@sjcrh/proteinpaint-client 2.63.0 → 2.63.2

package/README.md

@@ -11,20 +11,22 @@ This should be installed as a workspace, follow the README at the project root.
 From the proteinpaint/client directory:
 ```bash
 npm run dev # generates bundles to public/bin
-npm test # tests the client code
-npm run browser # bundles the front-end spec files for use at localhost:[port]/testrun.html
-npm run gdc # runs the gdc tests
+# the client dev script is usually called together with server start
+# for St. Jude developers, that's `npm run dev` from the supermodule/parent repo
 ```
 
 ## Test
 
-NOTE: Running `npm test` at the project root will run both client and server tests.
+You can view and run tests from `http://localhost:3000`, if you have a full dev environment running.
 
-`npm test` to run all available client-side tests.
+```bash
+
+npm run test:unit
+npm run test:integration
 
-To run a specific file with a $namepattern (such as filter): `node ./test/import-specs.js name=$namepattern && npm run tape`.
-For example, `node ./test/import-specs.js name=**/termsetting* && npm run tape`
+./test.sh *tvs.*.spec.*
 
+# not recommended: `npm test` to run all available client-side tests.
 
 ## Build
 

package/dist/{2dmaf-70c0b6bb.js → 2dmaf-0cabb4a4.js}

@@ -1 +1 @@
-import{M as t,bq as e,br as s,o as a,E as n,bl as i,p as r,l,f as o,a as c,ay as p,aU as h,q as d,a0 as f,_ as u}from"./app-f91922b4.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"./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 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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 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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 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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 k)){k[t.class]=0}if(t.symbol){if(!b[t.symbol]){b[t.symbol]={numlines:0,label:t.symbollabel,hidden:false}}b[t.symbol].numlines++}k[t.class]++}const v=Math.min(window.innerWidth,window.innerHeight);const _=50,D=v*.5,w=v*.5,R=w/2,I=D/2,M=_/3,X=R/5,A=Math.min(20,12*v/500),z=v/40,C=z*.7,O=3;const S=l().domain([0,x]).range([z/2,z]);const W=t=>Math.PI*Math.pow(S(t),2);for(const t of f){t.radius=Math.max(t["TinD.D"]?S(t["TinD.D"]):0,t["TinD.R"]?S(t["TinD.R"]):0)}const E=e.append("table");const q=E.append("tr");const H=q.append("td").style("vertical-align","top");const G=q.append("td").style("vertical-align","top");G.append("div").style("margin","10px").text("Name: "+u);const U=H.append("div");U.append("button").text("Hide").on("click",(()=>{s.shown=false;if(s.handle){s.handle.attr("font-weight","normal")}E.remove()}));const P=new N({axiswidth:_,sp:M,sp2:X,sample1height:R,sample2height:I,shareheight:w,sharewidth:D,headerdiv:U});U.append("button").text("Screenshot").on("click",(()=>{h(Z.node(),"2dmaf_"+s.name)}));{const t=U.append("select").on("change",(t=>{const e=t.target.options[t.target.selectedIndex].value;if(e=="all"){at.transition().attr("transform",(t=>t.posstring+" scale(1)"));ot.transition().attr("transform",(t=>t.posstring+" scale(1)"));dt.transition().attr("transform",(t=>t.posstring+" scale(1)"));return}at.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));ot.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));dt.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"))}));t.append("option").text("Show all mutation classes").property("value","all");const e=[];for(const t in k){e.push([t,k[t]])}e.sort(((t,e)=>e[1]-t[1]));for(const s of e){t.append("option").text((s[0]in n?n[s[0]].label:s[0])+" ("+s[1]+")").property("value",s[0])}}const Z=H.append("svg").attr("width",_+M+I+D+M*2).attr("height",_+M+R+w+M*2);const J=Z.append("g").attr("transform","translate("+M+","+M+")");P.setWrapper(J.append("g"));const K=l().domain([0,1]).range([0,D]);const Q=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+R+M)+")").call(y().scale(K).tickSize(5));c({axis:Q,showline:true,fontsize:A*.8});const $=i.length+p.length;Q.append("text").text(s.setname[1]+", n="+$+(s.purity1?", purity="+s.purity1:"")).attr("x",D/2).attr("y",_-4).attr("text-anchor","middle").attr("font-size",A);const tt=l().domain([0,1]).range([w,0]);const et=J.append("g").attr("transform","translate("+_+",0)").call(g().scale(tt).tickSize(5));c({axis:et,showline:true,fontsize:A*.8});const st=o.length+p.length;et.append("text").text(s.setname[2]+", n="+st+(s.purity2?", purity="+s.purity2:"")).attr("transform","translate("+(A-_-10)+","+w/2+") 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Y){nt.filter(Y[t]).append(t).attr("rx",(t=>t.symbol?null:S(t["TinD.D"]))).attr("ry",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.D"])+W(t["TinD.R"])/2)())).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 it=l().domain([0,x]).range([R-X,0]);const rt=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const lt="#FFBEAD";rt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("x",0).attr("width",3).attr("height",R-X);c({axis:rt.call(g().scale(it).tickValues([0,x])),showline:true,fontsize:A*.8});rt.append("g").attr("transform","translate(-"+A/2+","+(R-X)/2+")").append("text").text("D total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("transform","rotate(-90)");const ot=rt.selectAll().data(i).enter().append("g").attr("transform",(t=>{t.posstring="translate("+K(t.maf1)+","+it(t["TinD.D"])+")";return t.posstring}));ot.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);ot.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=ot;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.R"]))).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 ct=l().domain([0,x]).range([0,I-X]);const pt=J.append("g").attr("transform","translate("+(_+M)+",0)");pt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("y",w).attr("width",I-X).attr("height",3);const ht=pt.append("g").attr("transform","translate(0,"+w+")").call(y().scale(ct).tickValues([0,x]));c({axis:ht,showline:true,fontsize:A*.8});pt.append("text").text("R total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("x",(I-X)/2).attr("y",w+A).attr("text-anchor","middle");const dt=pt.selectAll().data(o).enter().append("g").attr("transform",(t=>{t.posstring="translate("+ct(t["TinD.R"])+","+tt(t.maf2)+")";return t.posstring}));dt.