.push([e,"call_r is neither somatic nor wildtype",s]);continue}if(a.call_d=="somatic"){if(a.call_r=="somatic"){a.set_share=true}else{a.set_1=true}}else{if(a.call_r=="somatic"){a.set_2=true}}if(!a.type){f.push([e,"missing type",s]);continue}const i=a.type.toLowerCase();if(i=="snv"||i=="snp"||i=="mnv"||i=="complex"){a.issnv=true}else if(i=="indel"||i=="ins"||i=="del"){a.isindel=true}else{f.push([e,"type must be either SNV or INDEL",s]);continue}let r="MinD.D";let o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.D";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.D"]<a["MinD.D"]){f.push([e,"TinD.D value lower than MinD.D",s]);continue}r="MinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="MinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.R"]<a["MinD.R"]){f.push([e,"TinD.R value lower than MinD.R",s]);continue}r="MinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}if(a.symbol){if(!B[a.symbol]){f.push([e,"Invalid symbol value='"+a.symbol+"'",s]);continue}}if(a.class){const t=a.class.toUpperCase();if(t in u){a.class=u[t]}else{f.push([e,"invalid mutation class "+a.class,s]);continue}}a.style={fill:a.issnv?"white":"black",fillhl:a.class?n[a.class].color:"#ccc",stroke:a.chr=="chrX"?"black":a.issnv?"black":"none",strokehl:a.class?n[a.class].color:"black",fillopacity:a.issnv?0:.2,strokeopacity:.2};if(a["TinD.D"]>0){a.maf1=a["MinD.D"]/a["TinD.D"]}if(a["TinD.R"]>0){a.maf2=a["MinD.R"]/a["TinD.R"]}p[a.sample]=1;if(a.gene){h[a.gene]=1}if(!(a.sample in c)){c[a.sample]={name:a.sample,shown:false,header:l,mlst:[]}}const m=c[a.sample];m.mlst.push(a);if(a.purity1){let t=Number.parseFloat(a.purity1);if(Number.isNaN(t)){f.push([e,"diagnosis tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity1==undefined){m.purity1=t;d.purity1set=true}else if(m.purity1!=t){f.push([e,"diagnosis tumor purity value "+t+" is different from existing value "+m.purity1+" in "+a.sample,s])}}}if(a.purity2){let t=Number.parseFloat(a.purity2);if(Number.isNaN(t)){f.push([e,"relapse tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity2==undefined){m.purity2=t;d.purity2set=true}else if(m.purity2!=t){f.push([e,"relapse tumor purity value "+t+" is different from existing value "+m.purity2+" in "+a.sample,s])}}}d.good++}if(f.length>0){i(l,f)}if(d.good==0){return"No valid data."}a.append("p").text("File: "+s);let m=0;for(const t in h)m++;const y=16;const g=a.append("table");const x=g.append("tr");const b=x.append("td").attr("valign","top");b.append("div").html('<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+I+'"></div> Diagnosis only '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+X+'"></div> Shared '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+M+'"></div> Relapse only');const k=b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");const v=x.append("td").style("vertical-align","top");for(const t in c){const e=d.pairsetname[t];if(e){c[t].setname=e}else{c[t].setname={1:"Diagnosis",2:"Relapse"}}}const _={genome:e,pairs:c,color1:I,color2:M,colorshare:X,rowh:y,peoplewidth:150,genewidth:150,showholder:v,genelimit:Math.min(20,m),purity1set:d.purity1set,purity2set:d.purity2set};E(_,k)}function O(t){const e=t.toLowerCase().split("\t");const s=t.split("\t");if(s.length<=1){return["invalid file header"]}const a=(...t)=>{for(const s of t){const t=e.indexOf(s);if(t!=-1)return t}return-1};let i=a("person","sample","samplename","patient");if(i==-1)return["sample missing from header"];s[i]="sample";i=a("type");if(i==-1)return["type missing from header"];s[i]="type";i=a("mind.d1_g1","mind.d","mind");if(i==-1)return["MinD.D missing from header"];s[i]="MinD.D";i=a("tind.d1_g1","tind.d","tind");if(i==-1)return["TinD.D missing from header"];s[i]="TinD.D";i=a("mind.r1_g1","mind.r","minr");if(i==-1)return["MinD.R missing from header"];s[i]="MinD.R";i=a("tind.r1_g1","tind.r","tinr");if(i==-1)return["TinD.R missing from header"];s[i]="TinD.R";i=a("call_d1_g1","call_d");if(i==-1)return["call_d missing from header"];s[i]="call_d";i=a("call_r1_g1","call_r");if(i==-1)return["call_r missing from header"];s[i]="call_r";i=a("genename","gene");if(i==-1)return["gene missing from header"];s[i]="gene";i=a("amino_acid_change","annovar_sj_aachange","aachange","protein_change");if(i==-1)return["amino_acid_change missing from header"];s[i]="mname";i=a("class","mclass","variant_class","variant_classification","annovar_sj_class");if(i==-1)return["variant_class missing from header"];s[i]="class";i=a("chromosome","chr");if(i==-1)return["chromosome missing from header"];s[i]="chr";i=a("start","start_position","wu_hg19_pos","chr_position");if(i==-1)return["start missing from header"];s[i]="chrstart";i=a("minn.d1_g1","minn.d");if(i!=-1)s[i]="MinN.D";i=a("tinn.d1_g1","tinn.d");if(i!=-1)s[i]="TinN.D";i=a("minn.r1_g1","minn.r");if(i!=-1)s[i]="MinN.R";i=a("tinn.r1_g1","tinn.r");if(i!=-1)s[i]="TinN.R";i=a("mrna_accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq");if(i!=-1)s[i]="isoform";i=a("primary_purity","purity_d");if(i!=-1)s[i]="purity1";i=a("relapse_purity","purity_r");if(i!=-1)s[i]="purity2";i=a("tag_d_cnvloh","cnvloh_d");if(i!=-1)s[i]="Dcnvloh";i=a("tag_r_cnvloh","cnvloh_r");if(i!=-1)s[i]="Rcnvloh";const r=[];for(const t of s){switch(t){case"Dcnvloh":r.push({label:"D. CNV/LOH",get:t=>t.Dcnvlohraw});break;case"Rcnvloh":r.push({label:"R. CNV/LOH",get:t=>t.Rcnvlohraw});break;case"type":r.push({label:"Type",get:t=>t.type});break;case"chr":break;case"chrstart":r.push({label:"Genome Loc.",get:t=>t.chr+":"+(t.chrstart+1)});break;case"class":r.push({label:"Class",get:t=>{if(t.class==p){return t.originalclasslabel?t.originalclasslabel:n[t.class].label}return n[t.class].label}});break;case"mname":r.push({label:"Mutation",get:t=>{let e=t.mname;if(!e)e=t.cdna_change;return e}});break;case"MinD.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis,label:"D. tumor MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinD.D":break;case"MinD.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse,label:"R. tumor MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinD.R":break;case"MinN.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis_normal,label:"D. normal MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinN.D":break;case"MinN.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse_normal,label:"R. normal MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinN.R":break;case"call_d":r.push({label:"D. call",get:t=>t.call_d});break;case"call_r":r.push({label:"R. call",get:t=>t.call_r});break;case"purity1":r.push({label:"D. purity",get:t=>t.purity1});break;case"purity2":r.push({label:"R. purity",get:t=>t.purity2});break;default:r.push({label:t,get:e=>e[t]})}}return[null,s,r]}function S(e,s){const a=new t({border:"solid 1px black"});const i=[];const o=[];const p=[];const f=s.mlst;const u=f[0].sample;const m=T();let x=0;let b={};const k={};for(const t of f){if(t["TinD.D"]>0){x=Math.max(x,t["TinD.D"])}if(t["TinD.R"]>0){x=Math.max(x,t["TinD.R"])}if(t.set_share){p.push(t)}else if(t.set_1){i.push(t)}else if(t.set_2){o.push(t)}if(!(t.class in 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N({axiswidth:_,sp:M,sp2:X,sample1height:R,sample2height:I,shareheight:w,sharewidth:D,headerdiv:P});P.append("button").text("Screenshot").on("click",(()=>{h(Z.node(),"2dmaf_"+s.name)}));{const t=P.append("select").on("change",(t=>{const e=t.target.options[t.target.selectedIndex].value;if(e=="all"){at.transition().attr("transform",(t=>t.posstring+" scale(1)"));ot.transition().attr("transform",(t=>t.posstring+" scale(1)"));dt.transition().attr("transform",(t=>t.posstring+" scale(1)"));return}at.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));ot.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));dt.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"))}));t.append("option").text("Show all mutation classes").property("value","all");const e=[];for(const t in k){e.push([t,k[t]])}e.sort(((t,e)=>e[1]-t[1]));for(const s of e){t.append("option").text((s[0]in n?n[s[0]].label:s[0])+" 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pt=$.append("g").attr("transform","translate("+(_+M)+",0)");pt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("y",w).attr("width",I-X).attr("height",3);const ht=pt.append("g").attr("transform","translate(0,"+w+")").call(y().scale(ct).tickValues([0,x]));c({axis:ht,showline:true,fontsize:A*.8});pt.append("text").text("R total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("x",(I-X)/2).attr("y",w+A).attr("text-anchor","middle");const dt=pt.selectAll().data(o).enter().append("g").attr("transform",(t=>{t.posstring="translate("+ct(t["TinD.R"])+","+tt(t.maf2)+")";return t.posstring}));dt.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);dt.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=dt;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.D"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ft=$.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const 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a=ft.append("g").on("click",(()=>{s.hidden=!s.hidden;Z.selectAll(".twodmaf-"+e).style("display",s.hidden?"none":"");n.style("text-decoration",s.hidden?"line-through":"")}));t=gt+20;a.append("path").attr("transform","translate("+t+","+ut+")").attr("d",m.type(B[e]).size(100)()).attr("stroke","black").attr("fill","none").each((function(){t+=this.getBBox().width}));const n=a.append("text").text(s.label?s.label+" ("+s.numlines+")":"").attr("y",ut+2).attr("x",t).attr("dominant-baseline","middle").style("text-decoration",s.hidden?"line-through":"");ut+=30}ut+=30}const bt={},kt={},vt={},_t={};for(const t of f){if(!t.gene)continue;if(!(t.gene in bt)){bt[t.gene]=[]}bt[t.gene].push(t);if(t.set_1){kt[t.gene]=1}else if(t.set_2){vt[t.gene]=1}else if(t.set_share){_t[t.gene]=1}}const Dt=[];for(const t in kt){Dt.push(t)}for(const t in vt){if(!(t in kt)){Dt.push(t)}}for(const t in _t){if(!(t in kt)&&!(t in vt)){Dt.push(t)}}const 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e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,dt)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(i.length){for(const t of i){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,at)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}}function Nt(t,e,s){if(e.selected){t.style.border="";e.selected=false}else{t.style.border="solid 1px black";e.selected=true}const a=s.filter((t=>t.gene==e.gene&&t.class==e.class&&t.mname==e.mname));a.selectAll("rect").attr("fill-opacity",e.selected?.5:e.style.fillopacity).attr("fill",e.selected?e.style.fillhl:e.style.fill);a.selectAll("circle,ellipse,line").attr("stroke-opacity",e.selected?1:e.style.strokeopacity).attr("stroke",e.selected?e.style.strokehl:e.style.stroke).attr("stroke-width",e.selected?2:1);if(e.selected){let t=Math.max(20,e.radius),s=0;if((e.set_1||e.set_share)&&e.maf1>=.8){t=-e.radius;s=e.radius*2}const n=a.append("g").attr("class","sja_2dmaf_mlabel").attr("transform","translate("+t+","+s+")");let i;n.append("text").text(e.labelAs?e.labelAs:e.gene+" "+e.mname).attr("fill",e.style.fillhl).attr("dominant-baseline","middle").attr("text-anchor","start").attr("font-size",e.radius).each((function(){i=this.getBBox().width}));n.append("rect").attr("y",-e.radius/2).attr("width",i).attr("height",e.radius).attr("fill","black").attr("fill-opacity",0).on("mouseover",(t=>d(t.target).attr("fill-opacity",.2))).on("mouseout",(t=>d(t.target).attr("fill-opacity",0))).on("mousedown",(e=>{const a=t,i=s,r=e.clientX,l=e.clientY,o=d(document.body);o.on("mousemove",(e=>{e.preventDefault();t=a+e.clientX-r;s=i+e.clientY-l;n.attr("transform","translate("+t+","+s+")")}));o.on("mouseup",(()=>{o.on("mousemove",null).on("mouseup",null)}))}))}else{a.select(".sja_2dmaf_mlabel").remove()}}return E}function j(t,e,s){if(!e.selected){d(t.target).attr("fill",e.style.fillhl).attr("fill-opacity",.2)}s.clear();s.show(t.clientX,t.clientY);s.d.append("div").html((e.gene||"no gene")+' <span style="color:'+e.style.fillhl+'">'+(e.mname||"")+"</span>"+(e.class?' <span style="font-size:70%">'+n[e.class].label+"</span>":""))}function L(t,e,s){if(!e.selected){d(t.ele).attr("fill",e.style.fill).attr("fill-opacity",e.style.fillopacity).attr("stroke",e.style.stroke)}s.hide()}function V(t,e,s){const a=f({x:t.clientX+30,y:t.clientY-30});a.header.text((s.gene?s.gene:"No gene")+" "+(s.mname?s.mname:""));var n=[];for(let t=0;t<e.length;t++){n.push({k:e[t],v:s[e[t]]})}u(a.body,n)}function W(t,e){const s=t.pairs[e];if(s.shown){s.shown=false;s.holder.remove();if(s.handle){s.handle.attr("font-weight","normal")}}else{s.shown=true;if(s.holder){t.showholder.node().appendChild(s.holder.node())}else{s.holder=S(t.showholder,s)}if(s.handle){s.handle.attr("font-weight","bold")}}}function E(t,e){const s=[];for(const e in t.pairs){s.push([e,t.pairs[e].mlst.length])}e.selectAll("*").remove();const a=e.append("div").style("margin-bottom","5px");a.append("span").text(s.length+" individual"+(s.length>1?"s":""));const n=e.append("svg");const i=5,p=20,h=t.rowh;let d=0;for(const t of s){n.append("text").text(t[0]).attr("font-size",h).attr("font-family",r).each((function(){d=Math.max(d,this.getBBox().width)})).remove()}n.attr("width",d+i+t.peoplewidth+30).attr("height",p+i+h*s.length);s.sort(((t,e)=>e[1]-t[1]));let f=0;for(const e in t.pairs){f=Math.max(f,t.pairs[e].mlst.length)}const u=n.append("g").attr("transform","translate("+(d+i)+","+p+")").call(m().scale(l().domain([0,f]).range([0,t.peoplewidth])).tickFormat(o("d")).ticks(3));c({axis:u,showline:true,color:"black"});const y=t.peoplewidth/f;let g=p+i;for(const e of s){const s=e[0];t.pairs[s].handle=n.append("text").text(s).attr("class","sja_svgtext2").attr("font-size",h-2).attr("font-family",r).attr("x",d).attr("y",g+i+h/2).attr("text-anchor","end").on("click",(()=>{W(t,s)}));let a=0,l=0,o=0;for(const e of t.pairs[s].mlst){if(e.set_1)a++;else if(e.set_2)l++;else if(e.set_share)o++}const c=n.append("g").attr("transform","translate("+(d+i)+","+g+")");if(a>0){c.append("rect").attr("width",y*a).attr("height",h-1).attr("fill",t.color1)}if(o>0){c.append("rect").attr("x",y*a).attr("width",y*o).attr("height",h-1).attr("fill",t.colorshare)}if(l>0){c.append("rect").attr("x",y*(a+o)).attr("width",y*l).attr("height",h-1).attr("fill",t.color2)}g+=h}}export{z as d2mafparseinput,A as d2mafui};

