@sjcrh/proteinpaint-client 2.76.0 → 2.76.1

package/dist/{block.mds-3ad17dfa.js → block.mds-ebe7b58d.js}

@@ -1 +1 @@
-import{p as e,ac as t,ad as n}from"./app-b369b169.js";function i(e){for(const t in e.hash){const n=e.tk.cohortFilter.holderTable.append("tr");n.append("td").style("vertical-align","top").append("div").text(t).style("color","#858585").style("margin-top","7px");const i=n.append("td").append("div").style("display","inline-block");let o=[];const a=[];for(const n of e.hash[t]){if(n.depth==0){continue}if(n.depth==1){const[d,r]=s(e,n,i,t);if(d){o=[d]}a.push({nodeid:n.id,showhidebutton:r});continue}const d=o[n.depth-2];const[r,l]=s(e,n,d,t);if(r){o[n.depth-1]=r}a.push({nodeid:n.id,showhidebutton:l})}e.tk.cohortFilter.hierarchies.keys[t].allnodes=a}}function s(n,i,s,o){const a=s.append("div");const d=a.append("div").style("display","inline-block").style("margin-right","10px");n.makenodelabel(i,d);const r=a.append("div").style("display","inline-block").attr("class","sja_handle_green").text("SHOW").style("font-size",".8em").on("mousedown",(e=>{e.stopPropagation()})).on("click",(e=>{e.stopPropagation();n.clicknode(i,o)}));if(n.tk.subTracks.find((e=>e.permanentHierarchy.nodeid==i.id))){r.text("HIDE").attr("class","sja_handle_red")}let l;if(i.isleaf){a.style("padding","5px 10px")}else{a.attr("class","sja_clb").on("click",(()=>{if(l.style("display")=="none"){n.tk.cohortFilter.hierarchies.keys[o].opennodeids.add(i.id);e(l);return}t(l);n.tk.cohortFilter.hierarchies.keys[o].opennodeids.delete(i.id)}));l=s.append("div").style("display",n.tk.cohortFilter.hierarchies.keys[o].opennodeids.has(i.id)?"block":"none").style("margin-left","20px").style("border-left","solid 1px "+n.block.legend.legendcolor).style("padding-left","5px").style("background","white")}return[l,r]}function o(e,t,i){const s=e.subTracks.findIndex((e=>e.permanentHierarchy.nodeid==i.nodeid));if(s!=-1){const n=e.subTracks[s].tkid;e.subTracks.splice(s,1);t.tk_remove(t.tklst.findIndex((e=>e.tkid==n)));e.cohortFilter.hierarchies.keys[i.hierarchyname].allnodes.find((e=>e.nodeid==i.nodeid)).showhidebutton.text("SHOW").attr("class","sja_handle_green");return}const o={};{const t=e.mds.queries[e.querykey];for(const e in t){o[e]=t[e]}switch(t.type){case n.mdscnv:o.valueCutoff=e.valueCutoff;o.bplengthUpperLimit=e.bplengthUpperLimit;o.gain={color:e.gain.color,barheight:e.gain.barheight};o.loss={color:e.loss.color,barheight:e.loss.barheight};break;case n.mdsjunction:o.readcountCutoff=e.readcountCutoff;o.axisheight=e.axisheight;o.legheight=e.legheight;o.yscaleUseLog=e.yscaleUseLog;break}}const a=t.block_addtk_template(o);a.permanentHierarchy=i;delete a.subTracks;e.subTracks.push(a);a.querykey=e.querykey;a.mds=e.mds;a.parentTk=e;delete a.infoFilter;delete a.cohortFilter;t.tk_load(a);e.cohortFilter.hierarchies.keys[i.hierarchyname].allnodes.find((e=>e.nodeid==i.nodeid)).showhidebutton.text("HIDE").attr("class","sja_handle_red")}function a(e,t,n){return t.maketklefthandle(e,n||0).text("Close").on("click",(()=>{e.parentTk.subTracks.splice(e.parentTk.subTracks.findIndex((t=>t.tkid==e.tkid)),1);t.tk_remove(t.tklst.findIndex((t=>t.tkid==e.tkid)));e.parentTk.cohortFilter.hierarchies.keys[e.permanentHierarchy.hierarchyname].allnodes.find((t=>t.nodeid==e.permanentHierarchy.nodeid)).showhidebutton.text("SHOW").attr("class","sja_handle_green")}))}export{a,i as m,o as s};