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);dt.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=dt;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.D"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ft=J.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const mt=S(20),yt=S(x);ut+=A+yt;let gt;ft.append("text").text("SNV 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CNV/LOH").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt).attr("cy",ut+10).attr("r",O).attr("fill","black");ut+=30;ft.append("text").text("R. CNV/LOH").attr("y",ut).attr("dominant-baseline","central").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt-10).attr("cy",ut).attr("r",O).attr("fill","black");ut+=30;if(s.purity1!=undefined||s.purity2!=undefined){ft.append("text").text("Expected MAF").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=10;ft.append("rect").attr("fill",lt).attr("x",gt).attr("y",ut).attr("width",40).attr("height",3);ut+=30}const xt=Object.keys(b);if(xt.length){ft.append("text").text("Symbols").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));let t;for(const e in b){const s=b[e];const 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 wt=G.append("div").style("height",w+R+"px").style("margin","10px").style("padding","10px").style("border","solid 1px #ccc").style("overflow-y","scroll").style("resize","both").append("table");{const t=wt.append("tr");t.append("td").text("Gene");t.append("td").text(s.setname[1]+" only");t.append("td").text(s.setname[2]+" only");t.append("td").text("Shared")}let Tt=true;for(const t of Dt){const e=wt.append("tr");if(Tt){e.style("background-color","#f3f3f3")}Tt=!Tt;e.append("td").text(t);let s=[];if(t in bt){s=bt[t]}const a=[],n=[],i=[];for(const t of s){if(t.set_share)i.push(t);else if(t.set_1)a.push(t);else if(t.set_2)n.push(t)}let r=e.append("td");if(a.length){for(const t of a){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,ot)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(n.length){for(const t of n){const 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,bq as e,br as s,o as a,E as n,bl as i,p as r,l,f as o,a as c,ay as p,aU as h,q as d,a0 as f,_ as u}from"./app-71453429.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"./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 k)){k[t.class]=0}if(t.symbol){if(!b[t.symbol]){b[t.symbol]={numlines:0,label:t.symbollabel,hidden:false}}b[t.symbol].numlines++}k[t.class]++}const v=Math.min(window.innerWidth,window.innerHeight);const _=50,D=v*.5,w=v*.5,R=w/2,I=D/2,M=_/3,X=R/5,A=Math.min(20,12*v/500),z=v/40,C=z*.7,O=3;const S=l().domain([0,x]).range([z/2,z]);const W=t=>Math.PI*Math.pow(S(t),2);for(const t of f){t.radius=Math.max(t["TinD.D"]?S(t["TinD.D"]):0,t["TinD.R"]?S(t["TinD.R"]):0)}const E=e.append("table");const q=E.append("tr");const H=q.append("td").style("vertical-align","top");const G=q.append("td").style("vertical-align","top");G.append("div").style("margin","10px").text("Name: "+u);const U=H.append("div");U.append("button").text("Hide").on("click",(()=>{s.shown=false;if(s.handle){s.handle.attr("font-weight","normal")}E.remove()}));const P=new N({axiswidth:_,sp:M,sp2:X,sample1height:R,sample2height:I,shareheight:w,sharewidth:D,headerdiv:U});U.append("button").text("Screenshot").on("click",(()=>{h(Z.node(),"2dmaf_"+s.name)}));{const t=U.append("select").on("change",(t=>{const e=t.target.options[t.target.selectedIndex].value;if(e=="all"){at.transition().attr("transform",(t=>t.posstring+" scale(1)"));ot.transition().attr("transform",(t=>t.posstring+" scale(1)"));dt.transition().attr("transform",(t=>t.posstring+" scale(1)"));return}at.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));ot.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));dt.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"))}));t.append("option").text("Show all mutation classes").property("value","all");const e=[];for(const t in k){e.push([t,k[t]])}e.sort(((t,e)=>e[1]-t[1]));for(const s of e){t.append("option").text((s[0]in n?n[s[0]].label:s[0])+" ("+s[1]+")").property("value",s[0])}}const Z=H.append("svg").attr("width",_+M+I+D+M*2).attr("height",_+M+R+w+M*2);const J=Z.append("g").attr("transform","translate("+M+","+M+")");P.setWrapper(J.append("g"));const K=l().domain([0,1]).range([0,D]);const Q=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+R+M)+")").call(y().scale(K).tickSize(5));c({axis:Q,showline:true,fontsize:A*.8});const $=i.length+p.length;Q.append("text").text(s.setname[1]+", n="+$+(s.purity1?", purity="+s.purity1:"")).attr("x",D/2).attr("y",_-4).attr("text-anchor","middle").attr("font-size",A);const tt=l().domain([0,1]).range([w,0]);const et=J.append("g").attr("transform","translate("+_+",0)").call(g().scale(tt).tickSize(5));c({axis:et,showline:true,fontsize:A*.8});const st=o.length+p.length;et.append("text").text(s.setname[2]+", n="+st+(s.purity2?", purity="+s.purity2:"")).attr("transform","translate("+(A-_-10)+","+w/2+") 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Y){nt.filter(Y[t]).append(t).attr("rx",(t=>t.symbol?null:S(t["TinD.D"]))).attr("ry",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.D"])+W(t["TinD.R"])/2)())).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 it=l().domain([0,x]).range([R-X,0]);const rt=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const lt="#FFBEAD";rt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("x",0).attr("width",3).attr("height",R-X);c({axis:rt.call(g().scale(it).tickValues([0,x])),showline:true,fontsize:A*.8});rt.append("g").attr("transform","translate(-"+A/2+","+(R-X)/2+")").append("text").text("D total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("transform","rotate(-90)");const ot=rt.selectAll().data(i).enter().append("g").attr("transform",(t=>{t.posstring="translate("+K(t.maf1)+","+it(t["TinD.D"])+")";return t.posstring}));ot.