package/dist/{DEanalysis-38a34f76.js → DEanalysis-72075e47.js}

@@ -1 +1 @@
-import{M as t,aM as a,az as e,l as o,a as n,$ as l,q as s}from"./app-5ca65214.js";import{b as r,c as i}from"./axis-6cb4f314.js";import"path";const c="#ffa200";const d=new t;class p{constructor(){this.type="DEanalysis"}async init(t){const a=this.opts.holder.append("div");this.dom={holder:a,header:this.opts.header,controlsDiv:a.append("div")}}getState(t){const a=t.plots.find((t=>t.id===this.id));if(!a)throw`No plot with id='${this.id}' found`;return{config:a}}async main(){const t=await this.app.vocabApi.runDEanalysis(this.state.config);this.dom.header.style("opacity",.6).style("padding-left","10px").style("font-size","0.75em").text("DIFFERENTIAL EXPRESSION");h(this.dom.holder,t)}}function h(t,a){let e=0,l=0,s=0,d=0;for(const t of a){e=Math.min(e,t.fold_change);l=Math.max(l,t.fold_change);if(t.adjusted_p_value==0){continue}else{s=Math.min(s,t.adjusted_p_value);d=Math.max(d,t.adjusted_p_value)}}let p,h,u,g,f,m,x=50,y=50,k;const j=t.append("svg");const w=j.append("g");const b=j.append("g");const M=j.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const E=j.append("text").text("-log10(adjusted P value)").attr("fill","black").attr("text-anchor","middle");a.vo_dotarea=j.append("g");const P=a.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const D=o().domain([e,l]);const A=o().domain([s,d]);const I=a.vo_dotarea.selectAll().data(a).enter().append("g").each((function(t){t.vo_g=this}));let S=2;let N=3;let $=0;let z=0;const F=I.append("circle").attr("stroke",(t=>{let a;if(t.adjusted_p_value>N&&Math.abs(t.fold_change)>S){a="red";$+=1}else{a="black";z+=1}return a})).attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",c).attr("fill-opacity",0).each((function(t){t.vo_circle=this})).on("mouseover",_).on("mouseout",v);console.log("Percentage of significant genes:",$*100/($+z));const O=a.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function R(t,e){u=t;g=e;p=Math.max(50,u/8);h=Math.max(50,g/8);k=Math.max(u,g)/80;const o=k*3;F.each((t=>{t.vo_radius=k}));f=Math.max(o,u/50);m=Math.max(o,g/50);w.attr("transform","translate("+p+","+x+")");b.attr("transform","translate("+(p+f)+","+(x+g+m)+")");M.attr("x",p+f+u/2).attr("y",x+g+m+h-5);E.attr("transform","translate(15,"+(x+g/2)+") rotate(-90)");a.vo_dotarea.attr("transform","translate("+(p+f)+","+x+")");P.attr("width",u).attr("height",g);D.range([0,u]);A.range([g,0]);I.attr("transform",(t=>"translate("+D(t.fold_change)+","+A(t.adjusted_p_value)+")"));F.attr("r",(t=>t.vo_radius));O.attr("x1",D(0)).attr("x2",D(0)).attr("y2",g);j.attr("width",p+f+u+y).attr("height",x+g+m+h);n({axis:w.call(r().scale(A)),color:"black",showline:true});n({axis:b.call(i().scale(D)),color:"black",showline:true})}R(400,400);if(a[0].adjusted_p_value!=undefined){const e=t.append("div").style("margin","20px");e.append("span").text("Select P value for Volcano plot:");const o=e.append("select").style("margin-left","5px").on("change",(t=>{s=0;d=0;const e=o.node().selectedIndex==0;for(const t of a){const a=e?t.adjusted_p_value:t.original_p_value;if(a==0)continue;s=Math.min(s,a);d=Math.max(d,a)}A.domain([s,d]);n({axis:w.call(r().scale(A)),color:"black",showline:true});I.attr("transform",(t=>{const a=e?t.adjusted_p_value:t.original_p_value;return"translate("+D(t.fold_change)+","+A(a)+")"}));E.text(e?"-log10(adjusted P value)":"-log10(original P value)")}));o.append("option").text("Adjusted P value");o.append("option").text("Original P value")}return j}async function u(t,e){try{if(t.samplelst.groups.length!=2)throw"opts.samplelst.groups[].length!=2";if(t.samplelst.groups[0].values?.length<1)throw"group 1 not having >1 samples";if(t.samplelst.groups[1].values?.length<1)throw"group 2 not having >1 samples";const e={};return a(e,t)}catch(t){throw`${t} [DEanalysis getPlotConfig()]`}}const g=e(p);const f=g;function m(t,a){a.prepPlot({config:{chartType:"DEanalysis"}})}function _(t,a){d.clear().show(t.clientX,t.clientY);const e=[{k:"gene_name",v:a.gene_name},{k:"gene_symbol",v:a.gene_symbol},{k:"log fold change",v:a.fold_change},{k:"log original p-value",v:a.original_p_value},{k:"log adjusted p-value",v:a.adjusted_p_value}];l(d.d,e);if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",.9);s(a.vo_circle).attr("fill-opacity",.9)}}function v(t,a){d.hide();if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",0);s(a.vo_circle).attr("fill-opacity",0)}}export{g as DEanalysisInit,f as componentInit,u as getPlotConfig,m as makeChartBtnMenu};
+import{M as t,aM as a,az as e,l as o,a as n,$ as l,q as s}from"./app-172cc04d.js";import{b as r,c as i}from"./axis-6cb4f314.js";import"path";const c="#ffa200";const d=new t;class p{constructor(){this.type="DEanalysis"}async init(t){const a=this.opts.holder.append("div");this.dom={holder:a,header:this.opts.header,controlsDiv:a.append("div")}}getState(t){const a=t.plots.find((t=>t.id===this.id));if(!a)throw`No plot with id='${this.id}' found`;return{config:a}}async main(){const t=await this.app.vocabApi.runDEanalysis(this.state.config);this.dom.header.style("opacity",.6).style("padding-left","10px").style("font-size","0.75em").text("DIFFERENTIAL EXPRESSION");h(this.dom.holder,t)}}function h(t,a){let e=0,l=0,s=0,d=0;for(const t of a){e=Math.min(e,t.fold_change);l=Math.max(l,t.fold_change);if(t.adjusted_p_value==0){continue}else{s=Math.min(s,t.adjusted_p_value);d=Math.max(d,t.adjusted_p_value)}}let p,h,u,g,f,m,x=50,y=50,k;const j=t.append("svg");const w=j.append("g");const b=j.append("g");const M=j.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const E=j.append("text").text("-log10(adjusted P value)").attr("fill","black").attr("text-anchor","middle");a.vo_dotarea=j.append("g");const P=a.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const D=o().domain([e,l]);const A=o().domain([s,d]);const I=a.vo_dotarea.selectAll().data(a).enter().append("g").each((function(t){t.vo_g=this}));let S=2;let N=3;let $=0;let z=0;const F=I.append("circle").attr("stroke",(t=>{let a;if(t.adjusted_p_value>N&&Math.abs(t.fold_change)>S){a="red";$+=1}else{a="black";z+=1}return a})).attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",c).attr("fill-opacity",0).each((function(t){t.vo_circle=this})).on("mouseover",_).on("mouseout",v);console.log("Percentage of significant genes:",$*100/($+z));const O=a.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function R(t,e){u=t;g=e;p=Math.max(50,u/8);h=Math.max(50,g/8);k=Math.max(u,g)/80;const o=k*3;F.each((t=>{t.vo_radius=k}));f=Math.max(o,u/50);m=Math.max(o,g/50);w.attr("transform","translate("+p+","+x+")");b.attr("transform","translate("+(p+f)+","+(x+g+m)+")");M.attr("x",p+f+u/2).attr("y",x+g+m+h-5);E.attr("transform","translate(15,"+(x+g/2)+") rotate(-90)");a.vo_dotarea.attr("transform","translate("+(p+f)+","+x+")");P.attr("width",u).attr("height",g);D.range([0,u]);A.range([g,0]);I.attr("transform",(t=>"translate("+D(t.fold_change)+","+A(t.adjusted_p_value)+")"));F.attr("r",(t=>t.vo_radius));O.attr("x1",D(0)).attr("x2",D(0)).attr("y2",g);j.attr("width",p+f+u+y).attr("height",x+g+m+h);n({axis:w.call(r().scale(A)),color:"black",showline:true});n({axis:b.call(i().scale(D)),color:"black",showline:true})}R(400,400);if(a[0].adjusted_p_value!=undefined){const e=t.append("div").style("margin","20px");e.append("span").text("Select P value for Volcano plot:");const o=e.append("select").style("margin-left","5px").on("change",(t=>{s=0;d=0;const e=o.node().selectedIndex==0;for(const t of a){const a=e?t.adjusted_p_value:t.original_p_value;if(a==0)continue;s=Math.min(s,a);d=Math.max(d,a)}A.domain([s,d]);n({axis:w.call(r().scale(A)),color:"black",showline:true});I.attr("transform",(t=>{const a=e?t.adjusted_p_value:t.original_p_value;return"translate("+D(t.fold_change)+","+A(a)+")"}));E.text(e?"-log10(adjusted P value)":"-log10(original P value)")}));o.append("option").text("Adjusted P value");o.append("option").text("Original P value")}return j}async function u(t,e){try{if(t.samplelst.groups.length!=2)throw"opts.samplelst.groups[].length!=2";if(t.samplelst.groups[0].values?.length<1)throw"group 1 not having >1 samples";if(t.samplelst.groups[1].values?.length<1)throw"group 2 not having >1 samples";const e={};return a(e,t)}catch(t){throw`${t} [DEanalysis getPlotConfig()]`}}const g=e(p);const f=g;function m(t,a){a.prepPlot({config:{chartType:"DEanalysis"}})}function _(t,a){d.clear().show(t.clientX,t.clientY);const e=[{k:"gene_name",v:a.gene_name},{k:"gene_symbol",v:a.gene_symbol},{k:"log fold change",v:a.fold_change},{k:"log original p-value",v:a.original_p_value},{k:"log adjusted p-value",v:a.adjusted_p_value}];l(d.d,e);if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",.9);s(a.vo_circle).attr("fill-opacity",.9)}}function v(t,a){d.hide();if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",0);s(a.vo_circle).attr("fill-opacity",0)}}export{g as DEanalysisInit,f as componentInit,u as getPlotConfig,m as makeChartBtnMenu};

package/dist/{Disco-34abd456.js → Disco-d319a184.js}

@@ -1 +1 @@
-import{M as t,aN as e,E as s,q as n,aM as i,az as o}from"./app-5ca65214.js";import"./transform-f2cc07e6.js";import{d as r}from"./arc-3d6751aa.js";import{c as a,p as l}from"./constant-426a1483.js";import{s as c}from"./svg.legend-56e87ee9.js";import{a as h,l as u}from"./line-264f8f9e.js";import{t as d}from"./math-2fb199c6.js";import"path";function p(t,e){return e<t?-1:e>t?1:e>=t?0:NaN}function g(t){return t}function m(){var t=g,e=p,s=null,n=a(0),i=a(d),o=a(0);function r(r){var a,l=(r=h(r)).length,c,u,p=0,g=new Array(l),m=new Array(l),f=+n.apply(this,arguments),v=Math.min(d,Math.max(-d,i.apply(this,arguments)-f)),A,x=Math.min(Math.abs(v)/l,o.apply(this,arguments)),R=x*(v<0?-1:1),b;for(a=0;a<l;++a){if((b=m[g[a]=a]=+t(r[a],a,r))>0){p+=b}}if(e!=null)g.sort((function(t,s){return e(m[t],m[s])}));else if(s!=null)g.sort((function(t,e){return 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e=y,s=I,n=L,i=L,o=E,r=S,a=w,c=null;function h(){var h,u=e.apply(this,arguments),d=s.apply(this,arguments),p=a.apply(this,arguments)/2,g=M.call(arguments),m=+n.apply(this,(g[0]=u,g)),x=o.apply(this,g)-R,C=r.apply(this,g)-R,y=+i.apply(this,(g[0]=d,g)),I=o.apply(this,g)-R,L=r.apply(this,g)-R;if(!c)c=h=l();if(p>b){if(f(C-x)>p*2+b)C>x?(x+=p,C-=p):(x-=p,C+=p);else x=C=(x+C)/2;if(f(L-I)>p*2+b)L>I?(I+=p,L-=p):(I-=p,L+=p);else I=L=(I+L)/2}c.moveTo(m*v(x),m*A(x));c.arc(0,0,m,x,C);if(x!==I||C!==L){if(t){var E=+t.apply(this,arguments),S=y-E,w=(I+L)/2;c.quadraticCurveTo(0,0,S*v(I),S*A(I));c.lineTo(y*v(w),y*A(w));c.lineTo(S*v(L),S*A(L))}else{c.quadraticCurveTo(0,0,y*v(I),y*A(I));c.arc(0,0,y,I,L)}}c.quadraticCurveTo(0,0,m*v(x),m*A(x));c.closePath();if(h)return c=null,h+""||null}if(t)h.headRadius=function(e){return arguments.length?(t=typeof e==="function"?e:C(+e),h):t};h.radius=function(t){return arguments.length?(n=i=typeof t==="function"?t:C(+t),h):n};h.sourceRadius=function(t){return arguments.length?(n=typeof t==="function"?t:C(+t),h):n};h.targetRadius=function(t){return arguments.length?(i=typeof t==="function"?t:C(+t),h):i};h.startAngle=function(t){return arguments.length?(o=typeof t==="function"?t:C(+t),h):o};h.endAngle=function(t){return arguments.length?(r=typeof t==="function"?t:C(+t),h):r};h.padAngle=function(t){return arguments.length?(a=typeof t==="function"?t:C(+t),h):a};h.source=function(t){return arguments.length?(e=t,h):e};h.target=function(t){return arguments.length?(s=t,h):s};h.context=function(t){return arguments.length?(c=t==null?null:t,h):c};return h}function N(){return O()}class D{constructor(t,e,s){this.radius=t;this.width=e;this.color=s}render(t){const e=r();const s={startAngle:0,endAngle:Math.PI*2,innerRadius:this.radius,outerRadius:this.radius+this.width,color:this.color,text:"No label"};const n=[];n.push(s);const i=t.append("g");i.selectAll("path").data(n).enter().append("path").attr("d",(t=>e(t))).attr("fill",(t=>t.color))}}class V{static create(){const e=new t({padding:5});e.d.style("border","1px solid #FFF").style("position","absolute").style("z-index",1001);return e}}var T;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(T||(T={}));class z{static getColor(t,e){if(t!