@sjcrh/proteinpaint-client 2.29.4 → 2.29.5

package/dist/{2dmaf-265a1d29.js → 2dmaf-8395f6f5.js}

@@ -1 +1 @@
-import{M as t,bd as e,be as s,o as a,E as n,ba as i,p as r,l,f as o,a as c,ay as p,aN as h,q as d,w as f,$ as u}from"./app-3a0d2197.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,be as e,bf as s,o as a,E as n,bb as i,p as r,l,f as o,a as c,ay as p,aO as h,q as d,w as f,$ as u}from"./app-b89f072e.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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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-d0c7ab8d.js → DEanalysis-7d43b61d.js}

@@ -1 +1 @@
-import{M as t,aL as a,az as e,l as o,a as l,$ as n,q as s}from"./app-3a0d2197.js";import{d as r}from"./lasso-4b18148d.js";import{b as i,c}from"./axis-6cb4f314.js";import"path";import"./drag-af780349.js";import"./nodrag-b2d2fedc.js";import"./pointer-c7475677.js";const d="#ffa200";const p=new t;class u{constructor(){this.type="DEanalysis"}async init(t){const a=this.opts.holder.append("div");this.dom={holder:a,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);f(this.dom.holder,t)}}function f(t,a){let e=0,n=0,s=0,r=0;for(const t of a){e=Math.min(e,t.fold_change);n=Math.max(n,t.fold_change);if(t.adjusted_p_value==0){continue}else{s=Math.min(s,t.adjusted_p_value);r=Math.max(r,t.adjusted_p_value)}}let p,u,f,h,g,m,_=50,b=50,j;const k=t.append("svg");const w=k.append("g");const M=k.append("g");const P=k.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const A=k.append("text").text("-log(P value)").attr("fill","black").attr("text-anchor","middle");a.vo_dotarea=k.append("g");const E=a.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const D=o().domain([e,n]);const $=o().domain([s,r]);const I=a.vo_dotarea.selectAll().data(a).enter().append("g").each((function(t){t.vo_g=this}));const S=I.append("circle").attr("stroke","black").attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",d).attr("fill-opacity",0).each((function(t){t.vo_circle=this})).on("mouseover",v).on("mouseout",x).on("click",((t,e)=>{circleclick(e,a,t.clientX,t.clientY)}));const X=a.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function Y(t,e){f=t;h=e;p=Math.max(50,f/8);u=Math.max(50,h/8);j=Math.max(f,h)/80;const o=j*3;S.each((t=>{t.vo_radius=j}));g=Math.max(o,f/50);m=Math.max(o,h/50);w.attr("transform","translate("+p+","+_+")");M.attr("transform","translate("+(p+g)+","+(_+h+m)+")");P.attr("x",p+g+f/2).attr("y",_+h+m+u-5);A.attr("transform","translate(15,"+(_+h/2)+") rotate(-90)");a.vo_dotarea.attr("transform","translate("+(p+g)+","+_+")");E.attr("width",f).attr("height",h);D.range([0,f]);$.range([h,0]);I.attr("transform",(t=>"translate("+D(t.fold_change)+","+$(t.adjusted_p_value==0?r:t.adjusted_p_value,10)+")"));S.attr("r",(t=>t.vo_radius));X.attr("x1",D(0)).attr("x2",D(0)).attr("y2",h);k.attr("width",p+g+f+b).attr("height",_+h+m+u);l({axis:w.call(i().scale($)),color:"black",showline:true});l({axis:M.call(c().scale(D)),color:"black",showline:true})}Y(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;r=0;const e=o.node().selectedIndex==0;for(const t of a){const a=e?t.original_p_value:t.adjusted_p_value;if(a==0)continue;s=Math.min(s,a);r=Math.max(r,a)}$.domain([s,r]);l({axis:w.call(i().scale($)),color:"black",showline:true});I.attr("transform",(t=>{const a=e?t.original_p_value:t.adjusted_p_value;return"translate("+D(t.fold_change)+","+$(a==0?r:a)+")"}));A.text(e?"-log10(P value)":"-log10(adjusted P value)")}));o.append("option").text("Original P value");o.append("option").text("Adjusted P value")}y(I.selectAll("circle"),k,"ma_circle");return k}async function h(t,e){try{if(t.samplelst.groups?.length!=2)throw"opts.samplelst.groups[].length!=2";if(t.samplelst.groups[0].values?.length<1)throw"group 1 not having >1 samples";if(t.samplelst.groups[1].values?.length<1)throw"group 2 not having >1 samples";const e={};return a(e,t)}catch(t){throw`${t} [DEanalysis getPlotConfig()]`}}const g=e(u);const m=g;function _(t,a){a.prepPlot({config:{chartType:"DEanalysis"}})}function v(t,a){p.