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);ot.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=ot;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.R"]))).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 ct=l().domain([0,x]).range([0,I-X]);const pt=J.append("g").attr("transform","translate("+(_+M)+",0)");pt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("y",w).attr("width",I-X).attr("height",3);const ht=pt.append("g").attr("transform","translate(0,"+w+")").call(y().scale(ct).tickValues([0,x]));c({axis:ht,showline:true,fontsize:A*.8});pt.append("text").text("R total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("x",(I-X)/2).attr("y",w+A).attr("text-anchor","middle");const dt=pt.selectAll().data(o).enter().append("g").attr("transform",(t=>{t.posstring="translate("+ct(t["TinD.R"])+","+tt(t.maf2)+")";return t.posstring}));dt.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);dt.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=dt;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.D"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ft=J.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const mt=S(20),yt=S(x);ut+=A+yt;let gt;ft.append("text").text("SNV coverage").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",mt).attr("stroke","black").attr("fill","none");ft.append("text").text(20).attr("x",gt).attr("y",ut).attr("text-anchor","middle").attr("dominant-baseline","middle");gt+=mt+yt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",yt).attr("stroke","black").attr("fill","none");ft.append("text").text(x).attr("x",gt).attr("y",ut).attr("text-anchor","middle").attr("dominant-baseline","middle");ut+=yt+10;ft.append("text").text("Indel").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));ft.append("circle").attr("cx",gt+10+C/2).attr("cy",ut).attr("r",C/2).attr("fill","black").attr("fill-opacity",.3);ut+=30;ft.append("text").text("chrX").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("stroke-dasharray","5,5").attr("fill","none");ut+=30;ft.append("text").text("D. CNV/LOH").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt).attr("cy",ut+10).attr("r",O).attr("fill","black");ut+=30;ft.append("text").text("R. CNV/LOH").attr("y",ut).attr("dominant-baseline","central").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt-10).attr("cy",ut).attr("r",O).attr("fill","black");ut+=30;if(s.purity1!=undefined||s.purity2!=undefined){ft.append("text").text("Expected MAF").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=10;ft.append("rect").attr("fill",lt).attr("x",gt).attr("y",ut).attr("width",40).attr("height",3);ut+=30}const xt=Object.keys(b);if(xt.length){ft.append("text").text("Symbols").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));let t;for(const e in b){const s=b[e];const 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 wt=G.append("div").style("height",w+R+"px").style("margin","10px").style("padding","10px").style("border","solid 1px #ccc").style("overflow-y","scroll").style("resize","both").append("table");{const t=wt.append("tr");t.append("td").text("Gene");t.append("td").text(s.setname[1]+" only");t.append("td").text(s.setname[2]+" only");t.append("td").text("Shared")}let Tt=true;for(const t of Dt){const e=wt.append("tr");if(Tt){e.style("background-color","#f3f3f3")}Tt=!Tt;e.append("td").text(t);let s=[];if(t in bt){s=bt[t]}const a=[],n=[],i=[];for(const t of s){if(t.set_share)i.push(t);else if(t.set_1)a.push(t);else if(t.set_2)n.push(t)}let r=e.append("td");if(a.length){for(const t of a){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,ot)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(n.length){for(const t of n){const 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/{ColorScale-b44d51ef.js → ColorScale-9800a609.js}

@@ -1 +1 @@
-import{a as t}from"./axisstyle-fac7f76b.js";import{l as a,p as s}from"./app-f91922b4.js";import{d as i,c as r}from"./axis-6cb4f314.js";class o{constructor(t){this.barheight=t.barheight||14;this.barwidth=t.barwidth||100;this.startColor=t.startColor||"white";this.midColor=t.midColor||"white";this.endColor=t.endColor||"red";this.data=t.data;this.position=t.position||"0,0";this.svg={width:t.width||100,height:t.height||30};this.topTicks=t.topTicks||false;this.ticks=t.ticks||5;this.tickSize=t.tickSize||1;this.fontSize=t.fontSize||10;this.markedValue=t.markedValue&&t.markedValue>.001?t.markedValue:null;if(!t.holder)throw new Error("No holder provided for color scale.");if(!t.data)throw new Error("No data provided for color scale.");this.formatData();const a=t.holder.append("svg").attr("data-testid","sjpp-color-scale").attr("width",this.svg.width).attr("height",this.svg.height);const s=a.append("g").attr("transform",`translate(${this.position})`);const i=Math.random().toString();if(this.topTicks===true){const{scale:t,scaleAxis:a}=this.makeAxis(s,i);const{gradientStart:r,gradientMid:o,gradientEnd:e}=this.makeColorBar(s,i);this.dom={scale:t,scaleAxis:a,gradientStart:r,gradientMid:o,gradientEnd:e}}else{const{gradientStart:t,gradientMid:a,gradientEnd:r}=this.makeColorBar(s,i);const{scale:o,scaleAxis:e}=this.makeAxis(s,i);this.dom={scale:o,scaleAxis:e,gradientStart:t,gradientMid:a,gradientEnd:r};if(this.markedValue!