=e){return T.Interchromosomal.valueOf()}else{return T.Intrachromosomal.valueOf()}}}class k{render(t,e){let s=0;if(e.length>0){s=e[0].target.radius;const n=new D(s,2,"#6464641A");n.render(t)}const n=N().radius(s);const i=t.selectAll(".chord").data(e);const o=V.create();i.enter().append("path").attr("class","chord").attr("d",n).attr("fill",(t=>z.getColor(t.source.positionInChromosome.chromosome,t.target.positionInChromosome.chromosome))).on("mouseover",((t,e)=>{o.d.style("padding","2px").html(this.getTooltip(e));o.show(t.x,t.y)})).on("mouseout",(()=>{o.hide()}))}getTooltip(t){let e="";if(t.source.gene){e+=t.source.gene}const s=t.source.positionInChromosome;e+=` ${s.chromosome}:${s.position}<br />`;if(t.target.gene){e+=t.target.gene}const n=t.target.positionInChromosome;e+=` ${n.chromosome}:${n.position}`;return e}}class P{constructor(t){this.downloadClickListener=t}render(t,e){t.append("span").append("button").style("margin","2px 0 2px 30px").text("Download image").on("click",(()=>{const t=e.select("svg").node();this.downloadClickListener(t)}))}}class ${constructor(t){this.checkBoxClickListener=t}render(t,e,s,n,i){if(s){const s=t.append("span").append("input").attr("type","checkbox").attr("id","genes-checkbox").property("checked",e);t.append("label").attr("for","genes-checkbox").text(`Prioritize Cancer Gene Census (${n} mutations out of ${i} total)`);s.on("change",(()=>{this.checkBoxClickListener(s.property("checked"))}))}}}class B{constructor(t,e,s,n){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new k;this.downloadButtonRenderer=new P(s);this.prioritizeGenesCheckboxRenderer=new $(n)}render(t,e){const s=t.append("div");s.append("div");const n=s.append("div").style("display","inline-block").style("font-family","Arial");const i=n.append("div");this.downloadButtonRenderer.render(i,n);this.prioritizeGenesCheckboxRenderer.render(i,e.settings.label.prioritizeGeneLabelsByGeneSets,e.settings.label.showPrioritizeGeneLabelsByGeneSets,e.filteredSnvDataLength,e.svnDataLength);const o=n.append("svg").attr("width",e.width).attr("height",e.height+e.legendHeight);const r=o.append("g").attr("class","mainG").attr("transform",`translate(${e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+100},${e.height/2})`);for(const[t,s]of this.renders){const n=e.getElements(t);const i=e.getCollisions(t);s.render(r,n,i)}this.fusionRenderer.render(r,e.fusions);this.legendRenderer.render(r,e.legend,-1*(e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+50),e.width,e.height/2)}}class G{constructor(t){this.downloadImgName=t.state.settings.downloadImgName||"disco.plot";this.cappingClickCallback=(e,s)=>{const n=t.app.tip;n.clear();const i=t.app.tip.d;const o=i.append("span").html("Capping:").append("input").attr("type","number").on("change",(()=>{t.app.dispatch({type:"plot_edit",id:t.opts.id,config:{settings:{cnv:{capping:Number(o.property("value"))}}}});n.hide()}));const r=s.node().getBoundingClientRect();const a=r.left-20;const l=r.top-40;n.show(a,l)};this.downloadClickListener=t=>{const e=document.createElement("a");document.body.appendChild(e);e.addEventListener("click",(()=>{const s=new XMLSerializer;const n=new Blob([s.serializeToString(t)],{type:"image/svg+xml"});e.download=this.downloadImgName+".svg";e.href=URL.createObjectURL(n);document.body.removeChild(e)}),false);e.click()};this.geneClickListener=(s,n)=>e(this,void 0,void 0,(function*(){const e={holder:t.app.opts.holder,genome:t.app.opts.state.args.genome,nobox:true,query:s,tklst:[{type:"mds3",dslabel:t.app.opts.state.dslabel,hlaachange:n.join(",")}]};const i=yield import("./app-5ca65214.js").then((function(t){return t.bX}));yield i.default(e)}));this.prioritizeGenesCheckboxListener=e=>{t.app.dispatch({type:"plot_edit",id:t.opts.id,config:{settings:{label:{prioritizeGeneLabelsByGeneSets:e}}}})}}}class W{constructor(t,e,s){this.chromosomes=[];this.chromosomesOrder=[];this.keysArray=[];this.totalSizeArray=[];this.chrSizesArray=[];const n=s||e;this.settings=t;this.chromosomesOrder=[];let i=0;this.totalPadAngle=Object.keys(n).length*this.settings.padAngle;this.totalChromosomesAngle=2*Math.PI-this.totalPadAngle;for(const t in n){const e=t.slice(0,3)==="chr"?t.slice(3):t;this.chromosomesOrder.push(t);this.keysArray.push(e);this.totalSizeArray.push(i);this.chrSizesArray.push(n[t]);i+=n[t]}this.totalSize=i;let o=0;for(let t=0;t<this.keysArray.length;t++){const e=this.totalChromosomesAngle*(this.chrSizesArray[t]/i);const s=t==0?this.settings.padAngle/2:o+this.settings.padAngle;const n=t==0?this.settings.padAngle/2+e:o+this.settings.padAngle+e;const r={start:this.totalSizeArray[t],size:this.chrSizesArray[t],factor:1,startAngle:s,endAngle:n,angle:(s+n)/2,innerRadius:this.settings.chromosomeInnerRadius,outerRadius:this.settings.chromosomeInnerRadius+this.settings.chromosomeWidth,color:"#AAA",text:this.keysArray[t]};this.chromosomes.push(r);if(r.endAngle!=null){o=r.endAngle}}}}class F{constructor(t,e){this.sampleName=t;this.prioritizedGenes=e}map(t){return{dt:t.dt,mname:t.mname,mClass:t.class,gene:t.gene,chr:t.chr,ref:t.ref,alt:t.alt,position:t.pos?t.pos:t.position,poschr:t.poschr,posbins:t.posbins,poslabel:t.poslabel,sampleName:this.sampleName,ssm_id:t.ssm_id,start:t.start,stop:t.stop,value:t.value,segmean:t.segmean,isPrioritized:this.prioritizedGenes.some((e=>e==t.gene)),chrA:t.chrA,chrB:t.chrB,geneA:t.geneA,geneB:t.geneB,posA:t.posA,posB:t.posB,strandA:t.strandA,strandB:t.strandB}}}var H;(function(t){t[t["SNV"]=1]="SNV";t[t["FUSION"]=2]="FUSION";t[t["CNV"]=4]="CNV";t[t["SV"]=5]="SV";t[t["LOH"]=10]="LOH"})(H||(H={}));class j{constructor(t,e,s,n=[]){this.labelData=[];this.nonExonicSnvData=[];this.nonExonicInnerRadius=0;this.snvRingDataMap=new Map;this.snvInnerRadius=0;this.snvData=[];this.bpx=0;this.onePxArcAngle=0;this.filteredSnvData=[];this.lohData=[];this.lohInnerRadius=0;this.cnvData=[];this.cnvInnerRadius=0;this.fusionData=[];this.fusionRadius=0;this.hasPrioritizedGenes=false;this.cnvMaxValue=undefined;this.cnvMinValue=undefined;this.lohMaxValue=undefined;this.lohMinValue=undefined;this.snvFilter=t=>t.dt==H.SNV;this.fusionFilter=t=>t.dt==H.FUSION||t.dt==H.SV;this.cnvFilter=t=>t.dt==H.CNV;this.lohFilter=t=>t.dt==H.LOH;this.compareData=(t,e)=>{const s=this.reference.chromosomesOrder.indexOf(t.chr)-this.reference.chromosomesOrder.indexOf(e.chr);if(s!=0){return s}const n=t.pos?t.pos:t.start;const i=e.pos?e.pos:e.start;return n-i};this.settings=t;this.reference=e;this.sample=s;this.lastInnerRadious=this.settings.rings.chromosomeInnerRadius;this.nonExonicFilter=e=>t.rings.nonExonicFilterValues.includes(mt.snvClassLayer[e.mClass]);this.snvRingFilter=e=>{if(n.length>0&&this.settings.label.prioritizeGeneLabelsByGeneSets){return n.includes(e.gene)&&t.rings.snvRingFilters.includes(mt.snvClassLayer[e.mClass])}else{return t.rings.snvRingFilters.includes(mt.snvClassLayer[e.mClass])}};this.dataObjectMapper=new F(s,n)}map(t){const e=[];t.forEach((t=>{const s=this.reference.chromosomesOrder.indexOf(t.chr);const n=this.reference.chromosomesOrder.indexOf(t.chrA);const i=this.reference.chromosomesOrder.indexOf(t.chrB);if(t.dt==H.SNV){if(s!=-1&&this.snvData.length<this.settings.snv.maxMutationCount){this.addData(t,e)}}else if(t.dt==H.FUSION||t.dt==H.SV){if(n!=-1&&i!=-1){this.addData(t,e)}}else if([H.CNV,H.LOH].includes(Number(t.dt))){this.addData(t,e)}else{throw Error("Unknown mutation type!")}}));const s=e.sort(this.compareData);if(this.settings.rings.nonExonicRingEnabled){s.forEach((t=>{this.filterNonExonicSnvData(t)}))}if(this.nonExonicSnvData.length>0){this.nonExonicInnerRadius=this.lastInnerRadious-this.settings.rings.nonExonicRingWidth;this.lastInnerRadious=this.nonExonicInnerRadius}s.forEach((t=>{this.filterSnvs(t)}));s.forEach((t=>{this.filterLohs(t)}));if(this.lohData.length>0){this.lohInnerRadius=this.lastInnerRadious-this.settings.rings.lohRingWidth;this.lastInnerRadious=this.lohInnerRadius}s.forEach((t=>{this.filterCnvs(t)}));if(this.cnvData.length>0){this.cnvInnerRadius=this.lastInnerRadious-this.settings.rings.cnvRingWidth;this.lastInnerRadious=this.cnvInnerRadius}s.forEach((t=>{this.filterFusion(t)}));if(this.fusionData.length>0){this.fusionRadius=this.lastInnerRadious}const n={labelData:this.labelData,nonExonicSnvData:this.nonExonicSnvData,nonExonicInnerRadius:this.nonExonicInnerRadius,snvRingDataMap:this.snvRingDataMap,snvInnerRadius:this.snvInnerRadius,snvData:this.snvData,bpx:this.bpx,onePxArcAngle:this.onePxArcAngle,filteredSnvData:this.filteredSnvData,lohData:this.lohData,lohInnerRadius:this.lohInnerRadius,cnvData:this.cnvData,cnvInnerRadius:this.cnvInnerRadius,fusionData:this.fusionData,fusionRadius:this.fusionRadius,hasPrioritizedGenes:this.hasPrioritizedGenes,cnvMaxValue:this.cnvMaxValue,cnvMinValue:this.cnvMinValue,lohMaxValue:this.lohMaxValue,lohMinValue:this.lohMinValue};return n}addData(t,e){const s=this.dataObjectMapper.map(t);if(s.isPrioritized){this.hasPrioritizedGenes=true}e.push(s)}filterNonExonicSnvData(t){if(this.snvFilter(t)){if(this.settings.rings.nonExonicRingEnabled&&this.nonExonicFilter(t)){this.nonExonicSnvData.push(t)}}}filterSnvs(t){if(this.snvFilter(t)){this.snvData.push(t);if(this.snvRingFilter(t)){if(this.snvInnerRadius==0){this.snvInnerRadius=this.lastInnerRadious-this.settings.rings.snvRingWidth;this.lastInnerRadious=this.snvInnerRadius;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*this.snvInnerRadius));this.onePxArcAngle=1/this.snvInnerRadius}this.filteredSnvData.push(t);this.labelData.push(t);const e=this.calculateArcAngle(t);let s=this.snvRingDataMap.get(e);if(!s){s=new Array}s.push(t);this.snvRingDataMap.set(e,s)}}}filterFusion(t){if(this.fusionFilter(t)){t.isPrioritized=true;this.fusionData.push(t);this.labelData.push(t)}}filterLohs(t){if(this.lohFilter(t)){if(this.lohMaxValue==undefined||this.lohMaxValue<t.value){this.lohMaxValue=t.segmean}if(this.lohMinValue==undefined||this.lohMinValue>t.value){this.lohMinValue=t.segmean}this.lohData.push(t)}}filterCnvs(t){if(this.cnvFilter(t)){if(this.cnvMaxValue==undefined||this.cnvMaxValue<t.value){this.cnvMaxValue=t.value}if(this.cnvMinValue==undefined||this.cnvMinValue>t.value){this.cnvMinValue=t.value}this.cnvData.push(t)}}calculateArcAngle(t){const e=this.reference.chromosomes[this.reference.chromosomesOrder.findIndex((e=>t.chr==e))];const s=Math.floor(t.position/this.bpx);return e.startAngle+s*this.onePxArcAngle}}class U{constructor(t,e,s,n,i,o,r,a){this.snvTitle=t;this.cnvTitle=e;this.lohTitle=s;this.fusionTitle=n;this.snvClassMap=i;this.cnvClassMap=o;this.lohLegend=a;this.fusionLegend=r}legendCount(){return(this.snvClassMap.size>0?1:0)+(this.cnvClassMap.size>0?1:0)+(this.lohLegend?1:0)+(this.fusionLegend?1:0)}}class X{constructor(t,e,s,n,i){this.source=t;this.target=e;this.genes=s;this.count=n;this.endpts=i}}class q{constructor(t,e,s,n,i,o,r){this.startAngle=t;this.endAngle=e;this.radius=s;this.gene=n;this.value=i;this.genes=o;this.positionInChromosome=r}}class _{constructor(t,e,s){this.radius=t;this.sampleName=e;this.reference=s}map(t){const e=[];t.forEach((t=>{const s=new Set;s.add(t.geneA);s.add(t.geneB);const n=new q(this.calculateStartAngle(t.chrA,t.posA),this.calculateEndAngle(t.chrA,t.posA),this.radius,t.geneA,t.value,s,{chromosome:t.chrA,position:t.posA});const i=new q(this.calculateStartAngle(t.chrB,t.posB),this.calculateEndAngle(t.chrB,t.posB),this.radius,t.geneB,t.value,s,{chromosome:t.chrB,position:t.posB});const o=new X(n,i,"genes",-1,"Endpoints");e.push(o)}));return e}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)-.01}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return.01+n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class J{static provide(t){const e=Math.min(Math.max(t,0),1);const s=Math.round(e*255);return`rgb(${s}, ${s}, ${s})`}}class K{constructor(t,e){this.minValue=t;this.maxValue=e;this.colorStartValue=J.provide(t);this.colorEndValue=J.provide(e)}}var Q;(function(t){t[t["CHROMOSOME"]=0]="CHROMOSOME";t[t["LABEL"]=1]="LABEL";t[t["NONEXONICSNV"]=2]="NONEXONICSNV";t[t["SNV"]=3]="SNV";t[t["CNV"]=4]="CNV";t[t["LOH"]=5]="LOH";t[t["FUSION"]=6]="FUSION"})(Q||(Q={}));class Y{constructor(t,e,s,n,i,o){this.settings=t;this.rings=e;this.legend=s;this.fusions=n;this.width=1.2*(this.settings.horizontalPadding+this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance);this.height=2*(this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance+this.settings.verticalPadding);this.legendHeight=this.calculateLegendHeight(s);this.svnDataLength=o;this.filteredSnvDataLength=i}getElements(t){switch(t){case Q.CHROMOSOME:return this.rings.chromosomesRing?this.rings.chromosomesRing.elements:[];case Q.LABEL:return this.rings.labelsRing.elementsToDisplay;case Q.NONEXONICSNV:return this.rings.nonExonicArcRing?this.rings.nonExonicArcRing.elements:[];case Q.SNV:return this.rings.snvArcRing?this.rings.snvArcRing.elements:[];case Q.CNV:return this.rings.cnvArcRing?this.rings.cnvArcRing.elements:[];case Q.LOH:return this.rings.lohArcRing?this.rings.lohArcRing.elements:[];default:throw new Error(`ringType ${t} not defined`)}}getCollisions(t){if(t==Q.LABEL){return this.rings.labelsRing.collisions}else{return undefined}}calculateLegendHeight(t){const e=this.settings.legend.rowHeight;return e*t.legendCount()}}class Z{constructor(t,e,s){this.innerRadius=t;this.outerRadius=t+e;this.width=e;this.elements=s}}class tt{constructor(){const t={};for(const e in s){t[s[e].label]=s[e];t[e]=s[e]}this.mlabel=t}static getInstance(){if(!tt.instance){tt.instance=new tt}return tt.instance}}class et{constructor(t,e,s){this.snvType=t;this.color=e;this.count=s}}class st{constructor(t,e,s,n){this.snvClassMap=new Map;this.svnInnerRadius=t;this.svnWidth=e;this.sampleName=s;this.reference=n;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*t));this.onePxArcAngle=1/t}map(t){const e=[];for(const s of t.keys()){const n=t.get(s);if(n){const t=n.length;for(let i=0;i<n.length;i++){const o=n[i];const r=this.snvClassMap.get(o.mClass);if(r){this.snvClassMap.set(o.mClass,this.createSnvLegend(o.mClass,++r.count))}else{this.snvClassMap.set(o.mClass,this.createSnvLegend(o.mClass,1))}const a=s;const l=s+this.onePxArcAngle;const c=tt.getInstance().mlabel?tt.getInstance().mlabel[o.mClass]:undefined;const h={startAngle:a,endAngle:l,innerRadius:this.svnInnerRadius+i*this.svnWidth/t,outerRadius:this.svnInnerRadius+(i+1)*this.svnWidth/t,color:c.color,text:o.gene,dataClass:c.label,mname:o.mname,chr:o.chr,pos:o.position};e.push(h)}}}return e}createSnvLegend(t,e){const s=tt.getInstance().mlabel[t];return new