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}];n(p.d,e);if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",.9);s(a.vo_circle).attr("fill-opacity",.9)}}function x(t,a){p.hide();if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",0);s(a.vo_circle).attr("fill-opacity",0)}}function y(t,a,e){const o=r().items(t).targetArea(a);function l(){a.selectAll(".possible").style("fill-opacity",0).classed("not_possible",true).classed("selected",false).each((t=>{s(t[e]).attr("fill-opacity",0)}))}function n(){o.possibleItems().style("fill-opacity",.9).classed("not_possible",false).classed("possible",true).each((t=>{s(t[e]).attr("fill-opacity",.9)}))}function i(){}o.on("start",l).on("draw",n).on("end",i);a.call(o)}export{g as DEanalysisInit,m as componentInit,h as getPlotConfig,_ as makeChartBtnMenu};
+import{M as t,aL as a,az as e,l as o,a as l,$ as n,q as s}from"./app-b89f072e.js";import{d as r}from"./lasso-075c320f.js";import{b as i,c}from"./axis-6cb4f314.js";import"path";import"./drag-f3cefb68.js";import"./nodrag-b5457f59.js";import"./pointer-c7475677.js";const p="#ffa200";const d=new t;class f{constructor(){this.type="DEanalysis"}async init(t){const a=this.opts.holder.append("div");this.dom={holder:a,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);u(this.dom.holder,t)}}function u(t,a){let e=0,n=0,s=0,r=0;for(const t of a){e=Math.min(e,t.fold_change);n=Math.max(n,t.fold_change);if(t.adjusted_p_value==0){continue}else{s=Math.min(s,t.adjusted_p_value);r=Math.max(r,t.adjusted_p_value)}}let d,f,u,h,g,m,_=50,b=50,j;const k=t.append("svg");const w=k.append("g");const M=k.append("g");const P=k.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const A=k.append("text").text("-log(P value)").attr("fill","black").attr("text-anchor","middle");a.vo_dotarea=k.append("g");const E=a.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const D=o().domain([e,n]);const $=o().domain([s,r]);const I=a.vo_dotarea.selectAll().data(a).enter().append("g").each((function(t){t.vo_g=this}));const S=I.append("circle").attr("stroke","black").attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",p).attr("fill-opacity",0).each((function(t){t.vo_circle=this})).on("mouseover",v).on("mouseout",x).on("click",((t,e)=>{circleclick(e,a,t.clientX,t.clientY)}));const X=a.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function Y(t,e){u=t;h=e;d=Math.max(50,u/8);f=Math.max(50,h/8);j=Math.max(u,h)/80;const o=j*3;S.each((t=>{t.vo_radius=j}));g=Math.max(o,u/50);m=Math.max(o,h/50);w.attr("transform","translate("+d+","+_+")");M.attr("transform","translate("+(d+g)+","+(_+h+m)+")");P.attr("x",d+g+u/2).attr("y",_+h+m+f-5);A.attr("transform","translate(15,"+(_+h/2)+") rotate(-90)");a.vo_dotarea.attr("transform","translate("+(d+g)+","+_+")");E.attr("width",u).attr("height",h);D.range([0,u]);$.range([h,0]);I.attr("transform",(t=>"translate("+D(t.fold_change)+","+$(t.adjusted_p_value==0?r:t.adjusted_p_value,10)+")"));S.attr("r",(t=>t.vo_radius));X.attr("x1",D(0)).attr("x2",D(0)).attr("y2",h);k.attr("width",d+g+u+b).attr("height",_+h+m+f);l({axis:w.call(i().scale($)),color:"black",showline:true});l({axis:M.call(c().scale(D)),color:"black",showline:true})}Y(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;r=0;const e=o.node().selectedIndex==0;for(const t of a){const a=e?t.original_p_value:t.adjusted_p_value;if(a==0)continue;s=Math.min(s,a);r=Math.max(r,a)}$.domain([s,r]);l({axis:w.call(i().scale($)),color:"black",showline:true});I.attr("transform",(t=>{const a=e?t.original_p_value:t.adjusted_p_value;return"translate("+D(t.fold_change)+","+$(a==0?r:a)+")"}));A.text(e?"-log10(P value)":"-log10(adjusted P value)")}));o.append("option").text("Original P value");o.append("option").text("Adjusted P value")}y(I.selectAll("circle"),k,"ma_circle");return k}async function h(t,e){try{if(t.samplelst.groups?.length!