==null)this.markedValueInColorBar(s)}}formatData(){this.data=this.data.map((t=>Number(t.toFixed(2))))}makeColorBar(t,a){const s=t.append("defs");const i=s.append("linearGradient").attr("data-testid","sjpp-color-scale-bar").attr("id",a);const r=i.append("stop").attr("offset","0%").attr("stop-color",this.startColor);const o=i.append("stop").attr("offset","100%").attr("stop-color",this.midColor);const e=i.append("stop").attr("offset","100%").attr("stop-color",this.endColor);return{gradientStart:r,gradientMid:o,gradientEnd:e}}makeAxis(t,s){t.append("rect").attr("height",this.barheight).attr("width",this.barwidth).attr("fill","url(#"+s+")");const i=t.append("g").attr("data-testid","sjpp-color-scale-axis");if(this.topTicks===false)i.attr("transform",`translate(0, ${this.barheight+2})`);const r=a().domain(this.data).range([0,this.barwidth]);return{scale:r,scaleAxis:i}}markedValueInColorBar(t){if(!this.markedValue||this.topTicks==true)return;this.dom.line=t.append("line").classed("sjpp-color-scale-marked",true).attr("data-testid","sjpp-color-scale-marked-tick").attr("y1",this.barheight-2).attr("y2",this.barheight+1).attr("stroke","black");this.dom.label=t.append("text").classed("sjpp-color-scale-marked",true).attr("data-testid","sjpp-color-scale-marked-label").attr("text-anchor","middle").attr("font-family",s).attr("font-size",this.fontSize).attr("y",this.barheight-3);this.updateValueInColorBar()}render(){const a=this.getAxis();t({axis:this.dom.scaleAxis.call(a),showline:false,fontsize:this.fontSize})}getAxis(){const t=this.topTicks===true?i(this.dom.scale):r(this.dom.scale);t.ticks(this.ticks).tickSize(this.tickSize);return t}setAxis(t){if(this.topTicks===true){return i(this.dom.scale).tickValues(t).tickSize(this.tickSize)}else{return r(this.dom.scale).tickValues(t).tickSize(this.tickSize)}}updateColors(){this.dom.gradientStart.attr("stop-color",this.startColor);this.dom.gradientMid.attr("stop-color",this.midColor);this.dom.gradientEnd.attr("stop-color",this.endColor)}updateAxis(){this.formatData();const t=this.data[0];const s=this.data[this.data.length-1];const i=[t,s];this.dom.scaleAxis.selectAll("*").remove();if(t<0&&s>0){i.splice(this.data.length/2,0,0);this.dom.scale=a().domain(i).range([0,this.barwidth/2,this.barwidth]);this.dom.gradientStart.attr("offset","0%").attr("stop-color",this.startColor);this.dom.gradientMid.attr("offset","50%").attr("stop-color",this.midColor);this.dom.gradientEnd.attr("offset","100%").attr("stop-color",this.endColor)}else{this.dom.scale=a().domain(i).range([0,this.barwidth]);this.dom.gradientStart.attr("offset","0%").attr("stop-color",this.startColor);this.dom.gradientMid.attr("offset",t>=0?"0%":"100%").attr("stop-color",t>=0?this.startColor:this.endColor);this.dom.gradientEnd.attr("offset","100%").attr("stop-color",this.endColor)}this.dom.scaleAxis.transition().duration(500).call(this.setAxis(i))}updateValueInColorBar(){if(!this.markedValue||this.topTicks==true)return;if(!this.dom.line||!this.dom.label)throw new Error("Missing dom elements to update value in color bar.");const t=Math.min(this.barwidth,this.dom.scale(this.markedValue));this.dom.line.attr("x1",t).attr("x2",t);this.dom.label.attr("x",t).text(Math.floor(this.markedValue))}updateScale(){this.updateColors();this.updateAxis();this.updateValueInColorBar()}}export{o as C};
+import{a as t}from"./axisstyle-fac7f76b.js";import{l as a,p as s}from"./app-71453429.js";import{d as i,c as r}from"./axis-6cb4f314.js";class o{constructor(t){this.barheight=t.barheight||14;this.barwidth=t.barwidth||100;this.startColor=t.startColor||"white";this.midColor=t.midColor||"white";this.endColor=t.endColor||"red";this.data=t.data;this.position=t.position||"0,0";this.svg={width:t.width||100,height:t.height||30};this.topTicks=t.topTicks||false;this.ticks=t.ticks||5;this.tickSize=t.tickSize||1;this.fontSize=t.fontSize||10;this.markedValue=t.markedValue&&t.markedValue>.001?t.markedValue:null;if(!t.holder)throw new Error("No holder provided for color scale.");if(!t.data)throw new Error("No data provided for color scale.");this.formatData();const a=t.holder.append("svg").attr("data-testid","sjpp-color-scale").attr("width",this.svg.width).attr("height",this.svg.height);const s=a.append("g").attr("transform",`translate(${this.position})`);const i=Math.random().toString();if(this.topTicks===true){const{scale:t,scaleAxis:a}=this.makeAxis(s,i);const{gradientStart:r,gradientMid:o,gradientEnd:e}=this.makeColorBar(s,i);this.dom={scale:t,scaleAxis:a,gradientStart:r,gradientMid:o,gradientEnd:e}}else{const{gradientStart:t,gradientMid:a,gradientEnd:r}=this.makeColorBar(s,i);const{scale:o,scaleAxis:e}=this.makeAxis(s,i);this.dom={scale:o,scaleAxis:e,gradientStart:t,gradientMid:a,gradientEnd:r};if(this.markedValue!==null)this.markedValueInColorBar(s)}}formatData(){this.data=this.data.map((t=>Number(t.toFixed(2))))}makeColorBar(t,a){const s=t.append("defs");const i=s.append("linearGradient").attr("data-testid","sjpp-color-scale-bar").attr("id",a);const r=i.append("stop").attr("offset","0%").attr("stop-color",this.startColor);const o=i.append("stop").attr("offset","100%").attr("stop-color",this.midColor);const e=i.append("stop").attr("offset","100%").attr("stop-color",this.endColor);return{gradientStart:r,gradientMid:o,gradientEnd:e}}makeAxis(t,s){t.append("rect").attr("height",this.barheight).attr("width",this.barwidth).attr("fill","url(#"+s+")");const i=t.append("g").attr("data-testid","sjpp-color-scale-axis");if(this.topTicks===false)i.attr("transform",`translate(0, ${this.barheight+2})`);const r=a().domain(this.data).range([0,this.barwidth]);return{scale:r,scaleAxis:i}}markedValueInColorBar(t){if(!this.markedValue||this.topTicks==true)return;this.dom.line=t.append("line").classed("sjpp-color-scale-marked",true).attr("data-testid","sjpp-color-scale-marked-tick").attr("y1",this.barheight-2).attr("y2",this.barheight+1).attr("stroke","black");this.dom.label=t.append("text").classed("sjpp-color-scale-marked",true).attr("data-testid","sjpp-color-scale-marked-label").attr("text-anchor","middle").attr("font-family",s).attr("font-size",this.fontSize).attr("y",this.barheight-3);this.updateValueInColorBar()}render(){const a=this.getAxis();t({axis:this.dom.scaleAxis.call(a),showline:false,fontsize:this.fontSize})}getAxis(){const t=this.topTicks===true?i(this.dom.scale):r(this.dom.scale);t.ticks(this.ticks).tickSize(this.tickSize);return t}setAxis(t){if(this.topTicks===true){return i(this.dom.scale).tickValues(t).tickSize(this.tickSize)}else{return r(this.dom.scale).tickValues(t).tickSize(this.tickSize)}}updateColors(){this.dom.gradientStart.attr("stop-color",this.startColor);this.dom.gradientMid.attr("stop-color",this.midColor);this.dom.gradientEnd.attr("stop-color",this.endColor)}updateAxis(){this.formatData();const