et(s.label,s.color,e)}}class nt{constructor(t,e,s,n){this.text=t;this.cnvType=e;this.color=s;this.value=n}}var it;(function(t){t[t["Loss"]=0]="Loss";t[t["Gain"]=1]="Gain";t[t["Cap"]=2]="Cap"})(it||(it={}));class ot{static getColor(t,e){const s=e.cnv;const n=e.cnv.capping;const i=-1*e.cnv.capping;if(t<i){return s.cappedLossColor}else if(t>=i&&t<=0){return s.lossColor}else if(t>0&&t<=n){return s.ampColor}else{return s.cappedAmpColor}}}class rt{constructor(t,e,s,n,i,o=0,r=0,a=""){this.cnvClassMap=new Map;this.cnvInnerRadius=t;this.cnvWidth=e;this.settings=s;this.sampleName=n;this.reference=i;this.cnvMaxValue=o;this.cnvMinValue=r;this.cnvUnit=a;this.gainCapped=this.settings.cnv.capping;this.lossCapped=-1*this.settings.cnv.capping;this.lossOnly=o<=0;this.gainOnly=r>=0;this.onePxArcAngle=1/this.cnvInnerRadius;const l=new nt("Max",o>0?it.Gain:it.Loss,this.getColor(o),o);const c=new nt("Min",r>0?it.Gain:it.Loss,this.getColor(r),r);const h=new nt("Capping",it.Loss,this.getColor(r>0?r:o),this.settings.cnv.capping);this.cnvClassMap.set(it.Gain,l);this.cnvClassMap.set(it.Loss,c);this.cnvClassMap.set(it.Cap,h);this.maxAbsValue=Math.max(Math.abs(this.capMaxValue(r)),Math.abs(this.capMaxValue(o)))}map(t){const e=[];t.forEach((t=>{let s=this.calculateStartAngle(t);let n=this.calculateEndAngle(t);if(n-s<this.onePxArcAngle){const t=this.onePxArcAngle-(n-s);s=s-t/2;n=s+t/2}const i=this.calculateInnerRadius(t);const o=this.calculateOuterRadius(t);const r=this.getColor(t.value);const a={startAngle:s,endAngle:n,innerRadius:i,outerRadius:o,color:r,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.value,unit:this.cnvUnit};e.push(a)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}getColor(t){return ot.getColor(t,this.settings)}calculateInnerRadius(t){if(this.gainOnly){return this.cnvInnerRadius}if(this.lossOnly){const e=this.cnvInnerRadius+this.cnvWidth;return e-this.capMinValue(this.cnvWidth*this.capMaxValue(t.value)/this.maxAbsValue)}const e=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return e}if(Math.sign(t.value)==-1){return e+this.capMinValue(this.capMaxValue(t.value)/this.maxAbsValue*(this.cnvWidth/2))}return 1}calculateOuterRadius(t){const e=this.cnvInnerRadius+this.cnvWidth;if(this.gainOnly){return this.cnvInnerRadius+this.capMinValue(this.cnvWidth*this.capMaxValue(t.value)/this.maxAbsValue)}if(this.lossOnly){return e}const s=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return s+this.capMinValue(this.capMaxValue(t.value)/this.maxAbsValue*(this.cnvWidth/2))}if(Math.sign(t.value)==-1){return s}return 1}capMaxValue(t){if(Math.sign(t)==1){return t>this.gainCapped?this.gainCapped:t}if(Math.sign(t)==-1){return t<this.lossCapped?this.lossCapped:t}return 0}capMinValue(t,e=1){if(Math.sign(t)==1){return t>e?t:e}if(Math.sign(t)==-1){return t<-1*e?t:-1*e}return 1}}class at{constructor(t,e){this.points=new Array;this.points=t;this.color=e}}class lt{static createLabel(t,e,s,n,i,o,r,a,l,c,h=false,u,d,p){const g=(t+e)/2;const m=g-Math.PI/2;const f=`rotate(${g*180/Math.PI-90}) translate(${n})${g>Math.PI?"rotate(180)":""}`;const v=g>Math.PI?"end":"";const A=s;const x=n-u;const R=[];const b={x:A*Math.cos(m),y:A*Math.sin(m)};const M={x:x*Math.cos(m),y:x*Math.sin(m)};R.push(b);R.push(M);const C=new at(R,r);const y={startAngle:t,endAngle:e,innerRadius:s,outerRadius:n,angle:g,value:i,text:o,color:r,transform:f,textAnchor:v,ccAngle:m,line:C,isPrioritized:h,start:c,stop:c,chr:l,mutationsTooltip:d?[d]:undefined,fusionTooltip:p?[p]:undefined};return y}static createMovedLabel(t,e){const s=t.startAngle+e;const n=t.endAngle+e;const i=(s+n)/2;const o=i-Math.PI/2;const r=t.innerRadius;const a=t.outerRadius-2;const l=(a-r)/3;const c=Math.cos(t.ccAngle);const h=Math.sin(t.ccAngle);const u=Math.cos(t.ccAngle+e);const d=Math.sin(t.ccAngle+e);const p=[];const g={x:r*c,y:r*h};const m={x:(r+l)*c,y:(r+l)*h};const f={x:(r+2*l)*u,y:(r+2*l)*d};const v={x:(r+3*l)*u,y:(r+3*l)*d};p.push(g);p.push(m);p.push(f);p.push(v);const A=new at(p,t.color);const x="rotate("+(i*180/Math.PI-90)+")"+"translate("+t.outerRadius+")"+(i>Math.PI?"rotate(180)":"");const R=i>Math.PI?"end":"";const b=t.mutationsTooltip?t.mutationsTooltip[0].color:t.fusionTooltip?t.fusionTooltip[0].color:undefined;const M={startAngle:s,endAngle:n,innerRadius:t.innerRadius,outerRadius:t.outerRadius,angle:i,value:t.value,text:t.text,transform:x,textAnchor:R,ccAngle:o,color:b,line:A,isPrioritized:t.isPrioritized,start:t.start,stop:t.stop,chr:t.chr,mutationsTooltip:t.mutationsTooltip,fusionTooltip:t.fusionTooltip};return M}}class ct{constructor(t,e,s){this.labelMap=new Map;this.settings=t;this.sampleName=e;this.reference=s}map(t,e=[]){const s=this.settings.rings.labelLinesInnerRadius;const n=s+this.settings.rings.labelsToLinesDistance;t.forEach((t=>{if(t.dt==H.SNV){const e=this.calculateStartAngle(t.chr,t.position);const i=this.calculateEndAngle(t.chr,t.position);const o=tt.getInstance().mlabel?tt.getInstance().mlabel[t.mClass]:undefined;this.addLabelOrMutation(t,t.gene,t.mname,e,i,s,n,o.color,o.label)}if(t.dt==H.FUSION){const e=z.getColor(t.chrA,t.chrB);if(t.geneA){const i=this.calculateStartAngle(t.chrA,t.posA);const o=this.calculateEndAngle(t.chrA,t.posA);this.addLabelOrFusion(t,t.geneA,t.posA,i,o,s,n,e)}if(t.geneB&&t.geneA!=t.geneB){const i=this.calculateStartAngle(t.chrB,t.posB);const o=this.calculateEndAngle(t.chrB,t.posB);this.addLabelOrFusion(t,t.geneB,t.posB,i,o,s,n,e)}}}));const i=Array.from(this.labelMap.values());i.forEach((t=>{e.forEach((e=>{if(t.stop>=e.start&&e.stop>=t.start&&t.chr==e.chr){const s={value:e.value,color:ot.getColor(e.value,this.settings),chr:e.chr,start:e.start,stop:e.stop};if(t.cnvTooltip){t.cnvTooltip.push(s)}else{t.cnvTooltip=[];t.cnvTooltip.push(s)}}}))}));return Array.from(this.labelMap.values())}addLabelOrMutation(t,e,s,n,i,o,r,a,l){const c=this.labelMap.get(e);const h={mname:s,color:a,dataClass:l,chr:t.chr,position:t.position};if(!c){this.labelMap.set(e,lt.createLabel(n,i,o,r,t.value,e,a,l,t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,h))}else{if(c.mutationsTooltip){c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}else{c.mutationsTooltip=[];c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}}}addLabelOrFusion(t,e,s,n,i,o,r,a){const l=this.labelMap.get(e);const c={color:a,chrA:t.chrA,chrB:t.chrB,posA:t.posA,posB:t.posB,geneA:t.geneA,geneB:t.geneB,strandA:t.strandA,strandB:t.strandB};if(!l){this.labelMap.set(e,lt.createLabel(n,i,o,r,t.value,e,a,"Fusion transcript",t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,undefined,c))}else{if(l.fusionTooltip){l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}else{l.fusionTooltip=[];l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}}}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class ht extends Z{constructor(t,e,s){super(t.rings.labelLinesInnerRadius,t.rings.labelsToLinesDistance,e.sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0)));this.elementsToDisplay=[];this.settings=t;this.hasPrioritizedGenes=s;const n=2*Math.PI*(t.rings.labelLinesInnerRadius+t.rings.labelsToLinesDistance);this.overlapAngle=this.settings.label.overlapAngleFactor*this.settings.label.fontSize/n;this.calculateCollisions()}calculateCollisions(){this.collisions=[];let t=[];t=this.elements.filter((t=>t.isPrioritized));if(this.settings.label.prioritizeGeneLabelsByGeneSets){this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(t)}else if(this.hasPrioritizedGenes){const t=this.elements.filter((t=>t.isPrioritized));const e=this.getLabelsWithPrioritizedGenes(t);const s=this.elements.filter((t=>!t.isPrioritized));const n=[...s,...e].sort(((t,e)=>t.startAngle-e.startAngle));this.elementsToDisplay=this.getAllLabels(n)}else{this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(this.elements)}}getLabelsWithPrioritizedGenes(t){const e=[];let s={endAngle:0};t.forEach(((t,n)=>{if(n==0){e.push(t);s=t}else{const n=s.endAngle-t.startAngle+this.overlapAngle;if(n>0&&n<this.settings.label.maxDeltaAngle){const i=lt.createMovedLabel(t,n);e===null||e===void 0?void 0:e.push(i);s=i}if(n<=0){e.push(t);s=t}}}));return e}getAllLabels(t){var e;const s=[];let n={endAngle:0};const i=t.length;let o=-1;for(let r=0;r<t.length;r++){const a=t[r];if(a.isPrioritized){s.push(a);o=r;n=a;continue}if(r==0){if(i>1){if(this.isElementOverlappingNextCancerGene(t,o,a,0)){continue}s.push(a);n=a}continue}const l=n.endAngle-a.startAngle+this.overlapAngle;if(l>0&&l<this.settings.label.maxDeltaAngle){if(r==length-1){s.push(a);continue}if(this.isElementOverlappingNextCancerGene(t,o,a,l)){continue}const i=lt.createMovedLabel(a,l);(e=this.collisions)===null||e===void 0?void 0:e.push(i);s.push(a);n=i}if(l<=0){if(this.isElementOverlappingNextCancerGene(t,o,a,0)){continue}s.push(a);n=a}}return s}isElementOverlappingNextCancerGene(t,e,s,n){const i=this.getNextLabelWithCancerGene(t,e);if(i){const t=s.endAngle+n-i.startAngle+this.overlapAngle;if(t>0){return true}}return false}getNextLabelWithCancerGene(t,e){return t.find(((t,s)=>t.isPrioritized&&s>e))}}class ut{constructor(t,e,s,n){this.nonExonicInnerRadius=t;this.nonExonicWidht=e;this.sampleName=s;this.reference=n;this.onePxArcAngle=1/t}map(t){const e=this.nonExonicInnerRadius;const s=e+this.nonExonicWidht;const n=[];t.forEach((t=>{const i=tt.getInstance().mlabel?tt.getInstance().mlabel[t.mClass]:undefined;const o=this.calculateStartAngle(t);const r=this.calculateEndAngle(t);const a={startAngle:o,endAngle:r,innerRadius:e,outerRadius:s,color:i.color,text:t.gene,dataClass:i.label,mname:t.mname,chr:t.chr,pos:t.position};n.push(a)}));return n}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)-this.onePxArcAngle}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return this.onePxArcAngle+s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)}}class dt{constructor(t,e,s,n){this.lohInnerRadius=t;this.lohWidth=e;this.sampleName=s;this.reference=n}map(t){const e=[];t.forEach((t=>{const s=this.calculateStartAngle(t);const n=this.calculateEndAngle(t);const i=this.lohInnerRadius;const o=i+this.lohWidth;const r=J.provide(t.segmean);const a={startAngle:s,endAngle:n,innerRadius:i,outerRadius:o,color:r,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.segmean};e.push(a)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}}class pt{constructor(t,e,s,n,i,o){this.labelsRing=t;this.chromosomesRing=e;this.nonExonicArcRing=s;this.snvArcRing=n;this.cnvArcRing=i;this.lohArcRing=o}}class gt{constructor(t,e,s,n){this.nonExonicArcRing=undefined;this.settings=t;this.dataMapper=e;this.reference=s;this.sampleName=n}map(t){const e=this.dataMapper.map(t);const s=new ct(this.settings,this.sampleName,this.reference);const n=s.map(e.labelData,e.cnvData);const i=new ht(this.settings,n,e.hasPrioritizedGenes);const o=new Z(this.settings.rings.chromosomeInnerRadius,this.settings.rings.chromosomeWidth,this.reference.chromosomes);const r=new ut(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,this.sampleName,this.reference);const a=r.map(e.nonExonicSnvData);if(a.length>0){this.nonExonicArcRing=new Z(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,a)}this.snvArcsMapper=new st(e.snvInnerRadius,this.settings.rings.snvRingWidth,this.sampleName,this.reference);const l=this.snvArcsMapper.map(e.snvRingDataMap);if(l.length>0){this.snvArcRing=new Z(e.snvInnerRadius,this.settings.rings.snvRingWidth,l)}const c=new dt(e.lohInnerRadius,this.settings.rings.lohRingWidth,this.sampleName,this.reference);const h=c.map(e.lohData);if(h.length>0){this.lohArcRing=new Z(e.lohInnerRadius,this.settings.rings.lohRingWidth,h)}this.cnvArcsMapper=new rt(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,this.settings,this.sampleName,this.reference,e.cnvMaxValue,e.cnvMinValue,this.settings.cnv.unit);const u=this.cnvArcsMapper.map(e.cnvData);if(u.length>0){this.cnvArcRing=new Z(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,u)}const d=new _(e.fusionRadius,this.sampleName,this.reference);const p=d.map(e.fusionData);let g;if(this.settings.legend.lohLegendEnabled&&e.lohMinValue&&e.lohMaxValue){g=new K(e.lohMinValue,e.lohMaxValue)}const m=new U(this.settings.legend.snvTitle,this.settings.legend.cnvTitle,this.settings.legend.lohTitle,this.settings.legend.fusionTitle,this.snvArcsMapper?this.snvArcsMapper.snvClassMap:new Map,this.cnvArcsMapper?this.cnvArcsMapper.cnvClassMap:new Map,p.length>0,g);const f=new pt(i,o,this.nonExonicArcRing,this.snvArcRing,this.cnvArcRing,this.lohArcRing);return new Y(this.settings,f,m,p,e.filteredSnvData.length,e.snvData.length-e.nonExonicSnvData.length)}}class mt{constructor(t){this.settings=t}map(t){var e;const s=t.args.chromosomes;const n=t.args.genome.majorchr;const i=t.args.sampleName;const o=t.args.genome;const r=((e=o===null||o===void 0?void 0:o.geneset)===null||e===void 0?void 0:e[0])?o.geneset[0].lst:[];const a=t.args.data;const l=new W(this.settings,n,s);const c=new j(this.settings,l,i,r);return new gt(this.settings,c,l,i).map(a)}}mt.dtNums=[2,5,4,10,1,"exonic","non-exonic"];mt.dtAlias={1:"snv",2:"sv",3:"geneexpression",4:"cnv",5:"sv",6:"snv",7:"snv",8:"snv",9:"snv",10:"loh"};mt.snvClassLayer={M:"exonic",E:"exonic",F:"exonic",N:"exonic",S:"exonic",D:"exonic",I:"exonic",P:"exonic",L:"exonic",Utr3:"exonic",Utr5:"exonic",mnv:"non-exonic",ITD:"non-exonic",insertion:"non-exonic",deletion:"non-exonic",Intron:"non-exonic",X:"non-exonic",noncoding:"non-exonic"};class ft{constructor(t,e){this.cvnCapping=t;this.onClickCallback=e}map(t){const e=[];let s=0;if(t.snvClassMap){this.mapSnv(t,e,s++)}if(t.cnvClassMap){this.mapCnv(t,e,s++)}if(t.lohLegend){this.mapLoh(t,e,s++)}if(t.fusionLegend){this.mapFusion(t,e,s++)}return e}mapSnv(t,e,s){const n=[];let i=0;for(const[e,s]of t.snvClassMap){n.push({termid:t.snvTitle,key:e,text:`${s.snvType} (${s.count})`,color:s.color,order:i++,border:"1px solid #ccc"})}e.push({name:t.snvTitle,order:s,items:n})}mapCnv(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(it.Gain);const i=t.cnvClassMap.get(it.Loss);const o=t.cnvClassMap.get(it.Cap);if(n&&i&&o){let r=0;const a=[];if(n.value>0){a.push({termid:t.cnvTitle,key:it.Gain,text:`Max: ${n.value}`,color:n.color,order:r++,border:"1px solid #ccc"})}if(i.value<0){a.push({termid:t.cnvTitle,key:it.Loss,text:`Min: ${i.value}`,color:i.color,order:r++,border:"1px solid #ccc"})}a.push({termid:t.cnvTitle,key:it.Cap,text:`Capping: ${o.value}`,color:o.color,order:r++,border:"1px solid #ccc",onClickCallback:this.onClickCallback});e.push({name:t.cnvTitle,order:s,items:a})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:T.Interchromosomal,text:"Interchromosomal",color:T.