+import{p as e,ac as t,ad as n}from"./app-2cd97738.js";function i(e){for(const t in e.hash){const n=e.tk.cohortFilter.holderTable.append("tr");n.append("td").style("vertical-align","top").append("div").text(t).style("color","#858585").style("margin-top","7px");const i=n.append("td").append("div").style("display","inline-block");let o=[];const a=[];for(const n of e.hash[t]){if(n.depth==0){continue}if(n.depth==1){const[d,r]=s(e,n,i,t);if(d){o=[d]}a.push({nodeid:n.id,showhidebutton:r});continue}const d=o[n.depth-2];const[r,l]=s(e,n,d,t);if(r){o[n.depth-1]=r}a.push({nodeid:n.id,showhidebutton:l})}e.tk.cohortFilter.hierarchies.keys[t].allnodes=a}}function s(n,i,s,o){const a=s.append("div");const d=a.append("div").style("display","inline-block").style("margin-right","10px");n.makenodelabel(i,d);const r=a.append("div").style("display","inline-block").attr("class","sja_handle_green").text("SHOW").style("font-size",".8em").on("mousedown",(e=>{e.stopPropagation()})).on("click",(e=>{e.stopPropagation();n.clicknode(i,o)}));if(n.tk.subTracks.find((e=>e.permanentHierarchy.nodeid==i.id))){r.text("HIDE").attr("class","sja_handle_red")}let l;if(i.isleaf){a.style("padding","5px 10px")}else{a.attr("class","sja_clb").on("click",(()=>{if(l.style("display")=="none"){n.tk.cohortFilter.hierarchies.keys[o].opennodeids.add(i.id);e(l);return}t(l);n.tk.cohortFilter.hierarchies.keys[o].opennodeids.delete(i.id)}));l=s.append("div").style("display",n.tk.cohortFilter.hierarchies.keys[o].opennodeids.has(i.id)?"block":"none").style("margin-left","20px").style("border-left","solid 1px "+n.block.legend.legendcolor).style("padding-left","5px").style("background","white")}return[l,r]}function o(e,t,i){const s=e.subTracks.findIndex((e=>e.permanentHierarchy.nodeid==i.nodeid));if(s!=-1){const n=e.subTracks[s].tkid;e.subTracks.splice(s,1);t.tk_remove(t.tklst.findIndex((e=>e.tkid==n)));e.cohortFilter.hierarchies.keys[i.hierarchyname].allnodes.find((e=>e.nodeid==i.nodeid)).showhidebutton.text("SHOW").attr("class","sja_handle_green");return}const o={};{const t=e.mds.queries[e.querykey];for(const e in t){o[e]=t[e]}switch(t.type){case n.mdscnv:o.valueCutoff=e.valueCutoff;o.bplengthUpperLimit=e.bplengthUpperLimit;o.gain={color:e.gain.color,barheight:e.gain.barheight};o.loss={color:e.loss.color,barheight:e.loss.barheight};break;case n.mdsjunction:o.readcountCutoff=e.readcountCutoff;o.axisheight=e.axisheight;o.legheight=e.legheight;o.yscaleUseLog=e.yscaleUseLog;break}}const a=t.block_addtk_template(o);a.permanentHierarchy=i;delete a.subTracks;e.subTracks.push(a);a.querykey=e.querykey;a.mds=e.mds;a.parentTk=e;delete a.infoFilter;delete a.cohortFilter;t.tk_load(a);e.cohortFilter.hierarchies.keys[i.hierarchyname].allnodes.find((e=>e.nodeid==i.nodeid)).showhidebutton.text("HIDE").attr("class","sja_handle_red")}function a(e,t,n){return t.maketklefthandle(e,n||0).text("Close").on("click",(()=>{e.parentTk.subTracks.splice(e.parentTk.subTracks.findIndex((t=>t.tkid==e.tkid)),1);t.tk_remove(t.tklst.findIndex((t=>t.tkid==e.tkid)));e.parentTk.cohortFilter.hierarchies.keys[e.permanentHierarchy.hierarchyname].allnodes.find((t=>t.nodeid==e.permanentHierarchy.nodeid)).showhidebutton.text("SHOW").attr("class","sja_handle_green")}))}export{a,i as m,o as s};

package/dist/{block.mds.cnv-857ba868.js → block.mds.cnv-99f0a414.js}

@@ -1 +1 @@