t=this.data[0];const s=this.data[this.data.length-1];const i=[t,s];this.dom.scaleAxis.selectAll("*").remove();if(t<0&&s>0){i.splice(this.data.length/2,0,0);this.dom.scale=a().domain(i).range([0,this.barwidth/2,this.barwidth]);this.dom.gradientStart.attr("offset","0%").attr("stop-color",this.startColor);this.dom.gradientMid.attr("offset","50%").attr("stop-color",this.midColor);this.dom.gradientEnd.attr("offset","100%").attr("stop-color",this.endColor)}else{this.dom.scale=a().domain(i).range([0,this.barwidth]);this.dom.gradientStart.attr("offset","0%").attr("stop-color",this.startColor);this.dom.gradientMid.attr("offset",t>=0?"0%":"100%").attr("stop-color",t>=0?this.startColor:this.endColor);this.dom.gradientEnd.attr("offset","100%").attr("stop-color",this.endColor)}this.dom.scaleAxis.transition().duration(500).call(this.setAxis(i))}updateValueInColorBar(){if(!this.markedValue||this.topTicks==true)return;if(!this.dom.line||!this.dom.label)throw new Error("Missing dom elements to update value in color bar.");const t=Math.min(this.barwidth,this.dom.scale(this.markedValue));this.dom.line.attr("x1",t).attr("x2",t);this.dom.label.attr("x",t).text(Math.floor(this.markedValue))}updateScale(){this.updateColors();this.updateAxis();this.updateValueInColorBar()}}export{o as C};

package/dist/{DEanalysis-b86d0874.js → DEanalysis-567989ff.js}

@@ -1 +1 @@
-import{a as e}from"./axisstyle-fac7f76b.js";import{M as t,aS as a,az as s,l,bo as o,q as i,S as n}from"./app-f91922b4.js";import{d as r,r as c}from"./table-d6c411fd.js";import{controlsInit as d}from"./controls-8d4972c8.js";import{b as p,c as g}from"./axis-6cb4f314.js";import"./controls.btns-bad9e4cf.js";import"./controls.config-e0f394cb.js";import"./controls.overlay-3ac8773d.js";import"./termsetting-9a7511e6.js";import"path";import"./FilterRxComp-0e75dd8d.js";import"./controls.term1-008f4be4.js";import"./controls.divide-d8ac5a9b.js";const u="#ffa200";const h=new t;class m{constructor(){this.type="DEanalysis"}async init(e){e.plots.find((e=>e.id===this.id));const t=this.opts.holder.append("div").style("display","inline-block");const a=this.opts.holder.append("div").style("display","inline-block").style("margin-left","50px");const s=a.append("div").style("display","inline-block");const l=a.append("div").style("display","inline-block").style("vertical-align","top").style("margin-top","50px");const o=this.opts.holder.append("div").style("margin-left","50px");this.dom={holder:s,header:this.opts.header,controlsDiv:t,detailsDiv:l,tableDiv:o}}async setControls(e){this.dom.controlsDiv.selectAll("*").remove();const t=[{label:"Minimum read count",type:"number",chartType:"DEanalysis",settingsKey:"min_count",title:"Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset",min:0,max:1e4},{label:"Minimum total read count",type:"number",chartType:"DEanalysis",settingsKey:"min_total_count",title:"Minimum total read count required for each sample",min:0,max:1e4},{label:"P-value significance (linear scale)",type:"number",chartType:"DEanalysis",settingsKey:"pvalue",title:"P-value significance",min:0,max:1},{label:"Fold change (log scale)",type:"number",chartType:"DEanalysis",settingsKey:"foldchange",title:"Fold change",min:-10,max:10},{label:"P-value table",type:"checkbox",chartType:"DEanalysis",settingsKey:"pvaluetable",title:"Display table showing original and adjusted pvalues for all significant genes",boxLabel:""},{label:"P-value",type:"radio",chartType:"DEanalysis",settingsKey:"adjusted_original_pvalue",title:"Toggle between original and adjusted pvalues for volcano plot",options:[{label:"adjusted",value:"adjusted"},{label:"original",value:"original"}]}];if(e.mid_sample_size_cutoff>=e.sample_size1&&e.mid_sample_size_cutoff<e.sample_size2&&e.sample_size2<e.high_sample_size_cutoff||e.mid_sample_size_cutoff>=e.sample_size2&&e.mid_sample_size_cutoff<e.sample_size1&&e.sample_size1<e.high_sample_size_cutoff){t.push({label:"Method",type:"radio",chartType:"DEanalysis",settingsKey:"method",title:"Toggle between edgeR and wilcoxon test",options:[{label:"edgeR",value:"edgeR"},{label:"wilcoxon",value:"wilcoxon"}]});this.settings.method=e.method;this.state.config=e.method}if(this.app.opts.genome.termdbs){t.push({label:"Gene set overrepresentation analysis",type:"radio",chartType:"DEanalysis",settingsKey:"gene_ora",title:"Toggle between analyzing upregulated, downregulated or both genes",options:[{label:"upregulated",value:"upregulated"},{label:"downregulated",value:"downregulated"},{label:"both",value:"both"}]})}if(this.settings.pvaluetable==true){t.push({label:"Hierarchial Clustering",type:"radio",chartType:"DEanalysis",settingsKey:"hierCluster",title:"Toggle between various methods for selecting genes for hierarchial clustering",options:[{label:"Top 100 genes",value:"top100"},{label:"Top 100 upregulated",value:"top100up"},{label:"Top 100 downregulated",value:"top100down"}]});this.settings.hierCluster="top100"}this.components={controls:await d({app:this.app,id:this.id,holder:this.dom.controlsDiv,inputs:t})};this.components.controls.on("downloadClick.DEanalysis",(()=>{r(this.table_rows,this.table_cols)}))}getState(e){const t=e.plots.find((e=>e.id===this.id));if(!t)throw`No plot with id='${this.id}' found`;return{config:t}}async main(){this.config=JSON.parse(JSON.stringify(this.state.config));this.settings=this.config.settings.DEanalysis;if(this.dom.detailsDiv){this.dom.detailsDiv.selectAll("*").remove()}if(this.dom.holder){this.dom.holder.selectAll("*").remove()}const e=this.dom.detailsDiv.append("div").text("Loading...");const t=await D(this);e.remove();t.mid_sample_size_cutoff=8;t.high_sample_size_cutoff=30;await this.setControls(t);this.dom.header.style("opacity",.6).style("padding-left","10px").style("font-size","0.75em").text("DIFFERENTIAL GENE EXPRESSION");f(this,t)}}async function f(t,a){const s=a.sample_size1;const i=a.sample_size2;const n=a.data;const r=t.dom.holder;r.selectAll("*").remove();t.dom.detailsDiv.selectAll("*").remove();let d=0,h=0,m=0,f=0;for(const e of n){d=Math.min(d,e.fold_change);h=Math.max(h,e.fold_change);if(e.adjusted_p_value==0){continue}else{m=Math.min(m,e.adjusted_p_value);f=Math.max(f,e.adjusted_p_value)}}let _,v,b,y,j,D,M=50,E=50,k;const z=r.append("svg");const T=z.append("g");const P=z.append("g");const A=z.