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:T.Intrachromosomal,text:"Intrachromosomal",color:T.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class vt{constructor(t,e,s){this.fontSize=e;this.legendJSONMapper=new ft(t,s)}render(t,e,s,n,i){const o=c({holder:t.append("g"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const r={xOffset:s};const a=this.legendJSONMapper.map(e);o(a,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:r,fontsize:this.fontSize})})}}class At{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=m().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=r().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const o=t.append("g");o.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");o.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${i.centroid(t)}) rotate(${t.data.angle*180/Math.PI-90})${t.data.angle>Math.PI?"rotate(180)":""}`)).attr("dy","0.35em").attr("text-anchor","middle").text((t=>t.data.text)).style("fill","white")}}class xt{constructor(t,e){this.animationDuration=t;this.geneClickListener=e}render(t,e,s){const i=t.append("g");const o=u().x((t=>t.x)).y((t=>t.y));const r=V.create();i.selectAll(".group").data(e).enter().append("g").attr("class","group").each(((t,e,s)=>{const i=n(s[e]);i.append("text").attr("class","chord-text").attr("dy",".35em").attr("transform",t.transform).style("text-anchor",t.textAnchor).style("font-size","12px").style("fill",t.color).style("cursor","pointer").text(t.text).on("click",(()=>{if(t.mutationsTooltip){this.geneClickListener(t.text,t.mutationsTooltip.map((t=>t.mname)))}})).on("mouseover",(e=>{r.d.style("padding","2px").html(this.createTooltipHtml(t));r.show(e.x,e.y)})).on("mouseout",(()=>{r.hide()}));i.append("path").attr("class","chord-tick").datum(t.line.points).style("stroke",t.color).style("fill","none").attr("d",o)}));i.selectAll(".group").each(((t,e,i)=>{const r=s?s.find((e=>e.text===t.text)):undefined;if(r){const t=n(i[e]);t.selectAll(".chord-text").datum(r).transition().duration(this.animationDuration).attr("transform",r.transform).style("text-anchor",r.textAnchor);t.selectAll(".chord-tick").datum(r.line.points).transition().duration(this.animationDuration).style("fill","none").attr("d",o)}}))}createTooltipHtml(t){let e="";if(t.mutationsTooltip){e+=`Gene: ${t.text} <br />`;t.mutationsTooltip.forEach((t=>{e+=`Consequence: ${t.mname} <span style="color: ${t.color}" >${t.dataClass}</span> <br />Mutation: ${t.chr}:${t.position} <br />`}))}if(t.fusionTooltip){e+=`Data type: Fusion transcript <br />`;t.fusionTooltip.forEach((t=>{e+=`Break points: ${t.geneA?t.geneA:""} ${t.chrA}:${t.posA} ${t.strandA=="+"?"forward":"reverse"} > `+`${t.geneB?t.geneB:""} ${t.chrB}:${t.posB} ${t.strandB=="+"?"forward":"reverse"} <br /> `}))}if(t.cnvTooltip){t.cnvTooltip.forEach((t=>{e+=`CNV: <span style="color: ${t.color}">${t.value}</span> ${t.chr}:${t.start}-${t.stop}`}))}return e}}function Rt(t={}){const e={downloadImgName:"disco.plot",rings:{nonExonicRingWidth:20,snvRingWidth:20,lohRingWidth:20,cnvRingWidth:30,snvRingFilters:["exonic"],chromosomeInnerRadius:190,chromosomeWidth:20,labelLinesInnerRadius:210,labelsToLinesDistance:30,labelsToLinesGap:2,nonExonicRingEnabled:true,nonExonicFilterValues:["non-exonic"]},verticalPadding:70,horizontalPadding:500,layerScaler:1,padAngle:.002,label:{fontSize:12,maxDeltaAngle:.05,animationDuration:1e3,overlapAngleFactor:5,prioritizeGeneLabelsByGeneSets:false,showPrioritizeGeneLabelsByGeneSets:false},cnv:{capping:5,ampColor:"#D6683C",lossColor:"#67a9cf",cappedAmpColor:"#8B0000",cappedLossColor:"#00008B",unit:"Unit"},snv:{maxMutationCount:1e4},legend:{snvTitle:"SNV",cnvTitle:"CNV",lohTitle:"LOH",fusionTitle:"SV",lohLegendEnabled:true,fontSize:12,rowHeight:48},menu:{padding:5}};return i(e,t)}class bt{constructor(t){this.geneClickListener=t}render(t,e){const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Gene: ${e.text} <br />${e.mname} <br /> <span style="color:${e.color}">${e.dataClass}</span> <br /> ${e.chr}:${e.pos}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Mt{constructor(t,e){this.svnWidth=t;this.geneClickListener=e}render(t,e){if(e.length>0){const s=e[0].innerRadius;const n=new D(s,this.svnWidth,"#6464641A");n.render(t)}const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Gene: ${e.text} <br />${e.mname} <br /> <span style="color:${e.color}">${e.dataClass}</span> <br /> ${e.chr}:${e.pos}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Ct{render(t,e){const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Loss of Heterozygosity  <br /> ${e.chr}:${e.start}-${e.stop}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()}))}}class yt{constructor(t){this.menuPadding=t}render(t,e){const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Copy Number Variation <br /> ${e.chr}:${e.start}-${e.stop} <br /> ${e.unit}: ${e.value}  `);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()}))}}class It{constructor(t){this.type="Disco";this.opts=t}getState(t){return t.plots.find((t=>t.id===this.id))}main(){return e(this,void 0,void 0,(function*(){const t=new G(this);const e=this.state.settings;const s=new mt(e);const n=s.map(this.app.getState());const i=this.opts.holder;i.selectAll("*").remove();const o=new vt(e.cnv.capping,e.label.fontSize,t.cappingClickCallback);const r=new B(this.getRingRenderers(e,t.geneClickListener),o,t.downloadClickListener,t.prioritizeGenesCheckboxListener);r.render(i,n)}))}getRingRenderers(t,e){const s=new At(t.padAngle,t.rings.chromosomeInnerRadius,t.rings.chromosomeInnerRadius+t.rings.chromosomeWidth);const n=new xt(t.label.animationDuration,e);const i=new bt(e);const o=new Mt(t.rings.snvRingWidth,e);const r=new yt(t.menu.padding);const a=new Ct;const l=new Map;l.set(Q.CHROMOSOME,s);l.set(Q.LABEL,n);l.set(Q.NONEXONICSNV,i);l.set(Q.SNV,o);l.set(Q.CNV,r);l.set(Q.LOH,a);return l}}const Lt=o(It);const Et=Lt;function St(t){return e(this,void 0,void 0,(function*(){return{chartType:"Disco",subfolder:"disco",extension:"ts",settings:Rt(t.overrides)}}))}export{Et as componentInit,Lt as discoInit,St as getPlotConfig};
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e=y,s=I,n=L,i=L,o=E,r=S,a=w,c=null;function h(){var h,u=e.apply(this,arguments),d=s.apply(this,arguments),p=a.apply(this,arguments)/2,g=M.call(arguments),m=+n.apply(this,(g[0]=u,g)),x=o.apply(this,g)-R,C=r.apply(this,g)-R,y=+i.apply(this,(g[0]=d,g)),I=o.apply(this,g)-R,L=r.apply(this,g)-R;if(!c)c=h=l();if(p>b){if(f(C-x)>p*2+b)C>x?(x+=p,C-=p):(x-=p,C+=p);else x=C=(x+C)/2;if(f(L-I)>p*2+b)L>I?(I+=p,L-=p):(I-=p,L+=p);else I=L=(I+L)/2}c.moveTo(m*v(x),m*A(x));c.arc(0,0,m,x,C);if(x!==I||C!==L){if(t){var E=+t.apply(this,arguments),S=y-E,w=(I+L)/2;c.quadraticCurveTo(0,0,S*v(I),S*A(I));c.lineTo(y*v(w),y*A(w));c.lineTo(S*v(L),S*A(L))}else{c.quadraticCurveTo(0,0,y*v(I),y*A(I));c.arc(0,0,y,I,L)}}c.quadraticCurveTo(0,0,m*v(x),m*A(x));c.closePath();if(h)return c=null,h+""||null}if(t)h.headRadius=function(e){return arguments.length?(t=typeof e==="function"?e:C(+e),h):t};h.radius=function(t){return arguments.length?(n=i=typeof t==="function"?t:C(+t),h):n};h.sourceRadius=function(t){return arguments.length?(n=typeof t==="function"?t:C(+t),h):n};h.targetRadius=function(t){return arguments.length?(i=typeof t==="function"?t:C(+t),h):i};h.startAngle=function(t){return arguments.length?(o=typeof t==="function"?t:C(+t),h):o};h.endAngle=function(t){return arguments.length?(r=typeof t==="function"?t:C(+t),h):r};h.padAngle=function(t){return arguments.length?(a=typeof t==="function"?t:C(+t),h):a};h.source=function(t){return arguments.length?(e=t,h):e};h.target=function(t){return arguments.length?(s=t,h):s};h.context=function(t){return arguments.length?(c=t==null?null:t,h):c};return h}function N(){return O()}class D{constructor(t,e,s){this.radius=t;this.width=e;this.color=s}render(t){const e=r();const s={startAngle:0,endAngle:Math.PI*2,innerRadius:this.radius,outerRadius:this.radius+this.width,color:this.color,text:"No label"};const n=[];n.push(s);const i=t.append("g");i.selectAll("path").data(n).enter().append("path").attr("d",(t=>e(t))).attr("fill",(t=>t.color))}}class V{static create(){const e=new t({padding:5});e.d.style("border","1px solid #FFF").style("position","absolute").style("z-index",1001);return e}}var T;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(T||(T={}));class z{static getColor(t,e){if(t!=e){return T.Interchromosomal.valueOf()}else{return T.Intrachromosomal.valueOf()}}}class k{render(t,e){let s=0;if(e.length>0){s=e[0].target.radius;const n=new D(s,2,"#6464641A");n.render(t)}const n=N().radius(s);const i=t.selectAll(".chord").data(e);const o=V.create();i.enter().append("path").attr("class","chord").attr("d",n).attr("fill",(t=>z.getColor(t.source.positionInChromosome.chromosome,t.target.positionInChromosome.chromosome))).on("mouseover",((t,e)=>{o.d.style("padding","2px").html(this.getTooltip(e));o.show(t.x,t.y)})).on("mouseout",(()=>{o.hide()}))}getTooltip(t){let e="";if(t.source.gene){e+=t.source.gene}const s=t.source.positionInChromosome;e+=` ${s.chromosome}:${s.position}<br />`;if(t.target.gene){e+=t.target.gene}const n=t.target.positionInChromosome;e+=` ${n.chromosome}:${n.position}`;return e}}class P{constructor(t){this.downloadClickListener=t}render(t,e){t.append("span").append("button").style("margin","2px 0 2px 30px").text("Download image").on("click",(()=>{const t=e.select("svg").node();this.downloadClickListener(t)}))}}class ${constructor(t){this.checkBoxClickListener=t}render(t,e,s,n,i){if(s){const s=t.append("span").append("input").attr("type","checkbox").attr("id","genes-checkbox").property("checked",e);t.append("label").attr("for","genes-checkbox").text(`Prioritize Cancer Gene Census (${n} mutations out of ${i} total)`);s.on("change",(()=>{this.checkBoxClickListener(s.property("checked"))}))}}}class B{constructor(t,e,s,n){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new k;this.downloadButtonRenderer=new P(s);this.prioritizeGenesCheckboxRenderer=new $(n)}render(t,e){const s=t.append("div");s.append("div");const n=s.append("div").style("display","inline-block").style("font-family","Arial");const i=n.append("div");this.downloadButtonRenderer.render(i,n);this.prioritizeGenesCheckboxRenderer.render(i,e.settings.label.prioritizeGeneLabelsByGeneSets,e.settings.label.showPrioritizeGeneLabelsByGeneSets,e.filteredSnvDataLength,e.svnDataLength);const o=n.append("svg").attr("width",e.width).attr("height",e.height+e.legendHeight);const r=o.append("g").attr("class","mainG").attr("transform",`translate(${e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+100},${e.height/2})`);for(const[t,s]of this.renders){const n=e.getElements(t);const i=e.getCollisions(t);s.render(r,n,i)}this.fusionRenderer.render(r,e.fusions);this.legendRenderer.render(r,e.legend,-1*(e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+50),e.width,e.height/2)}}class G{constructor(t){this.downloadImgName=t.state.settings.downloadImgName||"disco.plot";this.cappingClickCallback=(e,s)=>{const n=t.app.tip;n.clear();const i=t.app.tip.d;const o=i.append("span").html("Capping:").append("input").attr("type","number").on("change",(()=>{t.app.dispatch({type:"plot_edit",id:t.opts.id,config:{settings:{cnv:{capping:Number(o.property("value"))}}}});n.hide()}));const r=s.node().getBoundingClientRect();const a=r.left-20;const l=r.top-40;n.show(a,l)};this.downloadClickListener=t=>{const e=document.createElement("a");document.body.appendChild(e);e.addEventListener("click",(()=>{const s=new XMLSerializer;const n=new Blob([s.serializeToString(t)],{type:"image/svg+xml"});e.download=this.downloadImgName+".svg";e.href=URL.createObjectURL(n);document.body.removeChild(e)}),false);e.click()};this.geneClickListener=(s,n)=>e(this,void 0,void 0,(function*(){const e={holder:t.app.opts.holder,genome:t.app.opts.state.args.genome,nobox:true,query:s,tklst:[{type:"mds3",dslabel:t.app.opts.state.dslabel,hlaachange:n.join(",")}]};const i=yield import("./app-172cc04d.js").then((function(t){return t.bX}));yield i.default(e)}));this.prioritizeGenesCheckboxListener=e=>{t.app.dispatch({type:"plot_edit",id:t.opts.id,config:{settings:{label:{prioritizeGeneLabelsByGeneSets:e}}}})}}}class W{constructor(t,e,s){this.chromosomes=[];this.chromosomesOrder=[];this.keysArray=[];this.totalSizeArray=[];this.chrSizesArray=[];const n=s||e;this.settings=t;this.chromosomesOrder=[];let i=0;this.totalPadAngle=Object.keys(n).length*this.settings.padAngle;this.totalChromosomesAngle=2*Math.PI-this.totalPadAngle;for(const t in n){const e=t.slice(0,3)==="chr"?t.slice(3):t;this.chromosomesOrder.push(t);this.keysArray.push(e);this.totalSizeArray.push(i);this.chrSizesArray.push(n[t]);i+=n[t]}this.totalSize=i;let o=0;for(let t=0;t<this.keysArray.length;t++){const e=this.totalChromosomesAngle*(this.chrSizesArray[t]/i);const s=t==0?this.settings.padAngle/2:o+this.settings.padAngle;const n=t==0?this.settings.padAngle/2+e:o+this.settings.padAngle+e;const r={start:this.totalSizeArray[t],size:this.chrSizesArray[t],factor:1,startAngle:s,endAngle:n,angle:(s+n)/2,innerRadius:this.settings.chromosomeInnerRadius,outerRadius:this.settings.chromosomeInnerRadius+this.settings.chromosomeWidth,color:"#AAA",text:this.keysArray[t]};this.chromosomes.push(r);if(r.endAngle!