=2)throw"opts.samplelst.groups[].length!=2";if(t.samplelst.groups[0].values?.length<1)throw"group 1 not having >1 samples";if(t.samplelst.groups[1].values?.length<1)throw"group 2 not having >1 samples";const e={};return a(e,t)}catch(t){throw`${t} [DEanalysis getPlotConfig()]`}}const g=e(f);const m=g;function _(t,a){a.prepPlot({config:{chartType:"DEanalysis"}})}function v(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}];n(d.d,e);if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",.9);s(a.vo_circle).attr("fill-opacity",.9)}}function x(t,a){d.hide();if(!a.ma_label){s(a.ma_circle).attr("fill-opacity",0);s(a.vo_circle).attr("fill-opacity",0)}}function y(t,a,e){const o=r().items(t).targetArea(a);function l(){a.selectAll(".possible").style("fill-opacity",0).classed("not_possible",true).classed("selected",false).each((t=>{s(t[e]).attr("fill-opacity",0)}))}function n(){o.possibleItems().style("fill-opacity",.9).classed("not_possible",false).classed("possible",true).each((t=>{s(t[e]).attr("fill-opacity",.9)}))}function i(){}o.on("start",l).on("draw",n).on("end",i);a.call(o)}export{g as DEanalysisInit,m as componentInit,h as getPlotConfig,_ as makeChartBtnMenu};

package/dist/Disco-f5027e5e.js

@@ -0,0 +1 @@
+import{M as t,aM as e,E as s,q as n,aL as i,az as o}from"./app-b89f072e.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-0cb59d4a.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=O,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),O=y-E,w=(I+L)/2;c.quadraticCurveTo(0,0,O*v(I),O*A(I));c.lineTo(y*v(w),y*A(w));c.lineTo(O*v(L),O*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 S()}class V{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 T{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 D;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(D||(D={}));class z{static getColor(t,e){if(t!=e){return D.Interchromosomal.valueOf()}else{return D.Intrachromosomal.valueOf()}}}class k{render(t,e){let s=0;if(e.length>0){s=e[0].target.radius;const n=new V(s,2,"#6464641A");n.render(t)}const n=N().radius(s);const i=t.selectAll(".chord").data(e);const o=T.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 B{constructor(t){this.checkBoxClickListener=t}render(t,e,s){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");s.on("change",(()=>{this.checkBoxClickListener(s.property("checked"))}))}}}class ${constructor(t,e,s,n){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new k;this.downloadButtonRenderer=new P(s);this.prioritizeGenesCheckboxRenderer=new B(n)}render(t,e){const s=t.append("div");s.append("div");const n=s.append("div").style("display","inline-block").style("font-family","Arial");const i=n.append("div");this.downloadButtonRenderer.render(i,n);this.prioritizeGenesCheckboxRenderer.render(i,e.settings.label.prioritizeGeneLabelsByGeneSets,e.settings.label.showPrioritizeGeneLabelsByGeneSets);const o=n.append("svg").attr("width",e.width).attr("height",e.height+e.legendHeight);const r=o.append("g").attr("class","mainG").attr("transform",`translate(${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.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",(function(){const s=new XMLSerializer;const n=new Blob([s.serializeToString(t)],{type:"image/svg+xml"});e.download="disco"+".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-b89f072e.js").then((function(t){return t.bT}));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,pos:t.pos,ref:t.ref,alt:t.alt,position:t.position,sample:this.sampleName,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=>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.