-import{ag as e,I as t,W as l,M as a}from"./app-b369b169.js";import{l as o}from"./block.legend-d3f61ef7.js";import{m as n,s as i,a as r}from"./block.mds-3ad17dfa.js";import{b as s}from"./axis-747c801e.js";import"./vcf-5cc55588.js";import"./partition-db811f6b.js";import"./arc-3d6751aa.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";import"./legacy-d3-polyfill-bdb2d792.js";function c(e,t){t.tkcloakon(e);t.block_setheight();if(e.uninitialized){u(e,t)}const l={jwt:t.jwt,genome:t.genome.name,rglst:t.tkarg_rglst(),regionspace:t.regionspace,dslabel:e.mds.label,querykey:e.querykey,gain:{barheight:e.gain.barheight,color:e.gain.color,color2:e.gain.color2},loss:{barheight:e.loss.barheight,color:e.loss.color,color2:e.loss.color2}};h(l,e);if(e.uninitialized){delete e.uninitialized}const a=new Request(t.hostURL+"/mdscnv",{method:"POST",body:JSON.stringify(l)});fetch(a).then((e=>e.json())).then((l=>{e.maxvalue=0;if(l.error)throw{message:l.error};if(!l.src)throw{message:".imgsrc missing"};e.img.attr("width",t.width).attr("height",e.gain.barheight+e.loss.barheight).attr("xlink:href",l.src);if(l.maxvalue){e.maxvalue=l.maxvalue}t.tkcloakoff(e,{});return{gain:l.gain,loss:l.loss,attributeSummary:l.attributeSummary,hierarchySummary:l.hierarchySummary}})).catch((l=>{e.img.attr("width",1).attr("height",1);t.tkcloakoff(e,{error:e.name+": "+l.message});if(l.stack){console.log(l)}return l.passover||{}})).then((l=>{if(l.gain&&l.gain.count){e.label_gain.text(l.gain.count+" gain"+(l.gain.count>1?"s":""))}else{e.label_gain.text("no copy number gain")}if(l.loss&&l.loss.count){e.label_loss.text(l.loss.count+" loss"+(l.loss.count>1?"es":""))}else{e.label_loss.text("no copy number loss")}p(e);if(e.parentTk);else{m(l,e,t)}e.height_main=e.toppad+e.gain.barheight+e.loss.barheight+e.bottompad;t.block_setheight();d(e,t)}))}function p(a){if(!a.maxvalue){a.gain.axis.selectAll("*").remove();a.loss.axis.selectAll("*").remove();return}a.loss.axis.attr("transform","translate(0,"+a.gain.barheight+")");e({axis:a.gain.axis.call(s().scale(t().domain([a.maxvalue,0]).range([0,a.gain.barheight])).tickValues([0,a.maxvalue]).tickFormat(l("d"))),color:"black",showline:true});e({axis:a.loss.axis.call(s().scale(t().domain([0,a.maxvalue]).range([0,a.gain.barheight])).tickValues([a.maxvalue,0]).tickFormat(l("d"))),color:"black",showline:true})}function h(e,t){if(t.valueCutoff){e.valueCutoff=t.valueCutoff}if(t.bplengthUpperLimit){e.bplengthUpperLimit=t.bplengthUpperLimit}if(t.permanentHierarchy){e.permanentHierarchy=t.permanentHierarchy}else{const l={};let a=false;for(const e in t.cohortFilter.hiddenAttr){let o=0;const n={};for(const l in t.cohortFilter.hiddenAttr[e]){o++;n[l]=1}if(o){a=true;l[e]=n}}if(a){e.cohortHiddenAttr=l}}}function d(e,t){const l=3;let a=e.gain.barheight/2;if(e.subhierarchylabel){e.tklabel.attr("y",a-l-t.labelfontsize);e.subhierarchylabel.attr("y",a);e.label_gain.attr("y",a+l+t.labelfontsize)}else{e.tklabel.attr("y",a-(l+t.labelfontsize)/2);e.label_gain.attr("y",a+(l+t.labelfontsize)/2)}a=e.gain.barheight+e.loss.barheight/2;if(e.closelabel){e.label_loss.attr("y",a-(l+t.labelfontsize)/2);e.closelabel.attr("y",a+(l+t.labelfontsize)/2)}else{e.label_loss.attr("y",a)}const o=[];e.tklabel.each((function(){o.push(this.getBBox().width)}));e.label_gain.each((function(){o.push(this.getBBox().width)}));e.label_loss.each((function(){o.push(this.getBBox().width)}));if(e.subhierarchylabel){e.subhierarchylabel.each((function(){o.push(this.getBBox().width)}))}e.leftLabelMaxwidth=Math.max(...o);t.setllabel()}function m(e,t,l){t.cohortFilter.holderTable.selectAll("*").remove();if(e.attributeSummary){g(e.attributeSummary,t,l)}if(e.hierarchySummary){if(!t.cohortFilter.hierarchies){t.cohortFilter.hierarchies={keys:{}};for(const l in e.hierarchySummary){t.cohortFilter.hierarchies.keys[l]={opennodeids:new Set}}}n({hash:e.hierarchySummary,tk:t,block:l,makenodelabel:(e,l)=>{b(e,l,t);const a=e.isleaf?"