=null){o=r.endAngle}}}}class F{constructor(t,e){this.sampleName=t;this.prioritizedGenes=e}map(t){return{dt:t.dt,mname:t.mname,mClass:t.class,gene:t.gene,chr:t.chr,ref:t.ref,alt:t.alt,position:t.pos?t.pos:t.position,poschr:t.poschr,posbins:t.posbins,poslabel:t.poslabel,sampleName:this.sampleName,ssm_id:t.ssm_id,start:t.start,stop:t.stop,value:t.value,segmean:t.segmean,isPrioritized:this.prioritizedGenes.some((e=>e==t.gene)),chrA:t.chrA,chrB:t.chrB,geneA:t.geneA,geneB:t.geneB,posA:t.posA,posB:t.posB,strandA:t.strandA,strandB:t.strandB}}}var H;(function(t){t[t["SNV"]=1]="SNV";t[t["FUSION"]=2]="FUSION";t[t["CNV"]=4]="CNV";t[t["SV"]=5]="SV";t[t["LOH"]=10]="LOH"})(H||(H={}));class j{constructor(t,e,s,n=[]){this.labelData=[];this.nonExonicSnvData=[];this.nonExonicInnerRadius=0;this.snvRingDataMap=new Map;this.snvInnerRadius=0;this.snvData=[];this.bpx=0;this.onePxArcAngle=0;this.filteredSnvData=[];this.lohData=[];this.lohInnerRadius=0;this.cnvData=[];this.cnvInnerRadius=0;this.fusionData=[];this.fusionRadius=0;this.hasPrioritizedGenes=false;this.cnvMaxValue=undefined;this.cnvMinValue=undefined;this.lohMaxValue=undefined;this.lohMinValue=undefined;this.snvFilter=t=>t.dt==H.SNV;this.fusionFilter=t=>t.dt==H.FUSION||t.dt==H.SV;this.cnvFilter=t=>t.dt==H.CNV;this.lohFilter=t=>t.dt==H.LOH;this.compareData=(t,e)=>{const s=this.reference.chromosomesOrder.indexOf(t.chr)-this.reference.chromosomesOrder.indexOf(e.chr);if(s!=0){return s}const n=t.pos?t.pos:t.start;const i=e.pos?e.pos:e.start;return n-i};this.settings=t;this.reference=e;this.sample=s;this.lastInnerRadious=this.settings.rings.chromosomeInnerRadius;this.nonExonicFilter=e=>t.rings.nonExonicFilterValues.includes(mt.snvClassLayer[e.mClass]);this.snvRingFilter=e=>{if(n.length>0&&this.settings.label.prioritizeGeneLabelsByGeneSets){return n.includes(e.gene)&&t.rings.snvRingFilters.includes(mt.snvClassLayer[e.mClass])}else{return t.rings.snvRingFilters.includes(mt.snvClassLayer[e.mClass])}};this.dataObjectMapper=new F(s,n)}map(t){const e=[];t.forEach((t=>{const s=this.reference.chromosomesOrder.indexOf(t.chr);const n=this.reference.chromosomesOrder.indexOf(t.chrA);const i=this.reference.chromosomesOrder.indexOf(t.chrB);if(t.dt==H.SNV){if(s!=-1&&this.snvData.length<this.settings.snv.maxMutationCount){this.addData(t,e)}}else if(t.dt==H.FUSION||t.dt==H.SV){if(n!=-1&&i!=-1){this.addData(t,e)}}else if([H.CNV,H.LOH].includes(Number(t.dt))){this.addData(t,e)}else{throw Error("Unknown mutation type!")}}));const s=e.sort(this.compareData);if(this.settings.rings.nonExonicRingEnabled){s.forEach((t=>{this.filterNonExonicSnvData(t)}))}if(this.nonExonicSnvData.length>0){this.nonExonicInnerRadius=this.lastInnerRadious-this.settings.rings.nonExonicRingWidth;this.lastInnerRadious=this.nonExonicInnerRadius}s.forEach((t=>{this.filterSnvs(t)}));s.forEach((t=>{this.filterLohs(t)}));if(this.lohData.length>0){this.lohInnerRadius=this.lastInnerRadious-this.settings.rings.lohRingWidth;this.lastInnerRadious=this.lohInnerRadius}s.forEach((t=>{this.filterCnvs(t)}));if(this.cnvData.length>0){this.cnvInnerRadius=this.lastInnerRadious-this.settings.rings.cnvRingWidth;this.lastInnerRadious=this.cnvInnerRadius}s.forEach((t=>{this.filterFusion(t)}));if(this.fusionData.length>0){this.fusionRadius=this.lastInnerRadious}const n={labelData:this.labelData,nonExonicSnvData:this.nonExonicSnvData,nonExonicInnerRadius:this.nonExonicInnerRadius,snvRingDataMap:this.snvRingDataMap,snvInnerRadius:this.snvInnerRadius,snvData:this.snvData,bpx:this.bpx,onePxArcAngle:this.onePxArcAngle,filteredSnvData:this.filteredSnvData,lohData:this.lohData,lohInnerRadius:this.lohInnerRadius,cnvData:this.cnvData,cnvInnerRadius:this.cnvInnerRadius,fusionData:this.fusionData,fusionRadius:this.fusionRadius,hasPrioritizedGenes:this.hasPrioritizedGenes,cnvMaxValue:this.cnvMaxValue,cnvMinValue:this.cnvMinValue,lohMaxValue:this.lohMaxValue,lohMinValue:this.lohMinValue};return n}addData(t,e){const s=this.dataObjectMapper.map(t);if(s.isPrioritized){this.hasPrioritizedGenes=true}e.push(s)}filterNonExonicSnvData(t){if(this.snvFilter(t)){if(this.settings.rings.nonExonicRingEnabled&&this.nonExonicFilter(t)){this.nonExonicSnvData.push(t)}}}filterSnvs(t){if(this.snvFilter(t)){this.snvData.push(t);if(this.snvRingFilter(t)){if(this.snvInnerRadius==0){this.snvInnerRadius=this.lastInnerRadious-this.settings.rings.snvRingWidth;this.lastInnerRadious=this.snvInnerRadius;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*this.snvInnerRadius));this.onePxArcAngle=1/this.snvInnerRadius}this.filteredSnvData.push(t);this.labelData.push(t);const e=this.calculateArcAngle(t);let s=this.snvRingDataMap.get(e);if(!s){s=new Array}s.push(t);this.snvRingDataMap.set(e,s)}}}filterFusion(t){if(this.fusionFilter(t)){t.isPrioritized=true;this.fusionData.push(t);this.labelData.push(t)}}filterLohs(t){if(this.lohFilter(t)){if(this.lohMaxValue==undefined||this.lohMaxValue<t.value){this.lohMaxValue=t.segmean}if(this.lohMinValue==undefined||this.lohMinValue>t.value){this.lohMinValue=t.segmean}this.lohData.push(t)}}filterCnvs(t){if(this.cnvFilter(t)){if(this.cnvMaxValue==undefined||this.cnvMaxValue<t.value){this.cnvMaxValue=t.value}if(this.cnvMinValue==undefined||this.cnvMinValue>t.value){this.cnvMinValue=t.value}this.cnvData.push(t)}}calculateArcAngle(t){const e=this.reference.chromosomes[this.reference.chromosomesOrder.findIndex((e=>t.chr==e))];const s=Math.floor(t.position/this.bpx);return e.startAngle+s*this.onePxArcAngle}}class U{constructor(t,e,s,n,i,o,r,a){this.snvTitle=t;this.cnvTitle=e;this.lohTitle=s;this.fusionTitle=n;this.snvClassMap=i;this.cnvClassMap=o;this.lohLegend=a;this.fusionLegend=r}legendCount(){return(this.snvClassMap.size>0?1:0)+(this.cnvClassMap.size>0?1:0)+(this.lohLegend?1:0)+(this.fusionLegend?1:0)}}class X{constructor(t,e,s,n,i){this.source=t;this.target=e;this.genes=s;this.count=n;this.endpts=i}}class q{constructor(t,e,s,n,i,o,r){this.startAngle=t;this.endAngle=e;this.radius=s;this.gene=n;this.value=i;this.genes=o;this.positionInChromosome=r}}class _{constructor(t,e,s){this.radius=t;this.sampleName=e;this.reference=s}map(t){const e=[];t.forEach((t=>{const s=new Set;s.add(t.geneA);s.add(t.geneB);const n=new q(this.calculateStartAngle(t.chrA,t.posA),this.calculateEndAngle(t.chrA,t.posA),this.radius,t.geneA,t.value,s,{chromosome:t.chrA,position:t.posA});const i=new q(this.calculateStartAngle(t.chrB,t.posB),this.calculateEndAngle(t.chrB,t.posB),this.radius,t.geneB,t.value,s,{chromosome:t.chrB,position:t.posB});const o=new X(n,i,"genes",-1,"Endpoints");e.push(o)}));return e}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)-.01}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return.01+n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class J{static provide(t){const e=Math.min(Math.max(t,0),1);const s=Math.round(e*255);return`rgb(${s}, ${s}, ${s})`}}class K{constructor(t,e){this.minValue=t;this.maxValue=e;this.colorStartValue=J.provide(t);this.colorEndValue=J.provide(e)}}var Q;(function(t){t[t["CHROMOSOME"]=0]="CHROMOSOME";t[t["LABEL"]=1]="LABEL";t[t["NONEXONICSNV"]=2]="NONEXONICSNV";t[t["SNV"]=3]="SNV";t[t["CNV"]=4]="CNV";t[t["LOH"]=5]="LOH";t[t["FUSION"]=6]="FUSION"})(Q||(Q={}));class Y{constructor(t,e,s,n,i,o){this.settings=t;this.rings=e;this.legend=s;this.fusions=n;this.width=1.2*(this.settings.horizontalPadding+this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance);this.height=2*(this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance+this.settings.verticalPadding);this.legendHeight=this.calculateLegendHeight(s);this.svnDataLength=o;this.filteredSnvDataLength=i}getElements(t){switch(t){case Q.CHROMOSOME:return this.rings.chromosomesRing?this.rings.chromosomesRing.elements:[];case Q.LABEL:return this.rings.labelsRing.elementsToDisplay;case Q.NONEXONICSNV:return this.rings.nonExonicArcRing?this.rings.nonExonicArcRing.elements:[];case Q.SNV:return this.rings.snvArcRing?this.rings.snvArcRing.elements:[];case Q.CNV:return this.rings.cnvArcRing?this.rings.cnvArcRing.elements:[];case Q.LOH:return this.rings.lohArcRing?this.rings.lohArcRing.elements:[];default:throw new Error(`ringType ${t} not defined`)}}getCollisions(t){if(t==Q.LABEL){return this.rings.labelsRing.collisions}else{return undefined}}calculateLegendHeight(t){const e=this.settings.legend.rowHeight;return e*t.legendCount()}}class Z{constructor(t,e,s){this.innerRadius=t;this.outerRadius=t+e;this.width=e;this.elements=s}}class tt{constructor(){const t={};for(const e in s){t[s[e].label]=s[e];t[e]=s[e]}this.mlabel=t}static getInstance(){if(!tt.instance){tt.instance=new tt}return tt.instance}}class et{constructor(t,e,s){this.snvType=t;this.color=e;this.count=s}}class st{constructor(t,e,s,n){this.snvClassMap=new Map;this.svnInnerRadius=t;this.svnWidth=e;this.sampleName=s;this.reference=n;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*t));this.onePxArcAngle=1/t}map(t){const e=[];for(const s of t.keys()){const n=t.get(s);if(n){const t=n.length;for(let i=0;i<n.length;i++){const o=n[i];const r=this.snvClassMap.get(o.mClass);if(r){this.snvClassMap.set(o.mClass,this.createSnvLegend(o.mClass,++r.count))}else{this.snvClassMap.set(o.mClass,this.createSnvLegend(o.mClass,1))}const a=s;const l=s+this.onePxArcAngle;const c=tt.getInstance().mlabel?tt.getInstance().mlabel[o.mClass]:undefined;const h={startAngle:a,endAngle:l,innerRadius:this.svnInnerRadius+i*this.svnWidth/t,outerRadius:this.svnInnerRadius+(i+1)*this.svnWidth/t,color:c.color,text:o.gene,dataClass:c.label,mname:o.mname,chr:o.chr,pos:o.position};e.push(h)}}}return e}createSnvLegend(t,e){const s=tt.getInstance().mlabel[t];return new et(s.label,s.color,e)}}class nt{constructor(t,e,s,n){this.text=t;this.cnvType=e;this.color=s;this.value=n}}var it;(function(t){t[t["Loss"]=0]="Loss";t[t["Gain"]=1]="Gain";t[t["Cap"]=2]="Cap"})(it||(it={}));class ot{static getColor(t,e){const s=e.cnv;const n=e.cnv.capping;const i=-1*e.cnv.capping;if(t<i){return s.cappedLossColor}else if(t>=i&&t<=0){return s.lossColor}else if(t>0&&t<=n){return s.ampColor}else{return s.cappedAmpColor}}}class rt{constructor(t,e,s,n,i,o=0,r=0,a=""){this.cnvClassMap=new Map;this.cnvInnerRadius=t;this.cnvWidth=e;this.settings=s;this.sampleName=n;this.reference=i;this.cnvMaxValue=o;this.cnvMinValue=r;this.cnvUnit=a;this.gainCapped=this.settings.cnv.capping;this.lossCapped=-1*this.settings.cnv.capping;this.lossOnly=o<=0;this.gainOnly=r>=0;this.onePxArcAngle=1/this.cnvInnerRadius;const l=new nt("Max",o>0?it.Gain:it.Loss,this.getColor(o),o);const c=new nt("Min",r>0?it.Gain:it.Loss,this.getColor(r),r);const h=new nt("Capping",it.Loss,this.getColor(r>0?r:o),this.settings.cnv.capping);this.cnvClassMap.set(it.Gain,l);this.cnvClassMap.set(it.Loss,c);this.cnvClassMap.set(it.Cap,h);this.maxAbsValue=Math.max(Math.abs(this.capMaxValue(r)),Math.abs(this.capMaxValue(o)))}map(t){const e=[];t.forEach((t=>{let s=this.calculateStartAngle(t);let n=this.calculateEndAngle(t);if(n-s<this.onePxArcAngle){const t=this.onePxArcAngle-(n-s);s=s-t/2;n=s+t/2}const i=this.calculateInnerRadius(t);const o=this.calculateOuterRadius(t);const r=this.getColor(t.value);const a={startAngle:s,endAngle:n,innerRadius:i,outerRadius:o,color:r,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.value,unit:this.cnvUnit};e.push(a)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}getColor(t){return ot.getColor(t,this.settings)}calculateInnerRadius(t){if(this.gainOnly){return this.cnvInnerRadius}if(this.lossOnly){const e=this.cnvInnerRadius+this.cnvWidth;return e-this.capMinValue(this.cnvWidth*this.capMaxValue(t.value)/this.maxAbsValue)}const e=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return e}if(Math.sign(t.value)==-1){return e+this.capMinValue(this.capMaxValue(t.value)/this.maxAbsValue*(this.cnvWidth/2))}return 1}calculateOuterRadius(t){const e=this.cnvInnerRadius+this.cnvWidth;if(this.gainOnly){return this.cnvInnerRadius+this.capMinValue(this.cnvWidth*this.capMaxValue(t.value)/this.maxAbsValue)}if(this.lossOnly){return e}const s=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return s+this.capMinValue(this.capMaxValue(t.value)/this.maxAbsValue*(this.cnvWidth/2))}if(Math.sign(t.value)==-1){return s}return 1}capMaxValue(t){if(Math.sign(t)==1){return t>this.gainCapped?this.gainCapped:t}if(Math.sign(t)==-1){return t<this.lossCapped?this.lossCapped:t}return 0}capMinValue(t,e=1){if(Math.sign(t)==1){return t>e?t:e}if(Math.sign(t)==-1){return t<-1*e?t:-1*e}return 1}}class at{constructor(t,e){this.points=new Array;this.points=t;this.color=e}}class lt{static createLabel(t,e,s,n,i,o,r,a,l,c,h=false,u,d,p){const g=(t+e)/2;const m=g-Math.PI/2;const f=`rotate(${g*180/Math.PI-90}) translate(${n})${g>Math.PI?"rotate(180)":""}`;const v=g>Math.PI?"end":"";const A=s;const x=n-u;const R=[];const b={x:A*Math.cos(m),y:A*Math.sin(m)};const M={x:x*Math.cos(m),y:x*Math.sin(m)};R.push(b);R.push(M);const C=new at(R,r);const y={startAngle:t,endAngle:e,innerRadius:s,outerRadius:n,angle:g,value:i,text:o,color:r,transform:f,textAnchor:v,ccAngle:m,line:C,isPrioritized:h,start:c,stop:c,chr:l,mutationsTooltip:d?[d]:undefined,fusionTooltip:p?