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.pos/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 q{constructor(t,e,s,n,i){this.source=t;this.target=e;this.genes=s;this.count=n;this.endpts=i}}class X{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 X(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 X(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 q(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){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)}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.pos};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.filteredPrioritizedGenesList=[];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=[];if(this.hasPrioritizedGenes){t=this.elements.filter((t=>t.isPrioritized));this.filteredPrioritizedGenesList=this.getLabelsWithoutPrioritizedGenes(t);const e=this.elements.filter((t=>!t.isPrioritized));const s=e.concat(this.filteredPrioritizedGenesList).sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0));this.elementsToDisplay=this.getAllLabels(s)}else{this.elementsToDisplay=this.getLabelsWithoutPrioritizedGenes(this.elements)}}getLabelsWithoutPrioritizedGenes(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.pos};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)}}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])&&this.settings.label.prioritizeGeneLabelsByGeneSets?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: ${o.value}`,color:o.color,order:r++,border:"1px solid #ccc",onClickCallback:this.onClickCallback});e.push({name:t.cnvTitle,order:s,items:a})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:D.Interchromosomal,text:"Interchromosomal",color:D.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:D.Intrachromosomal,text:"Intrachromosomal",color:D.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class vt{constructor(t,e,s){this.fontSize=e;this.legendJSONMapper=new ft(t,s)}render(t,e,s,n,i){const o=c({holder:t.append("g"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const r={xOffset:s};const a=this.legendJSONMapper.map(e);o(a,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:r,fontsize:this.fontSize})})}}class At{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=m().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=r().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const o=t.append("g");o.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");o.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${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=T.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={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"},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=T.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 V(s,this.svnWidth,"#6464641A");n.render(t)}const s=r();const n=t.append("g");const i=T.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=T.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=T.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;this.discoInteractions=new G(this)}getState(t){return t.plots.find((t=>t.id===this.id))}main(){return e(this,void 0,void 0,(function*(){const t=this.state.settings;const e=new mt(t);const s=e.map(this.app.getState());const n=this.opts.holder;n.selectAll("*").remove();const i=new vt(t.cnv.capping,t.label.fontSize,this.discoInteractions.cappingClickCallback);const o=new $(this.getRingRenderers(t,this.discoInteractions.geneClickListener),i,this.discoInteractions.downloadClickListener,this.discoInteractions.prioritizeGenesCheckboxListener);o.render(n,s)}))}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 Ot(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,Ot as getPlotConfig};

package/dist/Disco.UI-16d3a2b0.js

@@ -0,0 +1 @@