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const R=z.append("text").text("-log10(adjusted P value)").attr("fill","black").attr("text-anchor","middle");n.vo_dotarea=z.append("g");const S=n.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const C=l().domain([d,h]);const K=l().domain([m,f]);const N=n.vo_dotarea.selectAll().data(n).enter().append("g").each((function(e){e.vo_g=this}));const F=t.settings.foldchange;if(t.settings.pvalue==0)throw"p-value significance cannot be zero";const G=-Math.log10(t.settings.pvalue);const O=t.settings.adjusted_original_pvalue;let L=0;let I=0;t.table_rows=[];const q=N.append("circle").attr("stroke",(e=>{let a;if(O=="adjusted"&&e.adjusted_p_value>G&&Math.abs(e.fold_change)>F){a="red";L+=1;t.table_rows.push([{value:e.gene_name},{value:e.gene_symbol},{value:e.fold_change.toPrecision(4)},{value:Math.pow(10,-e.original_p_value).toPrecision(4)},{value:Math.pow(10,-e.adjusted_p_value).toPrecision(4)}])}else if(O=="original"&&e.original_p_value>G&&Math.abs(e.fold_change)>F){a="red";L+=1;t.table_rows.push([{value:e.gene_name},{value:e.gene_symbol},{value:e.fold_change},{value:Math.pow(10,-e.original_p_value)},{value:Math.pow(10,-e.adjusted_p_value)}])}else{a="black";I+=1}return a})).attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",u).attr("fill-opacity",0).each((function(e){e.vo_circle=this})).on("mouseover",x).on("mouseout",w);t.table_rows.sort(((e,t)=>e[2].value-t[2].value)).reverse();const H=n.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function J(t,a){b=t;y=a;_=Math.max(50,b/8);v=Math.max(50,y/8);k=Math.max(b,y)/80;const s=k*3;q.each((e=>{e.vo_radius=k}));j=Math.max(s,b/50);D=Math.max(s,y/50);T.attr("transform","translate("+_+","+M+")");P.attr("transform","translate("+(_+j)+","+(M+y+D)+")");A.attr("x",_+j+b/2).attr("y",M+y+D+v-5);R.attr("transform","translate(15,"+(M+y/2)+") rotate(-90)");n.vo_dotarea.attr("transform","translate("+(_+j)+","+M+")");S.attr("width",b).attr("height",y);C.range([0,b]);K.range([y,0]);N.attr("transform",(e=>"translate("+C(e.fold_change)+","+K(e.adjusted_p_value)+")"));q.attr("r",(e=>e.vo_radius));H.attr("x1",C(0)).attr("x2",C(0)).attr("y2",y);z.attr("width",_+j+b+E).attr("height",M+y+D+v);e({axis:T.call(p().scale(K)),color:"black",showline:true});e({axis:P.call(g().scale(C)),color:"black",showline:true})}J(400,400);if(n[0].adjusted_p_value!=undefined){r.append("div").style("margin","20px");m=0;f=0;let l;for(const e of n){let t;if(O=="adjusted"){t=e.adjusted_p_value}else{t=e.original_p_value}if(t==0)continue;m=Math.min(m,t);f=Math.max(f,t)}K.domain([m,f]);e({axis:T.call(p().scale(K)),color:"black",showline:true});N.attr("transform",(e=>{let t;if(O=="adjusted"){t=e.adjusted_p_value}else{t=e.original_p_value}return"translate("+C(e.fold_change)+","+K(t)+")"}));if(O=="adjusted"){l="-log10(adjusted P value)"}else{l="-log10(original P value)"}R.text(l);const d=o({holder:t.dom.detailsDiv});const g=[{label:"Percentage of significant genes",value:(L*100/(L+I)).toPrecision(2)},{label:"Number of significant genes",value:L},{label:"Number of total genes",value:L+I},{label:"Group1 sample size",value:s},{label:"Group2 sample size",value:i}];for(const e of g){const[t,a]=d.addRow();t.text(e.label);a.style("text-align","end").text(e.value)}t.table_cols=[{label:"Gene Name"},{label:"Gene Symbol"},{label:"log2 Fold change"},{label:"Original p-value (linear scale)"},{label:"Adjusted p-value (linear scale)"}];if(t.settings.pvaluetable==true){const e=t.dom.tableDiv.append("div").html(`<br>DE analysis results`);c({columns:t.table_cols,rows:t.table_rows,div:e,showLines:true,maxHeight:"150vh",resize:true})}else{t.dom.tableDiv.selectAll("*").remove()}if(t.settings.gene_ora&&t.app.opts.genome.termdbs){const e=[];const s=[];if(t.settings.gene_ora=="upregulated"){for(const t of a.data){if(t.gene_symbol.length>0){if(F<Math.abs(t.fold_change)&&t.fold_change>0){e.push(t.gene_symbol)}s.push(t.gene_symbol)}}}else if(t.settings.gene_ora=="downregulated"){for(const t of a.data){if(t.gene_symbol.length>0){if(F<Math.abs(t.fold_change)&&t.fold_change<0){e.push(t.gene_symbol)}s.push(t.gene_symbol)}}}else if(t.settings.gene_ora=="both"){for(const t of a.data){if(t.gene_symbol.length>0){if(F<Math.abs(t.fold_change)){e.push(t.gene_symbol)}s.push(t.gene_symbol)}}}else{console.log("Unrecognized option")}const l={sample_genes:e.toString(),background_genes:s.toString(),genome:t.app.vocabApi.opts.state.vocab.genome};const o={chartType:"geneORA",geneORAparams:l};t.app.dispatch({type:"plot_create",config:o})}}return z}async function _(e,t){try{if(e.samplelst.groups.length!=2)throw"opts.samplelst.groups[].length!=2";if(e.samplelst.groups[0].values?.length<1)throw"group 1 not having >1 samples";if(e.samplelst.groups[1].values?.length<1)throw"group 2 not having >1 samples";const t={settings:{DEanalysis:{pvalue:.05,foldchange:2,min_count:10,min_total_count:15,pvaluetable:false,adjusted_original_pvalue:"adjusted",method:undefined,gene_ora:undefined}}};return a(t,e)}catch(e){throw`${e} [DEanalysis getPlotConfig()]`}}const v=s(m);const b=v;function y(e,t){t.prepPlot({config:{chartType:"DEanalysis"}})}function x(e,t){h.clear().show(e.clientX,e.clientY);const a=[{k:"gene_name",v:t.gene_name},{k:"gene_symbol",v:t.gene_symbol},{k:"log fold change",v:t.fold_change.toPrecision(6)},{k:"log original p-value",v:t.original_p_value.toPrecision(6)},{k:"log adjusted p-value",v:t.adjusted_p_value.toPrecision(6)}];const s=o({holder:h.d});for(const e of a){const[t,a]=s.addRow();t.text(e.k);a.text(e.v)}if(!t.ma_label){i(t.ma_circle).attr("fill-opacity",.9);i(t.vo_circle).attr("fill-opacity",.9)}}function w(e,t){h.hide();if(!t.ma_label){i(t.ma_circle).attr("fill-opacity",0);i(t.vo_circle).attr("fill-opacity",0)}}async function j(e,t,a,s,l){e.term?e:{term:e};let o={chartType:"hierCluster",genes:["barchart",xxx]};if(s)o.insertBefore=s;if(l)o.id=l();await a.dispatch({type:"plot_create",config:o})}async function D(e){const t=await n("DEanalysis",{body:{genome:e.app.vocabApi.vocab.genome,dslabel:e.app.vocabApi.vocab.dslabel,samplelst:e.config.samplelst,min_count:e.settings.min_count,min_total_count:e.settings.min_total_count,method:e.settings.method}});if(t.error)console.log("server side error:",t.error);return t}export{v as DEanalysisInit,b as componentInit,_ as getPlotConfig,y as makeChartBtnMenu,j as openHiercluster};