[p]:undefined};return y}static createMovedLabel(t,e){const s=t.startAngle+e;const n=t.endAngle+e;const i=(s+n)/2;const o=i-Math.PI/2;const r=t.innerRadius;const a=t.outerRadius-2;const l=(a-r)/3;const c=Math.cos(t.ccAngle);const h=Math.sin(t.ccAngle);const u=Math.cos(t.ccAngle+e);const d=Math.sin(t.ccAngle+e);const p=[];const g={x:r*c,y:r*h};const m={x:(r+l)*c,y:(r+l)*h};const f={x:(r+2*l)*u,y:(r+2*l)*d};const v={x:(r+3*l)*u,y:(r+3*l)*d};p.push(g);p.push(m);p.push(f);p.push(v);const A=new at(p,t.color);const x="rotate("+(i*180/Math.PI-90)+")"+"translate("+t.outerRadius+")"+(i>Math.PI?"rotate(180)":"");const R=i>Math.PI?"end":"";const b=t.mutationsTooltip?t.mutationsTooltip[0].color:t.fusionTooltip?t.fusionTooltip[0].color:undefined;const M={startAngle:s,endAngle:n,innerRadius:t.innerRadius,outerRadius:t.outerRadius,angle:i,value:t.value,text:t.text,transform:x,textAnchor:R,ccAngle:o,color:b,line:A,isPrioritized:t.isPrioritized,start:t.start,stop:t.stop,chr:t.chr,mutationsTooltip:t.mutationsTooltip,fusionTooltip:t.fusionTooltip};return M}}class ct{constructor(t,e,s){this.labelMap=new Map;this.settings=t;this.sampleName=e;this.reference=s}map(t,e=[]){const s=this.settings.rings.labelLinesInnerRadius;const n=s+this.settings.rings.labelsToLinesDistance;t.forEach((t=>{if(t.dt==H.SNV){const e=this.calculateStartAngle(t.chr,t.position);const i=this.calculateEndAngle(t.chr,t.position);const o=tt.getInstance().mlabel?tt.getInstance().mlabel[t.mClass]:undefined;this.addLabelOrMutation(t,t.gene,t.mname,e,i,s,n,o.color,o.label)}if(t.dt==H.FUSION){const e=z.getColor(t.chrA,t.chrB);if(t.geneA){const i=this.calculateStartAngle(t.chrA,t.posA);const o=this.calculateEndAngle(t.chrA,t.posA);this.addLabelOrFusion(t,t.geneA,t.posA,i,o,s,n,e)}if(t.geneB&&t.geneA!=t.geneB){const i=this.calculateStartAngle(t.chrB,t.posB);const o=this.calculateEndAngle(t.chrB,t.posB);this.addLabelOrFusion(t,t.geneB,t.posB,i,o,s,n,e)}}}));const i=Array.from(this.labelMap.values());i.forEach((t=>{e.forEach((e=>{if(t.stop>=e.start&&e.stop>=t.start&&t.chr==e.chr){const s={value:e.value,color:ot.getColor(e.value,this.settings),chr:e.chr,start:e.start,stop:e.stop};if(t.cnvTooltip){t.cnvTooltip.push(s)}else{t.cnvTooltip=[];t.cnvTooltip.push(s)}}}))}));return Array.from(this.labelMap.values())}addLabelOrMutation(t,e,s,n,i,o,r,a,l){const c=this.labelMap.get(e);const h={mname:s,color:a,dataClass:l,chr:t.chr,position:t.position};if(!c){this.labelMap.set(e,lt.createLabel(n,i,o,r,t.value,e,a,l,t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,h))}else{if(c.mutationsTooltip){c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}else{c.mutationsTooltip=[];c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}}}addLabelOrFusion(t,e,s,n,i,o,r,a){const l=this.labelMap.get(e);const c={color:a,chrA:t.chrA,chrB:t.chrB,posA:t.posA,posB:t.posB,geneA:t.geneA,geneB:t.geneB,strandA:t.strandA,strandB:t.strandB};if(!l){this.labelMap.set(e,lt.createLabel(n,i,o,r,t.value,e,a,"Fusion transcript",t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,undefined,c))}else{if(l.fusionTooltip){l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}else{l.fusionTooltip=[];l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}}}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class ht extends Z{constructor(t,e,s){super(t.rings.labelLinesInnerRadius,t.rings.labelsToLinesDistance,e.sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0)));this.elementsToDisplay=[];this.settings=t;this.hasPrioritizedGenes=s;const n=2*Math.PI*(t.rings.labelLinesInnerRadius+t.rings.labelsToLinesDistance);this.overlapAngle=this.settings.label.overlapAngleFactor*this.settings.label.fontSize/n;this.calculateCollisions()}calculateCollisions(){this.collisions=[];let t=[];t=this.elements.filter((t=>t.isPrioritized));if(this.settings.label.prioritizeGeneLabelsByGeneSets){this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(t)}else if(this.hasPrioritizedGenes){const t=this.elements.filter((t=>t.isPrioritized));const e=this.getLabelsWithPrioritizedGenes(t);const s=this.elements.filter((t=>!t.isPrioritized));const n=[...s,...e].sort(((t,e)=>t.startAngle-e.startAngle));this.elementsToDisplay=this.getAllLabels(n)}else{this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(this.elements)}}getLabelsWithPrioritizedGenes(t){const e=[];let s={endAngle:0};t.forEach(((t,n)=>{if(n==0){e.push(t);s=t}else{const n=s.endAngle-t.startAngle+this.overlapAngle;if(n>0&&n<this.settings.label.maxDeltaAngle){const i=lt.createMovedLabel(t,n);e===null||e===void 0?void 0:e.push(i);s=i}if(n<=0){e.push(t);s=t}}}));return e}getAllLabels(t){var e;const s=[];let n={endAngle:0};const i=t.length;let o=-1;for(let r=0;r<t.length;r++){const a=t[r];if(a.isPrioritized){s.push(a);o=r;n=a;continue}if(r==0){if(i>1){if(this.isElementOverlappingNextCancerGene(t,o,a,0)){continue}s.push(a);n=a}continue}const l=n.endAngle-a.startAngle+this.overlapAngle;if(l>0&&l<this.settings.label.maxDeltaAngle){if(r==length-1){s.push(a);continue}if(this.isElementOverlappingNextCancerGene(t,o,a,l)){continue}const i=lt.createMovedLabel(a,l);(e=this.collisions)===null||e===void 0?void 0:e.push(i);s.push(a);n=i}if(l<=0){if(this.isElementOverlappingNextCancerGene(t,o,a,0)){continue}s.push(a);n=a}}return s}isElementOverlappingNextCancerGene(t,e,s,n){const i=this.getNextLabelWithCancerGene(t,e);if(i){const t=s.endAngle+n-i.startAngle+this.overlapAngle;if(t>0){return true}}return false}getNextLabelWithCancerGene(t,e){return t.find(((t,s)=>t.isPrioritized&&s>e))}}class ut{constructor(t,e,s,n){this.nonExonicInnerRadius=t;this.nonExonicWidht=e;this.sampleName=s;this.reference=n;this.onePxArcAngle=1/t}map(t){const e=this.nonExonicInnerRadius;const s=e+this.nonExonicWidht;const n=[];t.forEach((t=>{const i=tt.getInstance().mlabel?tt.getInstance().mlabel[t.mClass]:undefined;const o=this.calculateStartAngle(t);const r=this.calculateEndAngle(t);const a={startAngle:o,endAngle:r,innerRadius:e,outerRadius:s,color:i.color,text:t.gene,dataClass:i.label,mname:t.mname,chr:t.chr,pos:t.position};n.push(a)}));return n}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)-this.onePxArcAngle}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return this.onePxArcAngle+s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)}}class dt{constructor(t,e,s,n){this.lohInnerRadius=t;this.lohWidth=e;this.sampleName=s;this.reference=n}map(t){const e=[];t.forEach((t=>{const s=this.calculateStartAngle(t);const n=this.calculateEndAngle(t);const i=this.lohInnerRadius;const o=i+this.lohWidth;const r=J.provide(t.segmean);const a={startAngle:s,endAngle:n,innerRadius:i,outerRadius:o,color:r,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.segmean};e.push(a)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}}class pt{constructor(t,e,s,n,i,o){this.labelsRing=t;this.chromosomesRing=e;this.nonExonicArcRing=s;this.snvArcRing=n;this.cnvArcRing=i;this.lohArcRing=o}}class gt{constructor(t,e,s,n){this.nonExonicArcRing=undefined;this.settings=t;this.dataMapper=e;this.reference=s;this.sampleName=n}map(t){const e=this.dataMapper.map(t);const s=new ct(this.settings,this.sampleName,this.reference);const n=s.map(e.labelData,e.cnvData);const i=new ht(this.settings,n,e.hasPrioritizedGenes);const o=new Z(this.settings.rings.chromosomeInnerRadius,this.settings.rings.chromosomeWidth,this.reference.chromosomes);const r=new ut(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,this.sampleName,this.reference);const a=r.map(e.nonExonicSnvData);if(a.length>0){this.nonExonicArcRing=new Z(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,a)}this.snvArcsMapper=new st(e.snvInnerRadius,this.settings.rings.snvRingWidth,this.sampleName,this.reference);const l=this.snvArcsMapper.map(e.snvRingDataMap);if(l.length>0){this.snvArcRing=new Z(e.snvInnerRadius,this.settings.rings.snvRingWidth,l)}const c=new dt(e.lohInnerRadius,this.settings.rings.lohRingWidth,this.sampleName,this.reference);const h=c.map(e.lohData);if(h.length>0){this.lohArcRing=new Z(e.lohInnerRadius,this.settings.rings.lohRingWidth,h)}this.cnvArcsMapper=new rt(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,this.settings,this.sampleName,this.reference,e.cnvMaxValue,e.cnvMinValue,this.settings.cnv.unit);const u=this.cnvArcsMapper.map(e.cnvData);if(u.length>0){this.cnvArcRing=new Z(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,u)}const d=new _(e.fusionRadius,this.sampleName,this.reference);const p=d.map(e.fusionData);let g;if(this.settings.legend.lohLegendEnabled&&e.lohMinValue&&e.lohMaxValue){g=new K(e.lohMinValue,e.lohMaxValue)}const m=new U(this.settings.legend.snvTitle,this.settings.legend.cnvTitle,this.settings.legend.lohTitle,this.settings.legend.fusionTitle,this.snvArcsMapper?this.snvArcsMapper.snvClassMap:new Map,this.cnvArcsMapper?this.cnvArcsMapper.cnvClassMap:new Map,p.length>0,g);const f=new pt(i,o,this.nonExonicArcRing,this.snvArcRing,this.cnvArcRing,this.lohArcRing);return new Y(this.settings,f,m,p,e.filteredSnvData.length,e.snvData.length-e.nonExonicSnvData.length)}}class mt{constructor(t){this.settings=t}map(t){var e;const s=t.args.chromosomes;const n=t.args.genome.majorchr;const i=t.args.sampleName;const o=t.args.genome;const r=((e=o===null||o===void 0?void 0:o.geneset)===null||e===void 0?void 0:e[0])?o.geneset[0].lst:[];const a=t.args.data;const l=new W(this.settings,n,s);const c=new j(this.settings,l,i,r);return new gt(this.settings,c,l,i).map(a)}}mt.dtNums=[2,5,4,10,1,"exonic","non-exonic"];mt.dtAlias={1:"snv",2:"sv",3:"geneexpression",4:"cnv",5:"sv",6:"snv",7:"snv",8:"snv",9:"snv",10:"loh"};mt.snvClassLayer={M:"exonic",E:"exonic",F:"exonic",N:"exonic",S:"exonic",D:"exonic",I:"exonic",P:"exonic",L:"exonic",Utr3:"exonic",Utr5:"exonic",mnv:"non-exonic",ITD:"non-exonic",insertion:"non-exonic",deletion:"non-exonic",Intron:"non-exonic",X:"non-exonic",noncoding:"non-exonic"};class ft{constructor(t,e){this.cvnCapping=t;this.onClickCallback=e}map(t){const e=[];let s=0;if(t.snvClassMap){this.mapSnv(t,e,s++)}if(t.cnvClassMap){this.mapCnv(t,e,s++)}if(t.lohLegend){this.mapLoh(t,e,s++)}if(t.fusionLegend){this.mapFusion(t,e,s++)}return e}mapSnv(t,e,s){const n=[];let i=0;for(const[e,s]of t.snvClassMap){n.push({termid:t.snvTitle,key:e,text:`${s.snvType} (${s.count})`,color:s.color,order:i++,border:"1px solid #ccc"})}e.push({name:t.snvTitle,order:s,items:n})}mapCnv(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(it.Gain);const i=t.cnvClassMap.get(it.Loss);const o=t.cnvClassMap.get(it.Cap);if(n&&i&&o){let r=0;const a=[];if(n.value>0){a.push({termid:t.cnvTitle,key:it.Gain,text:`Max: ${n.value}`,color:n.color,order:r++,border:"1px solid #ccc"})}if(i.value<0){a.push({termid:t.cnvTitle,key:it.Loss,text:`Min: ${i.value}`,color:i.color,order:r++,border:"1px solid #ccc"})}a.push({termid:t.cnvTitle,key:it.Cap,text:`Capping: ${o.value}`,color:o.color,order:r++,border:"1px solid #ccc",onClickCallback:this.onClickCallback});e.push({name:t.cnvTitle,order:s,items:a})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:T.Interchromosomal,text:"Interchromosomal",color:T.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:T.Intrachromosomal,text:"Intrachromosomal",color:T.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class vt{constructor(t,e,s){this.fontSize=e;this.legendJSONMapper=new ft(t,s)}render(t,e,s,n,i){const o=c({holder:t.append("g"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const r={xOffset:s};const a=this.legendJSONMapper.map(e);o(a,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:r,fontsize:this.fontSize})})}}class At{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=m().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=r().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const o=t.append("g");o.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");o.