+import{aK as t,bs as e,aM as n}from"./app-b89f072e.js";import{m as i,a as l,b as a,c as s,e as o}from"./uiUtils-1cec39d5.js";import{launch as p}from"./launch.adhoc-e148580d.js";import"path";import"./plot.app-24c58f77.js";import"./recover-beec8c25.js";import"./filter-bbfd2df4.js";import"./table-00d6391b.js";import"./samplelst-717ec4af.js";import"./termsetting-c22c785c.js";function c(t,e,n){const a=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);const s={data:[]};i(a,"Select Genome").style("font-size","1.15em").style("padding","10px 0px").style("color","#003366");d(a,e,s);i(a,"Provide Data").style("font-size","1.15em").style("padding","10px 0px 5px 0px").style("color","#003366");a.append("div").style("opacity",.75).style("padding","10px 10px 15px 20px").text("The plot accepts multiple data types. Paste data for SNV Indel, SV, and CNV in each tab and submit.");const o=a.append("div").style("margin-left","2vw");r(o,s);const p=a.append("div").style("display","flex").style("align-items","center").style("margin","0px 0px 40px 130px");y(p,s,e,a,t);l(p,s,".disco_input");if(n)window.doms=s;return s}function d(t,e,n){const i=t.append("div").style("margin-left","40px");const l=a(i,e).style("border","1px solid rgb(138, 177, 212)");n.genome=l.node()}function r(e,i){const l=[{label:"SNV Indel",active:true,callback:(t,e)=>n(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>`;m(e,i,t)}))},{label:"SV",active:true,callback:(t,e)=>n(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>`;m(e,i,t)}))},{label:"CNV",active:true,callback:(t,e)=>n(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>`;m(e,i,t)}))}];new t({holder:e,tabs:l,tabsPosition:"vertical",linePosition:"right"}).main()}function m(t,e,n){t.contentHolder.style("border","none").style("display","block").style("padding-left","30px");x(t,e,t.key);t.contentHolder.append("div").style("margin","10px 0px 0px 10px").style("opacity",.75).text(`Provide ${t.label} data in tab delimited format with the following columns:`).append("span").html(n);delete t.callback}function x(t,e,i){const l=t.contentHolder.append("div").style("display","block");const a=o({div:l,cols:50}).style("border","1px solid rgb(138, 177, 212)").style("margin","0px 0px 0px 20px").classed("disco_input",true).on("keyup",(()=>n(this,void 0,void 0,(function*(){e.data[i+"Text"]=a.property("value").trim()}))))}function y(t,n,i,l,a){const o=s({div:t,text:"Create Disco Plot"});const c=t.append("div");o.style("margin-right","10px").style("font-size","16px").classed("sjpp-ui-submitBtn",true).attr("type","submit").on("click",(()=>{if(!n.data||n.data==undefined){const t=c.append("div").style("display","inline-block").style("max-width","20vw");e(t,"Please provide data");setTimeout((()=>t.remove()),2e3)}else{const t=i[n.genome.options[n.genome.selectedIndex].text];l.remove();p(n.data,t,a)}}))}export{c as init_discoplotUI};

package/dist/DragControls-dbbac7a8.js

@@ -0,0 +1 @@
+import{Plane as e,Raycaster as t,Vector2 as n,Vector3 as o,Matrix4 as r,EventDispatcher as i}from"./three.module-14830cb3.js";const s=new e;const a=new t;const c=new n;const l=new o;const u=new o;const p=new o;const d=new r;class f extends i{constructor(e,t,n){super();n.style.touchAction="none";let o=null,r=null;const i=[];const f=this;function m(){n.addEventListener("pointermove",g);n.addEventListener("pointerdown",E);n.addEventListener("pointerup",j);n.addEventListener("pointerleave",j)}function v(){n.removeEventListener("pointermove",g);n.removeEventListener("pointerdown",E);n.removeEventListener("pointerup",j);n.removeEventListener("pointerleave",j);n.style.cursor=""}function h(){v()}function y(){return e}function b(){return a}function g(m){if(f.enabled===false)return;x(m);a.setFromCamera(c,t);if(o){if(a.ray.intersectPlane(s,u)){o.position.copy(u.sub(l).applyMatrix4(d))}f.dispatchEvent({type:"drag",object:o});return}if(m.pointerType==="mouse"||m.pointerType==="pen"){i.length=0;a.setFromCamera(c,t);a.intersectObjects(e,true,i);if(i.length>0){const e=i[0].object;s.setFromNormalAndCoplanarPoint(t.getWorldDirection(s.normal),p.setFromMatrixPosition(e.matrixWorld));if(r!==e&&r!==null){f.dispatchEvent({type:"hoveroff",object:r});n.style.cursor="auto";r=null}if(r!