#858585":"inherit";l.append("span").style("margin-right","5px").style("color",a).text(e.label||e.name);if(e.totalCount){if(e.gain){l.append("span").style("font-size",".7em").style("color",t.gain.color).text(Math.ceil(100*e.gain/e.totalCount)+"%")}if(e.loss){l.append("span").style("font-size",".7em").style("color",t.loss.color).text((e.gain?", ":"")+Math.ceil(100*e.loss/e.totalCount)+"%")}}},clicknode:(e,a)=>{i(t,l,{hierarchyname:a,levelidx:e.depth-1,valuekey:e.name,valuelabel:e.label,nodeid:e.id})}})}}function g(e,t,l){for(const a of e){const e=t.cohortFilter.holderTable.append("tr").style("border-spacing","5px").style("border-collapse","separate");e.append("td").text(a.label).style("color","#858585");const o=e.append("td");for(const e of a.values){const n=o.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{f(t,l,a,e,n)}));if(e.label){n.property("title",e.label)}b(e,n,t);n.append("span").text(e.name)}if(t.cohortFilter.hiddenAttr[a.key]){for(const e in t.cohortFilter.hiddenAttr[a.key]){const n=o.append("div").style("display","inline-block").style("padding","8px").style("color","#858585").attr("class","sja_clb").style("text-decoration","line-through").text(e).on("click",(()=>{f(t,l,a,{name:e},n)}))}}}for(const a in t.cohortFilter.hiddenAttr){if(e.findIndex((e=>e.key==a))!=-1){continue}const o=t.cohortFilter.holderTable.append("tr").style("border-spacing","5px").style("border-collapse","separate");o.append("td").text(a).style("color","#858585");const n=o.append("td");for(const e in t.cohortFilter.hiddenAttr[a]){const o=n.append("div").style("display","inline-block").style("padding","8px").style("color","#858585").attr("class","sja_clb").style("text-decoration","line-through").text(e).on("click",(()=>{f(t,l,{key:a},{name:e},o)}))}}}function b(e,t,l){const a=t.append("div").style("display","inline-block").style("margin-right","5px");if(e.gain){a.append("span").style("padding","1px 3px").style("background",l.gain.color).style("color","white").style("font-size",".8em").text(e.gain)}if(e.loss){a.append("span").style("padding","1px 3px").style("background",l.loss.color).style("color","white").style("font-size",".8em").text(e.loss)}}function f(e,t,l,a,o){const n=e.legendMenu;n.clear().showunder(o.node());if(a.gain){n.d.append("div").html('<span style="color:white;background:'+e.gain.color+'">&nbsp;'+a.gain+"&nbsp;</span> sample"+(a.gain>1?"s":"")+" with copy number gain").style("margin","10px").style("font-size",".8em").style("color","#858585")}if(a.loss){n.d.append("div").html('<span style="color:white;background:'+e.loss.color+'">&nbsp;'+a.loss+"&nbsp;</span> sample"+(a.loss>1?"s":"")+" with copy number loss").style("margin","10px").style("font-size",".8em").style("color","#858585")}n.d.append("div").text((a.label||a.name)+(a.totalCount?", "+a.totalCount+" total":"")).style("margin","10px").style("font-size",".8em").style("color","#858585");if(e.cohortFilter.hiddenAttr[l.key]&&e.cohortFilter.hiddenAttr[l.key][a.name]){n.d.append("div").attr("class","sja_menuoption").text("Show").on("click",(()=>{n.hide();o.text("Loading ...");delete e.cohortFilter.hiddenAttr[l.key][a.name];c(e,t)}))}else{n.d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{n.hide();o.text("Loading ...");if(!e.cohortFilter.hiddenAttr[l.key]){e.cohortFilter.hiddenAttr[l.key]={}}e.cohortFilter.hiddenAttr[l.key][a.name]=1;c(e,t)}))}n.