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${i.centroid(t)}) rotate(${t.data.angle*180/Math.PI-90})${t.data.angle>Math.PI?"rotate(180)":""}`)).attr("dy","0.35em").attr("text-anchor","middle").text((t=>t.data.text)).style("fill","white")}}class xt{constructor(t,e){this.animationDuration=t;this.geneClickListener=e}render(t,e,s){const i=t.append("g");const o=u().x((t=>t.x)).y((t=>t.y));const r=V.create();i.selectAll(".group").data(e).enter().append("g").attr("class","group").each(((t,e,s)=>{const i=n(s[e]);i.append("text").attr("class","chord-text").attr("dy",".35em").attr("transform",t.transform).style("text-anchor",t.textAnchor).style("font-size","12px").style("fill",t.color).style("cursor","pointer").text(t.text).on("click",(()=>{if(t.mutationsTooltip){this.geneClickListener(t.text,t.mutationsTooltip.map((t=>t.mname)))}})).on("mouseover",(e=>{r.d.style("padding","2px").html(this.createTooltipHtml(t));r.show(e.x,e.y)})).on("mouseout",(()=>{r.hide()}));i.append("path").attr("class","chord-tick").datum(t.line.points).style("stroke",t.color).style("fill","none").attr("d",o)}));i.selectAll(".group").each(((t,e,i)=>{const r=s?s.find((e=>e.text===t.text)):undefined;if(r){const t=n(i[e]);t.selectAll(".chord-text").datum(r).transition().duration(this.animationDuration).attr("transform",r.transform).style("text-anchor",r.textAnchor);t.selectAll(".chord-tick").datum(r.line.points).transition().duration(this.animationDuration).style("fill","none").attr("d",o)}}))}createTooltipHtml(t){let e="";if(t.mutationsTooltip){e+=`Gene: ${t.text} <br />`;t.mutationsTooltip.forEach((t=>{e+=`Consequence: ${t.mname} <span style="color: ${t.color}" >${t.dataClass}</span> <br />Mutation: ${t.chr}:${t.position} <br />`}))}if(t.fusionTooltip){e+=`Data type: Fusion transcript <br />`;t.fusionTooltip.forEach((t=>{e+=`Break points: ${t.geneA?t.geneA:""} ${t.chrA}:${t.posA} ${t.strandA=="+"?"forward":"reverse"} > `+`${t.geneB?t.geneB:""} ${t.chrB}:${t.posB} ${t.strandB=="+"?"forward":"reverse"} <br /> `}))}if(t.cnvTooltip){t.cnvTooltip.forEach((t=>{e+=`CNV: <span style="color: ${t.color}">${t.value}</span> ${t.chr}:${t.start}-${t.stop}`}))}return e}}function Rt(t={}){const e={downloadImgName:"disco.plot",rings:{nonExonicRingWidth:20,snvRingWidth:20,lohRingWidth:20,cnvRingWidth:30,snvRingFilters:["exonic"],chromosomeInnerRadius:190,chromosomeWidth:20,labelLinesInnerRadius:210,labelsToLinesDistance:30,labelsToLinesGap:2,nonExonicRingEnabled:true,nonExonicFilterValues:["non-exonic"]},verticalPadding:70,horizontalPadding:500,layerScaler:1,padAngle:.002,label:{fontSize:12,maxDeltaAngle:.05,animationDuration:1e3,overlapAngleFactor:5,prioritizeGeneLabelsByGeneSets:false,showPrioritizeGeneLabelsByGeneSets:false},cnv:{capping:5,ampColor:"#D6683C",lossColor:"#67a9cf",cappedAmpColor:"#8B0000",cappedLossColor:"#00008B",unit:"Unit"},snv:{maxMutationCount:1e4},legend:{snvTitle:"SNV",cnvTitle:"CNV",lohTitle:"LOH",fusionTitle:"SV",lohLegendEnabled:true,fontSize:12,rowHeight:48},menu:{padding:5}};return i(e,t)}class bt{constructor(t){this.geneClickListener=t}render(t,e){const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Gene: ${e.text} <br />${e.mname} <br /> <span style="color:${e.color}">${e.dataClass}</span> <br /> ${e.chr}:${e.pos}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Mt{constructor(t,e){this.svnWidth=t;this.geneClickListener=e}render(t,e){if(e.length>0){const s=e[0].innerRadius;const n=new D(s,this.svnWidth,"#6464641A");n.render(t)}const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Gene: ${e.text} <br />${e.mname} <br /> <span style="color:${e.color}">${e.dataClass}</span> <br /> ${e.chr}:${e.pos}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Ct{render(t,e){const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Loss of Heterozygosity  <br /> ${e.chr}:${e.start}-${e.stop}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()}))}}class yt{constructor(t){this.menuPadding=t}render(t,e){const s=r();const n=t.append("g");const i=V.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Copy Number Variation <br /> ${e.chr}:${e.start}-${e.stop} <br /> ${e.unit}: ${e.value}  `);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()}))}}class It{constructor(t){this.type="Disco";this.opts=t}getState(t){return t.plots.find((t=>t.id===this.id))}main(){return e(this,void 0,void 0,(function*(){const t=new G(this);const e=this.state.settings;const s=new mt(e);const n=s.map(this.app.getState());const i=this.opts.holder;i.selectAll("*").remove();const o=new vt(e.cnv.capping,e.label.fontSize,t.cappingClickCallback);const r=new B(this.getRingRenderers(e,t.geneClickListener),o,t.downloadClickListener,t.prioritizeGenesCheckboxListener);r.render(i,n)}))}getRingRenderers(t,e){const s=new At(t.padAngle,t.rings.chromosomeInnerRadius,t.rings.chromosomeInnerRadius+t.rings.chromosomeWidth);const n=new xt(t.label.animationDuration,e);const i=new bt(e);const o=new Mt(t.rings.snvRingWidth,e);const r=new yt(t.menu.padding);const a=new Ct;const l=new Map;l.set(Q.CHROMOSOME,s);l.set(Q.LABEL,n);l.set(Q.NONEXONICSNV,i);l.set(Q.SNV,o);l.set(Q.CNV,r);l.set(Q.LOH,a);return l}}const Lt=o(It);const Et=Lt;function St(t){return e(this,void 0,void 0,(function*(){return{chartType:"Disco",subfolder:"disco",extension:"ts",settings:Rt(t.overrides)}}))}export{Et as componentInit,Lt as discoInit,St as getPlotConfig};

package/dist/{Disco.UI-cc32c0a1.js → Disco.UI-94541d4c.js}

@@ -1 +1 @@
-import{aL as t,bn as e,aN as l,R as n}from"./app-5ca65214.js";import{m as i,a,b as o,c as s,f as p,e as c}from"./uiUtils-1c2ec913.js";import{launch as d}from"./launch.adhoc-f28909a0.js";import"path";import"./plot.app-67392cda.js";import"./recover-ec7a9a86.js";import"./filter-bdf72439.js";import"./table-3e186b96.js";import"./samplelst-928b5cd5.js";import"./termsetting-893b59bb.js";function r(t,e,l){const n=t.append("div").style("margin","20px 20px 20px 40px").style("font-family","'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif").style("place-items","center left").style("overflow","hidden").classed("sjpp-app-ui",true).classed("sjpp-disco-ui",true);const o={data:[]};i(n,"Select Genome").style("font-size","1.15em").style("padding","10px 0px").style("color","#003366");y(n,e,o);i(n,"Provide Data").style("font-size","1.15em").style("padding","10px 0px 5px 0px").style("color","#003366");n.append("div").style("opacity",.75).style("padding","10px 10px 15px 20px").style("width","65vw").style("line-height","1.5em").html('<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>');const s=n.append("div").style("margin-left","2vw");m(s,o);const p=n.append("div").style("display","flex").style("align-items","center").style("padding","15px 0px");b(p,o,e,n,t);a(p,o,".disco_input");if(l)window["doms"]=o;return o}function y(t,e,l){const n=t.append("div").style("margin-left","40px");const i=o(n,e).style("border","1px solid rgb(138, 177, 212)");l.genome=i.node()}function m(e,n){const i=[{label:"SNV Indel",active:true,callback:(t,e)=>l(this,void 0,void 0,(function*(){e.key="snv";const t=`<ol>\n\t\t\t\t\t<li>chr</li>\n\t\t\t\t\t<li>position</li>\n\t\t\t\t\t<li>gene</li>\n\t\t\t\t\t<li>aachange</li>\n\t\t\t\t\t<li>class</li></ol>\n\t\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t226252135\tH3F3A\tK28M\tM\nchr2\t98765432\tTestGene\tTestMutation\tF\n</pre>`;f(e,n,t)}))},{label:"SV",active:false,callback:(t,e)=>l(this,void 0,void 0,(function*(){e.key="sv";const t=`<ol>\n\t\t\t\t\t<li>chrA</li>\n\t\t\t\t\t<li>posA</li>\n\t\t\t\t\t<li>geneA (optional)</li>\n\t\t\t\t\t<li>chrB</li>\n\t\t\t\t\t<li>posB</li>\n\t\t\t\t\t<li>geneB (optional)</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example (with genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tMDC1\tchr12\t61521661\tKMT2D\n</pre>\n\t\t\t\t<p>Example (without genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tchr12\t61521661\n</pre>`;f(e,n,t)}))},{label:"CNV",active:false,callback:(t,e)=>l(this,void 0,void 0,(function*(){e.key="cnv";const t=`<ol>\n\t\t\t\t<li>chr</li>\n\t\t\t\t<li>start</li>\n\t\t\t\t<li>stop</li>\n\t\t\t\t<li>value</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t1\t100000000\t0.5\nchr1\t100000000\t200000000\t-0.5\n</pre>`;f(e,n,t)}))}];new t({holder:e,tabs:i,tabsPosition:"vertical",linePosition:"right"}).main()}function f(t,e,l){t.contentHolder.style("border","none").style("display","block").style("padding-left","30px");x(t,e);t.contentHolder.append("div").style("padding","15px 0px 0px 10px").style("opacity",.75).text(`Provide ${t.label} data in tab delimited format with the following columns:`).append("span").html(l);delete t.callback}function x(e,i){const a=95;const o=[{label:"Select File",active:true,width:a,callback:(t,a)=>l(this,void 0,void 0,(function*(){const t=e.key;a.contentHolder.style("border","none").style("display","block");n(a.contentHolder);a.contentHolder.append("div").style("padding","0px 0px 5px 15px").style("opacity",.65).text(`Select a local file`);u(a,i,t);delete a.callback}))},{label:"Paste Data",active:false,width:a,callback:(t,a)=>l(this,void 0,void 0,(function*(){const t=e.key;a.contentHolder.style("border","none").style("display","block");n(a.contentHolder);v(a,i,t);delete a.callback}))}];new t({holder:e.contentHolder,tabs:o}).main()}function u(t,e,l){const n=t.contentHolder.append("div").style("display","inline-block");const i=p(n).classed("disco_input",true);i.on("change",(t=>{const n=t.target.files[0];const i=new FileReader;i.onload=t=>{e.data[l+"Text"]=t.target.result};i.readAsText(n,"utf8")}))}function v(t,e,n){const i=t.contentHolder.append("div").style("display","block");const a=c({div:i,cols:50}).style("border","1px solid rgb(138, 177, 212)").style("margin","0px 0px 0px 20px").classed("disco_input",true).on("keyup",(()=>l(this,void 0,void 0,(function*(){e.data[n+"Text"]=a.property("value").trim()}))))}function b(t,l,n,i,a){const o=s({div:t,text:"Create Disco Plot"});const p=t.append("div");o.style("margin-right","10px").style("font-size","16px").classed("sjpp-ui-submitBtn",true).attr("type","submit").on("click",(()=>{if(!l.data||l.data==undefined){const t=p.append("div").style("display","inline-block").style("max-width","20vw");e(t,"Please provide data");setTimeout((()=>t.remove()),2e3)}else{const t=n[l.genome.options[l.genome.selectedIndex].text];i.remove();d(l.data,t,a);h(a,n)}}))}function h(t,e){t.append("button").html("&#171; Back").on("click",(()=>{t.selectAll("*").remove();r(t,e,false)}))}export{r as init_discoplotUI};
+import{aL as t,bn as e,aN as l,R as n}from"./app-172cc04d.js";import{m as i,a,b as o,c as s,f as p,e as d}from"./uiUtils-5bef9618.js";import{launch as c}from"./launch.adhoc-ef3d90c1.js";import"path";import"./plot.app-364ceb6d.js";import"./recover-2d13e6d0.js";import"./filter-991b289b.js";import"./table-e393a076.js";import"./samplelst-33b0793a.js";import"./termsetting-19694d7c.js";function r(t,e,l){const n=t.append("div").style("margin","20px 20px 20px 40px").style("font-family","'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif").style("place-items","center left").style("overflow","hidden").classed("sjpp-app-ui",true).classed("sjpp-disco-ui",true);const o={data:[]};i(n,"Select Genome").style("font-size","1.15em").style("padding","10px 0px").style("color","#003366");y(n,e,o);i(n,"Provide Data").style("font-size","1.15em").style("padding","10px 0px 5px 0px").style("color","#003366");n.append("div").style("opacity",.75).style("padding","10px 10px 15px 20px").style("width","65vw").style("line-height","1.5em").html('<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>');const s=n.append("div").style("margin-left","2vw");m(s,o);const p=n.append("div").style("display","flex").style("align-items","center").style("padding","15px 0px");h(p,o,e,n,t);a(p,o,".disco_input");if(l)window["doms"]=o;return o}function y(t,e,l){const n=t.append("div").style("margin-left","40px");const i=o(n,e).style("border","1px solid rgb(138, 177, 212)");l.genome=i.node()}function m(e,n){const i=[{label:"SNV Indel",active:true,callback:(t,e)=>l(this,void 0,void 0,(function*(){e.key="snv";const t=`<ol>\n\t\t\t\t\t<li>chr</li>\n\t\t\t\t\t<li>position</li>\n\t\t\t\t\t<li>gene</li>\n\t\t\t\t\t<li>aachange</li>\n\t\t\t\t\t<li>class</li></ol>\n\t\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t226252135\tH3F3A\tK28M\tM\nchr2\t98765432\tTestGene\tTestMutation\tF\n</pre>`;f(e,n,t)}))},{label:"SV",active:false,callback:(t,e)=>l(this,void 0,void 0,(function*(){e.key="sv";const t=`<ol>\n\t\t\t\t\t<li>chrA</li>\n\t\t\t\t\t<li>posA</li>\n\t\t\t\t\t<li>geneA (optional)</li>\n\t\t\t\t\t<li>chrB</li>\n\t\t\t\t\t<li>posB</li>\n\t\t\t\t\t<li>geneB (optional)</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example (with genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tMDC1\tchr12\t61521661\tKMT2D\n</pre>\n\t\t\t\t<p>Example (without genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tchr12\t61521661\n</pre>`;f(e,n,t)}))},{label:"CNV",active:false,callback:(t,e)=>l(this,void 0,void 0,(function*(){e.key="cnv";const t=`<ol>\n\t\t\t\t<li>chr</li>\n\t\t\t\t<li>start</li>\n\t\t\t\t<li>stop</li>\n\t\t\t\t<li>value</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t1\t100000000\t0.5\nchr1\t100000000\t200000000\t-0.5\n</pre>`;f(e,n,t)}))}];new t({holder:e,tabs:i,tabsPosition:"vertical",linePosition:"right"}).main()}function f(t,e,l){t.contentHolder.style("border","none").style("display","block").style("padding-left","30px");x(t,e);t.contentHolder.append("div").style("padding","15px 0px 0px 10px").style("opacity",.75).text(`Provide ${t.label} data in tab delimited format with the following columns:`).append("span").html(l);delete t.callback}function x(e,i){const a=95;const o=[{label:"Select File",active:true,width:a,callback:(t,a)=>l(this,void 0,void 0,(function*(){const t=e.key;a.contentHolder.style("border","none").style("display","block");n(a.contentHolder);a.contentHolder.append("div").style("padding","0px 0px 5px 15px").style("opacity",.65).text(`Select a local file`);u(a,i,t);delete a.callback}))},{label:"Paste Data",active:false,width:a,callback:(t,a)=>l(this,void 0,void 0,(function*(){const t=e.key;a.contentHolder.style("border","none").style("display","block");n(a.contentHolder);v(a,i,t);delete a.callback}))}];new t({holder:e.contentHolder,tabs:o}).main()}function u(t,e,l){const n=t.contentHolder.append("div").style("display","inline-block");const i=p(n).classed("disco_input",true);i.on("change",(t=>{const n=t.target.files[0];const i=new FileReader;i.onload=t=>{e.data[l+"Text"]=t.target.result};i.readAsText(n,"utf8")}))}function v(t,e,n){const i=t.contentHolder.append("div").style("display","block");const a=d({div:i,cols:50}).style("border","1px solid rgb(138, 177, 212)").style("margin","0px 0px 0px 20px").classed("disco_input",true).on("keyup",(()=>l(this,void 0,void 0,(function*(){e.data[n+"Text"]=a.property("value").trim()}))))}function h(t,l,n,i,a){const o=s({div:t,text:"Create Disco Plot"});const p=t.append("div");o.style("margin-right","10px").style("font-size","16px").classed("sjpp-ui-submitBtn",true).attr("type","submit").on("click",(()=>{if(!l.data||l.data==undefined){const t=p.append("div").style("display","inline-block").style("max-width","20vw");e(t,"Please provide data");setTimeout((()=>t.remove()),2e3)}else{const t=n[l.genome.options[l.genome.selectedIndex].text];i.remove();c(l.data,t,a);b(a,n)}}))}function b(t,e){t.append("button").html("&#171; Back").on("click",(()=>{t.selectAll("*").remove();r(t,e,false)}))}export{r as init_discoplotUI};