+import{a as e}from"./axisstyle-fac7f76b.js";import{M as t,aS as a,az as s,l,bo as o,q as i,S as n}from"./app-71453429.js";import{d as r,r as c}from"./table-1dae543a.js";import{controlsInit as d}from"./controls-0467d2ec.js";import{b as p,c as g}from"./axis-6cb4f314.js";import"./controls.btns-ad7b28a2.js";import"./controls.config-6cf816fb.js";import"./controls.overlay-3a55c2ec.js";import"./termsetting-636d2271.js";import"path";import"./FilterRxComp-fc769f34.js";import"./controls.term1-59f4cd60.js";import"./controls.divide-3c0d52d7.js";const u="#ffa200";const h=new t;class m{constructor(){this.type="DEanalysis"}async init(e){e.plots.find((e=>e.id===this.id));const t=this.opts.holder.append("div").style("display","inline-block");const a=this.opts.holder.append("div").style("display","inline-block").style("margin-left","50px");const s=a.append("div").style("display","inline-block");const l=a.append("div").style("display","inline-block").style("vertical-align","top").style("margin-top","50px");const o=this.opts.holder.append("div").style("margin-left","50px");this.dom={holder:s,header:this.opts.header,controlsDiv:t,detailsDiv:l,tableDiv:o}}async setControls(e){this.dom.controlsDiv.selectAll("*").remove();const t=[{label:"Minimum read count",type:"number",chartType:"DEanalysis",settingsKey:"min_count",title:"Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset",min:0,max:1e4},{label:"Minimum total read count",type:"number",chartType:"DEanalysis",settingsKey:"min_total_count",title:"Minimum total read count required for each sample",min:0,max:1e4},{label:"P-value significance (linear scale)",type:"number",chartType:"DEanalysis",settingsKey:"pvalue",title:"P-value significance",min:0,max:1},{label:"Fold change (log scale)",type:"number",chartType:"DEanalysis",settingsKey:"foldchange",title:"Fold change",min:-10,max:10},{label:"P-value table",type:"checkbox",chartType:"DEanalysis",settingsKey:"pvaluetable",title:"Display table showing original and adjusted pvalues for all significant genes",boxLabel:""},{label:"P-value",type:"radio",chartType:"DEanalysis",settingsKey:"adjusted_original_pvalue",title:"Toggle between original and adjusted pvalues for volcano plot",options:[{label:"adjusted",value:"adjusted"},{label:"original",value:"original"}]}];if(e.mid_sample_size_cutoff>=e.sample_size1&&e.mid_sample_size_cutoff<e.sample_size2&&e.sample_size2<e.high_sample_size_cutoff||e.mid_sample_size_cutoff>=e.sample_size2&&e.mid_sample_size_cutoff<e.sample_size1&&e.sample_size1<e.high_sample_size_cutoff){t.push({label:"Method",type:"radio",chartType:"DEanalysis",settingsKey:"method",title:"Toggle between edgeR and wilcoxon test",options:[{label:"edgeR",value:"edgeR"},{label:"wilcoxon",value:"wilcoxon"}]});this.settings.method=e.method;this.state.config=e.method}if(this.app.opts.genome.termdbs){t.push({label:"Gene set overrepresentation analysis",type:"radio",chartType:"DEanalysis",settingsKey:"gene_ora",title:"Toggle between analyzing upregulated, downregulated or both genes",options:[{label:"upregulated",value:"upregulated"},{label:"downregulated",value:"downregulated"},{label:"both",value:"both"}]})}if(this.settings.pvaluetable==true){t.push({label:"Hierarchial Clustering",type:"radio",chartType:"DEanalysis",settingsKey:"hierCluster",title:"Toggle between various methods for selecting genes for hierarchial clustering",options:[{label:"Top 100 genes",value:"top100"},{label:"Top 100 upregulated",value:"top100up"},{label:"Top 100 downregulated",value:"top100down"}]});this.settings.hierCluster="top100"}this.components={controls:await d({app:this.app,id:this.id,holder:this.dom.controlsDiv,inputs:t})};this.components.controls.on("downloadClick.DEanalysis",(()=>{r(this.table_rows,this.table_cols)}))}getState(e){const t=e.plots.find((e=>e.id===this.id));if(!t)throw`No plot with id='${this.id}' found`;return{config:t}}async main(){this.config=JSON.parse(JSON.stringify(this.state.config));this.settings=this.config.settings.DEanalysis;if(this.dom.detailsDiv){this.dom.detailsDiv.selectAll("*").remove()}if(this.dom.holder){this.dom.holder.selectAll("*").remove()}const e=this.dom.detailsDiv.append("div").text("Loading...");const t=await D(this);e.remove();t.mid_sample_size_cutoff=8;t.high_sample_size_cutoff=30;await this.setControls(t);this.dom.header.style("opacity",.6).style("padding-left","10px").style("font-size","0.75em").text("DIFFERENTIAL GENE EXPRESSION");f(this,t)}}async function f(t,a){const s=a.sample_size1;const i=a.sample_size2;const n=a.data;const r=t.dom.holder;r.selectAll("*").remove();t.dom.detailsDiv.selectAll("*").remove();let d=0,h=0,m=0,f=0;for(const e of n){d=Math.min(d,e.fold_change);h=Math.max(h,e.fold_change);if(e.adjusted_p_value==0){continue}else{m=Math.min(m,e.adjusted_p_value);f=Math.max(f,e.adjusted_p_value)}}let _,v,b,y,j,D,M=50,E=50,k;const z=r.append("svg");const T=z.append("g");const P=z.append("g");const A=z.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const R=z.append("text").text("-log10(adjusted P value)").attr("fill","black").attr("text-anchor","middle");n.vo_dotarea=z.append("g");const S=n.