==e){f.dispatchEvent({type:"hoveron",object:e});n.style.cursor="pointer";r=e}}else{if(r!==null){f.dispatchEvent({type:"hoveroff",object:r});n.style.cursor="auto";r=null}}}}function E(r){if(f.enabled===false)return;x(r);i.length=0;a.setFromCamera(c,t);a.intersectObjects(e,true,i);if(i.length>0){o=f.transformGroup===true?e[0]:i[0].object;s.setFromNormalAndCoplanarPoint(t.getWorldDirection(s.normal),p.setFromMatrixPosition(o.matrixWorld));if(a.ray.intersectPlane(s,u)){d.copy(o.parent.matrixWorld).invert();l.copy(u).sub(p.setFromMatrixPosition(o.matrixWorld))}n.style.cursor="move";f.dispatchEvent({type:"dragstart",object:o})}}function j(){if(f.enabled===false)return;if(o){f.dispatchEvent({type:"dragend",object:o});o=null}n.style.cursor=r?"pointer":"auto"}function x(e){const t=n.getBoundingClientRect();c.x=(e.clientX-t.left)/t.width*2-1;c.y=-(e.clientY-t.top)/t.height*2+1}m();this.enabled=true;this.transformGroup=false;this.activate=m;this.deactivate=v;this.dispose=h;this.getObjects=y;this.getRaycaster=b}}export{f as DragControls};

package/dist/app-8675d1ab.js

@@ -0,0 +1 @@
+import{az as t,q as s,M as e,aA as r,a1 as o,ac as i}from"./app-b89f072e.js";import{r as a,s as n}from"./recover-beec8c25.js";import{v as p}from"./filter-bbfd2df4.js";import{n as c}from"./sampleScatter.interactivity-7670e074.js";import{summaryInit as l}from"./summary-39f2e235.js";import"path";import"./samplelst-717ec4af.js";import"./termsetting-c22c785c.js";import"./table-00d6391b.js";import"./app-f46a0548.js";import"./termInfo-4358632e.js";import"./violin-8495f665.js";import"./controls-d248ca8b.js";import"./controls.btns-a3a00dd9.js";import"./controls.config-4e2383d6.js";import"./controls.overlay-901775fa.js";import"./controls.term1-c0803929.js";import"./controls.divide-a74fa8d3.js";import"./violin.renderer-e4043630.js";import"./brush-79b3e1db.js";import"./pointer-c7475677.js";import"./nodrag-b5457f59.js";import"./transform-f2cc07e6.js";import"./axis-6cb4f314.js";import"./area-f56e50f9.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./log-1ba83249.js";import"./html.legend-ddfbe700.js";import"./violin.interactivity-e7704864.js";import"./barchart-b9b520a8.js";import"./bars.settings-f7884503.js";import"./bars.renderer-00c34250.js";import"./svg.legend-0cb59d4a.js";import"./barchart.events-4cc21ab5.js";import"./sampleScatter-23f44378.js";import"./zoom-b6b048e1.js";import"./lasso-075c320f.js";import"./drag-f3cefb68.js";import"./svg.download-86721342.js";import"./symbol-fc7cbd41.js";import"./math-2fb199c6.js";function m(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-7d43b61d.js");case"../plots/Disco.js":return import("./Disco-f5027e5e.js");case"../plots/barchart.data.js":return import("./filter-bbfd2df4.js").then((function(t){return t.p}));case"../plots/barchart.events.js":return import("./barchart.events-4cc21ab5.js");case"../plots/barchart.js":return import("./barchart-b9b520a8.js");case"../plots/bars.renderer.js":return import("./bars.renderer-00c34250.js");case"../plots/bars.settings.js":return import("./bars.settings-f7884503.js");case"../plots/boxplot.js":return import("./boxplot-4a473698.js");case"../plots/controls.btns.js":return import("./controls.btns-a3a00dd9.js");case"../plots/controls.config.js":return import("./controls.config-4e2383d6.js");case"../plots/controls.divide.js":return import("./controls.divide-a74fa8d3.js");case"../plots/controls.js":return import("./controls-d248ca8b.js");case"../plots/controls.overlay.js":return import("./controls.overlay-901775fa.js");case"../plots/controls.term1.js":return import("./controls.term1-c0803929.js");case"../plots/cuminc.js":return import("./cuminc-4c78009f.js");case"../plots/dataDownload.js":return import("./dataDownload-a978135b.js");case"../plots/dictionary.js":return import("./dictionary-7c726ae4.js");case"../plots/geneExpression.js":return import("./geneExpression-2499ed82.