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{n.hide();o.text("Loading ...");if(!e.cohortFilter.hiddenAttr[l.key]){e.cohortFilter.hiddenAttr[l.key]={}}for(const t of l.values){e.cohortFilter.hiddenAttr[l.key][t.name]=1}delete e.cohortFilter.hiddenAttr[l.key][a.name];c(e,t)}));if(e.cohortFilter.hiddenAttr[l.key]){let a=0;for(const t in e.cohortFilter.hiddenAttr[l.key]){a++}if(a){n.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{n.hide();o.text("Loading ...");delete e.cohortFilter.hiddenAttr[l.key];c(e,t)}))}}}function u(e,t){if(e.permanentHierarchy){e.subhierarchylabel=t.maketklefthandle(e).text(e.permanentHierarchy.hierarchyname+": "+e.permanentHierarchy.valuelabel).attr("class",null).attr("fill","#858585")}e.label_gain=t.maketklefthandle(e).on("click",(()=>{}));e.label_loss=t.maketklefthandle(e).on("click",(()=>{}));if(e.permanentHierarchy){e.closelabel=r(e,t)}e.config_handle=t.maketkconfighandle(e).on("click",(()=>{y(e,t)}));if(e.parentTk);else{e.legendMenu=new a({padding:"0px"});const[l,n]=o(t,e.name);e.tr_legend=l;e.td_legend=n;e.cohortFilter={holderTable:e.td_legend.append("table"),hiddenAttr:{}};if(e.mds.cohortHiddenAttr){for(const t in e.mds.cohortHiddenAttr){e.cohortFilter.hiddenAttr[t]={};for(const l in e.mds.cohortHiddenAttr[t]){e.cohortFilter.hiddenAttr[t][l]=1}}}}}function y(e,t){e.tkconfigtip.clear().showunder(e.config_handle.node());const l=e.tkconfigtip.d;{const a=l.append("div").style("margin-bottom","15px");a.append("span").html(e.valueLabel+" cutoff&nbsp;");a.append("input").property("value",e.valueCutoff||0).attr("type","number").style("width","50px").on("keyup",(l=>{if(l.code!="Enter"&&l.code!="NumpadEnter")return;let a=l.target.value;if(!a||a<0){a=0}if(a==0){if(e.valueCutoff){e.valueCutoff=0;c(e,t)}return}if(e.valueCutoff){if(e.valueCutoff==a);else{e.valueCutoff=a;c(e,t)}}else{e.valueCutoff=a;c(e,t)}}));a.append("div").style("font-size",".7em").style("color","#858585").html("Only shows CNV events with absolute "+e.valueLabel+" no less than cutoff.<br>Set to 0 to cancel.")}{const a=l.append("div").style("margin-bottom","15px");a.append("span").html("CNV segment size limit&nbsp;");a.append("input").property("value",e.bplengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(l=>{if(l.code!="Enter"&&l.code!="NumpadEnter")return;let a=l.target.value;if(!a||a<0){a=0}if(a==0){if(e.bplengthUpperLimit){e.bplengthUpperLimit=0;c(e,t)}return}if(e.bplengthUpperLimit){if(e.bplengthUpperLimit==a);else{e.bplengthUpperLimit=a;c(e,t)}}else{e.bplengthUpperLimit=a;c(e,t)}}));a.append("span").text("bp");a.append("div").style("font-size",".7em").style("color","#858585").html("Limit the CNV segment length to show only focal events.<br>Set to 0 to cancel.")}{const a=l.append("div").style("margin-bottom","15px");a.append("span").text("Track height");a.append("button").html("&nbsp;&nbsp;+&nbsp;&nbsp;").style("margin-left","10px").on("click",(()=>{e.gain.barheight+=10;e.loss.barheight+=10;c(e,t);t.block_setheight()}));a.append("button").html("&nbsp;&nbsp;-&nbsp;&nbsp;").style("margin-left","5px").on("click",(()=>{if(e.gain.barheight<=60)return;e.gain.barheight-=10;e.loss.barheight-=10;c(e,t);t.block_setheight()}))}{const a=l.append("div").style("margin-bottom","1px");a.append("span").html("Copy number gain&nbsp;");a.append("input").attr("type","color").property("value",e.gain.color).on("change",(l=>{e.gain.color=l.target.value;c(e,t)}));a.append("span").html("&nbsp;&nbsp;loss&nbsp;");a.append("input").attr("type","color").property("value",e.loss.color).on("change",(l=>{e.loss.color=l.target.value;c(e,t)}))}}export{c as loadTk};