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const C=l().domain([d,h]);const K=l().domain([m,f]);const N=n.vo_dotarea.selectAll().data(n).enter().append("g").each((function(e){e.vo_g=this}));const F=t.settings.foldchange;if(t.settings.pvalue==0)throw"p-value significance cannot be zero";const G=-Math.log10(t.settings.pvalue);const O=t.settings.adjusted_original_pvalue;let L=0;let I=0;t.table_rows=[];const q=N.append("circle").attr("stroke",(e=>{let a;if(O=="adjusted"&&e.adjusted_p_value>G&&Math.abs(e.fold_change)>F){a="red";L+=1;t.table_rows.push([{value:e.gene_name},{value:e.gene_symbol},{value:e.fold_change.toPrecision(4)},{value:Math.pow(10,-e.original_p_value).toPrecision(4)},{value:Math.pow(10,-e.adjusted_p_value).toPrecision(4)}])}else if(O=="original"&&e.original_p_value>G&&Math.abs(e.fold_change)>F){a="red";L+=1;t.table_rows.push([{value:e.gene_name},{value:e.gene_symbol},{value:e.fold_change},{value:Math.pow(10,-e.original_p_value)},{value:Math.pow(10,-e.adjusted_p_value)}])}else{a="black";I+=1}return a})).attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",u).attr("fill-opacity",0).each((function(e){e.vo_circle=this})).on("mouseover",x).on("mouseout",w);t.table_rows.sort(((e,t)=>e[2].value-t[2].value)).reverse();const H=n.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function J(t,a){b=t;y=a;_=Math.max(50,b/8);v=Math.max(50,y/8);k=Math.max(b,y)/80;const s=k*3;q.each((e=>{e.vo_radius=k}));j=Math.max(s,b/50);D=Math.max(s,y/50);T.attr("transform","translate("+_+","+M+")");P.attr("transform","translate("+(_+j)+","+(M+y+D)+")");A.attr("x",_+j+b/2).attr("y",M+y+D+v-5);R.attr("transform","translate(15,"+(M+y/2)+") rotate(-90)");n.vo_dotarea.attr("transform","translate("+(_+j)+","+M+")");S.attr("width",b).attr("height",y);C.range([0,b]);K.range([y,0]);N.attr("transform",(e=>"translate("+C(e.fold_change)+","+K(e.adjusted_p_value)+")"));q.attr("r",(e=>e.vo_radius));H.attr("x1",C(0)).attr("x2",C(0)).attr("y2",y);z.attr("width",_+j+b+E).attr("height",M+y+D+v);e({axis:T.call(p().scale(K)),color:"black",showline:true});e({axis:P.call(g().scale(C)),color:"black",showline:true})}J(400,400);if(n[0].adjusted_p_value!=undefined){r.append("div").style("margin","20px");m=0;f=0;let l;for(const e of n){let t;if(O=="adjusted"){t=e.adjusted_p_value}else{t=e.original_p_value}if(t==0)continue;m=Math.min(m,t);f=Math.max(f,t)}K.domain([m,f]);e({axis:T.call(p().scale(K)),color:"black",showline:true});N.attr("transform",(e=>{let t;if(O=="adjusted"){t=e.adjusted_p_value}else{t=e.original_p_value}return"translate("+C(e.fold_change)+","+K(t)+")"}));if(O=="adjusted"){l="-log10(adjusted P value)"}else{l="-log10(original P value)"}R.text(l);const d=o({holder:t.dom.detailsDiv});const g=[{label:"Percentage of significant genes",value:(L*100/(L+I)).toPrecision(2)},{label:"Number of significant genes",value:L},{label:"Number of total genes",value:L+I},{label:"Group1 sample size",value:s},{label:"Group2 sample size",value:i}];for(const e of g){const[t,a]=d.addRow();t.text(e.label);a.style("text-align","end").text(e.value)}t.table_cols=[{label:"Gene Name"},{label:"Gene Symbol"},{label:"log2 Fold change"},{label:"Original p-value (linear scale)"},{label:"Adjusted p-value (linear scale)"}];if(t.settings.pvaluetable==true){const e=t.dom.tableDiv.append("div").html(`<br>DE analysis results`);c({columns:t.table_cols,rows:t.table_rows,div:e,showLines:true,maxHeight:"150vh",resize:true})}else{t.dom.tableDiv.selectAll("*").remove()}if(t.settings.gene_ora&&t.app.opts.genome.termdbs){const e=[];const s=[];if(t.settings.gene_ora=="upregulated"){for(const t of a.data){if(t.gene_symbol.length>0){if(F<Math.abs(t.fold_change)&&t.fold_change>0){e.push(t.gene_symbol)}s.push(t.gene_symbol)}}}else if(t.settings.gene_ora=="downregulated"){for(const t of a.data){if(t.gene_symbol.length>0){if(F<Math.abs(t.fold_change)&&t.fold_change<0){e.push(t.gene_symbol)}s.push(t.gene_symbol)}}}else if(t.settings.gene_ora=="both"){for(const t of a.data){if(t.gene_symbol.length>0){if(F<Math.abs(t.fold_change)){e.push(t.gene_symbol)}s.push(t.gene_symbol)}}}else{console.log("Unrecognized option")}const l={sample_genes:e.toString(),background_genes:s.toString(),genome:t.app.vocabApi.opts.state.vocab.genome};const o={chartType:"geneORA",geneORAparams:l};t.app.dispatch({type:"plot_create",config:o})}}return z}async function _(e,t){try{if(e.samplelst.groups.length!=2)throw"opts.samplelst.groups[].length!=2";if(e.samplelst.groups[0].values?.length<1)throw"group 1 not having >1 samples";if(e.samplelst.groups[1].values?.length<1)throw"group 2 not having >1 samples";const t={settings:{DEanalysis:{pvalue:.05,foldchange:2,min_count:10,min_total_count:15,pvaluetable:false,adjusted_original_pvalue:"adjusted",method:undefined,gene_ora:undefined}}};return a(t,e)}catch(e){throw`${e} [DEanalysis getPlotConfig()]`}}const v=s(m);const b=v;function y(e,t){t.prepPlot({config:{chartType:"DEanalysis"}})}function x(e,t){h.clear().show(e.clientX,e.clientY);const a=[{k:"gene_name",v:t.gene_name},{k:"gene_symbol",v:t.gene_symbol},{k:"log fold change",v:t.fold_change.toPrecision(6)},{k:"log original p-value",v:t.original_p_value.toPrecision(6)},{k:"log adjusted p-value",v:t.adjusted_p_value.toPrecision(6)}];const s=o({holder:h.d});for(const e of a){const[t,a]=s.addRow();t.text(e.k);a.text(e.v)}if(!t.ma_label){i(t.ma_circle).attr("fill-opacity",.9);i(t.vo_circle).attr("fill-opacity",.9)}}function w(e,t){h.hide();if(!t.ma_label){i(t.ma_circle).attr("fill-opacity",0);i(t.vo_circle).attr("fill-opacity",0)}}async function j(e,t,a,s,l){e.term?e:{term:e};let o={chartType:"hierCluster",genes:["barchart",xxx]};if(s)o.insertBefore=s;if(l)o.id=l();await a.dispatch({type:"plot_create",config:o})}async function D(e){const t=await n("DEanalysis",{body:{genome:e.app.vocabApi.vocab.genome,dslabel:e.app.vocabApi.vocab.dslabel,samplelst:e.config.samplelst,min_count:e.settings.min_count,min_total_count:e.settings.min_total_count,method:e.settings.method}});if(t.error)console.log("server side error:",t.error);return t}export{v as DEanalysisInit,b as componentInit,_ as getPlotConfig,y as makeChartBtnMenu,j as openHiercluster};