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-0aa1fbbb.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-a6c8a9a0.js");case"../plots/hierCluster.js":return import("./hierCluster-8538a885.js");case"../plots/matrix.cells.js":return import("./matrix.cells-c66a1b06.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-c018157d.js");case"../plots/matrix.config.js":return import("./matrix.config-6d6c8c1b.js");case"../plots/matrix.controls.js":return import("./matrix.controls-77189f13.js");case"../plots/matrix.data.js":return import("./matrix.data-e52bf45f.js");case"../plots/matrix.dom.js":return import("./matrix.dom-43c08155.js");case"../plots/matrix.groups.js":return import("./matrix.groups-3ef82d87.js");case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-541ef9c8.js");case"../plots/matrix.js":return import("./matrix-0087ed29.js");case"../plots/matrix.layout.js":return import("./matrix.layout-d776f0e0.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-cd4c83b9.js");case"../plots/matrix.renderers.js":return import("./matrix.renderers-13daea8e.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-93188b26.js");case"../plots/matrix.sort.js":return import("./matrix.sort-f4811751.js");case"../plots/plot.app.js":return import("./plot.app-24c58f77.js");case"../plots/plot.disco.js":return import("./plot.disco-4fcf3ac1.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-59ac7d63.js");case"../plots/polar.js":return import("./polar-08ac21c8.js");case"../plots/profileBarchart.js":return import("./profileBarchart-9622c45c.js");case"../plots/profilePlot.js":return import("./profilePlot-6ca88101.js");case"../plots/profilePolar.js":return import("./profilePolar-8eeadbdc.js");case"../plots/profileRadar.js":return import("./profileRadar-6ad29652.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-f652fec4.js");case"../plots/regression.inputs.js":return import("./regression.inputs-77d7c1e6.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-77d7c1e6.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-5b7e7ae6.js");case"../plots/regression.js":return import("./regression.inputs-77d7c1e6.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-10c59099.js");case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-7670e074.js").then((function(t){return t.c}));case"../plots/sampleScatter.js":return import("./sampleScatter-23f44378.js").then((function(t){return t.a}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-23f44378.js").then((function(t){return t.s}));case"../plots/sampleView.js":return import("./sampleView-7e2bb630.js");case"../plots/scatter.js":return import("./scatter-2b17678e.js");case"../plots/stattable.js":return import("./stattable-3e74e4cd.js");case"../plots/summary.js":return import("./summary-39f2e235.js");case"../plots/survival.js":return import("./survival-0a53dac8.js");case"../plots/table.js":return import("./table-872b37c4.js");case"../plots/variantBrowser.js":return import("./variantBrowser-3709ae24.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-e7704864.js");case"../plots/violin.js":return import("./violin-8495f665.js");case"../plots/violin.renderer.js":return import("./violin.renderer-e4043630.js");default:return new Promise((function(s,e){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(e.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class d{constructor(t){this.type="plot";u(this);this.initUi(t)}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.endsWith("_group"))return true;if(t.type.startsWith("plot_"))return t.id===this.id;if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type=="app_refresh")return true;if(t.type.endsWith("customTerm"))return true}getState(t){const s=t.plots.find((t=>t.id===this.id));if(!s){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}return{config:s,groups:t.groups,_scope_:t._scope_}}async main(){this.dom.errdiv.style("display","none");if(!this.components)await this.setComponents(this.opts)}async setComponents(t){this.components={recover:await a({app:this.app,holder:this.dom.localRecoverDiv,getState:t=>this.getState(t),reactsTo:t=>t.id==this.id&&(t.type=="plot_edit"||t.type=="plot_nestedEdits")&&t._track_!="none",plot_id:this.id,maxHistoryLen:10})};const e=await m(`../plots/${t.chartType}.js`);this.components.chart=await e.componentInit({app:this.app,holder:this.dom.viz,header:this.dom.paneTitleDiv,id:this.id,plotDiv:s(this.dom.holder.app_div.node().parentNode)})}destroy(){this.dom.holder.app_div.selectAll("*").remove();this.dom.holder.app_div.remove();for(const t in this.dom){delete this.dom[t]}}}const j=t(d);function u(t){t.initUi=function(s){const r=s.holder;r.header.style("padding",0);try{t.dom={tip:new e({padding:"0px"}),holder:r,paneTitleDiv:r.header.append("div").style("display","inline-block").style("color","#999").style("padding-left","7px").style("vertical-align","sub"),localRecoverDiv:r.header.append("div").style("display","inline-block"),body:r.body.style("white-space","nowrap").style("overflow-x","auto"),errdiv:r.body.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),viz:r.body.append("div")}}catch(s){t.dom.errdiv.style("display","none").text(s)}}}class h{constructor(t){if(t.addLoginCallback){t.addLoginCallback((()=>this.api.dispatch({type:"app_refresh"})))}this.type="app";this.dom={holder:t.holder,topbar:t.holder.append("div"),errdiv:t.holder.append("div"),plotDiv:t.holder.append("div")};this.plotIdToSandboxId={}}validateOpts(t={}){if(!t.holder)throw`missing opts.holder in the MassApp constructor argument`;if(!t.callbacks)t.callbacks={};if(!t.state.vocab)t.state.vocab={};if(typeof t.state.vocab!="object")throw"opts.state.vocab{} is not an object";if(t.state.genome){t.state.vocab.genome=t.state.genome;delete t.state.genome}if(t.state.dslabel){t.state.vocab.dslabel=t.state.dslabel;delete t.state.dslabel}return t}async preApiFreeze(t){try{t.tip=new e({padding:"5px"});t.printError=t=>this.printError(t);const s=this.opts.state.vocab;t.vocabApi=await p({app:t,state:{vocab:this.opts.state.vocab},fetchOpts:this.opts.fetchOpts,getDatasetAccessToken:this.opts.getDatasetAccessToken});t.hasWebGL=function(){try{var t=document.createElement("canvas");return!!(window.WebGLRenderingContext&&(t.getContext("webgl")||t.getContext("experimental-webgl")))}catch(t){return false}};this.opts.state.vocab=t.vocabApi.vocab}catch(t){throw t}}async init(){try{const t="debounceInterval"in this.opts?this.opts.debounceInterval:0;this.store=await n({app:this.api,state:this.opts.state,debounceInterval:t});this.state=await this.store.copyState();this.components={};if(this.state.nav.header_mode!="hidden"){this.components.nav=await c({app:this.api,holder:this.dom.topbar,header_mode:this.state&&this.state.nav&&this.state.nav.header_mode,vocab:this.state.vocab,massSessionDuration:this.state.termdbConfig.massSessionDuration})}this.components.plots={};await this.api.dispatch()}catch(t){this.printError(t);throw t}}async main(){await this.api.vocabApi.main();const t={};let s;for(const e of this.state.plots){if(!(e.id in this.components.plots)){s=o(this.dom.plotDiv,{close:()=>{this.api.dispatch({type:"plot_delete",id:e.id})},plotId:e.id,beforePlotId:e.insertBefore||null,style:{width:"98.5%"}});if(e.chartType=="summary")t[e.id]=l(Object.assign({app:this.api,holder:s},e));else t[e.id]=j(Object.assign({app:this.api,holder:s},e))}}const e=Object.keys(t).length;if(e){await Promise.all(Object.values(t));for(const s in t){this.components.plots[s]=await t[s]}}for(const t in this.components.plots){if(!this.state.plots.find((s=>s.id===t))){this.components.plots[t].destroy();delete this.components.plots[t]}}}printError(t){i(this.dom.errdiv||this.opts.holder,"Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}const f=r(h);export{f as appInit};