+import{ag as e,I as t,W as l,M as a}from"./app-2cd97738.js";import{l as o}from"./block.legend-d2b7f1cb.js";import{m as n,s as i,a as r}from"./block.mds-ebe7b58d.js";import{b as s}from"./axis-747c801e.js";import"./vcf-145bf5dd.js";import"./partition-db811f6b.js";import"./arc-3d6751aa.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";import"./legacy-d3-polyfill-bdb2d792.js";function c(e,t){t.tkcloakon(e);t.block_setheight();if(e.uninitialized){u(e,t)}const l={jwt:t.jwt,genome:t.genome.name,rglst:t.tkarg_rglst(),regionspace:t.regionspace,dslabel:e.mds.label,querykey:e.querykey,gain:{barheight:e.gain.barheight,color:e.gain.color,color2:e.gain.color2},loss:{barheight:e.loss.barheight,color:e.loss.color,color2:e.loss.color2}};h(l,e);if(e.uninitialized){delete e.uninitialized}const a=new Request(t.hostURL+"/mdscnv",{method:"POST",body:JSON.stringify(l)});fetch(a).then((e=>e.json())).then((l=>{e.maxvalue=0;if(l.error)throw{message:l.error};if(!l.src)throw{message:".imgsrc missing"};e.img.attr("width",t.width).attr("height",e.gain.barheight+e.loss.barheight).attr("xlink:href",l.src);if(l.maxvalue){e.maxvalue=l.maxvalue}t.tkcloakoff(e,{});return{gain:l.gain,loss:l.loss,attributeSummary:l.attributeSummary,hierarchySummary:l.hierarchySummary}})).catch((l=>{e.img.attr("width",1).attr("height",1);t.tkcloakoff(e,{error:e.name+": "+l.message});if(l.stack){console.log(l)}return l.passover||{}})).then((l=>{if(l.gain&&l.gain.count){e.label_gain.text(l.gain.count+" gain"+(l.gain.count>1?"s":""))}else{e.label_gain.text("no copy number gain")}if(l.loss&&l.loss.count){e.label_loss.text(l.loss.count+" loss"+(l.loss.count>1?"es":""))}else{e.label_loss.text("no copy number loss")}p(e);if(e.parentTk);else{m(l,e,t)}e.height_main=e.toppad+e.gain.barheight+e.loss.barheight+e.bottompad;t.block_setheight();d(e,t)}))}function p(a){if(!a.maxvalue){a.gain.axis.selectAll("*").remove();a.loss.axis.selectAll("*").remove();return}a.loss.axis.attr("transform","translate(0,"+a.gain.barheight+")");e({axis:a.gain.axis.call(s().scale(t().domain([a.maxvalue,0]).range([0,a.gain.barheight])).tickValues([0,a.maxvalue]).tickFormat(l("d"))),color:"black",showline:true});e({axis:a.loss.axis.call(s().scale(t().domain([0,a.maxvalue]).range([0,a.gain.barheight])).tickValues([a.maxvalue,0]).tickFormat(l("d"))),color:"black",showline:true})}function h(e,t){if(t.valueCutoff){e.valueCutoff=t.valueCutoff}if(t.bplengthUpperLimit){e.bplengthUpperLimit=t.bplengthUpperLimit}if(t.permanentHierarchy){e.permanentHierarchy=t.permanentHierarchy}else{const l={};let a=false;for(const e in t.cohortFilter.hiddenAttr){let o=0;const n={};for(const l in t.cohortFilter.hiddenAttr[e]){o++;n[l]=1}if(o){a=true;l[e]=n}}if(a){e.cohortHiddenAttr=l}}}function d(e,t){const l=3;let a=e.gain.barheight/2;if(e.subhierarchylabel){e.tklabel.attr("y",a-l-t.labelfontsize);e.subhierarchylabel.attr("y",a);e.label_gain.attr("y",a+l+t.labelfontsize)}else{e.tklabel.attr("y",a-(l+t.labelfontsize)/2);e.label_gain.attr("y",a+(l+t.labelfontsize)/2)}a=e.gain.barheight+e.loss.barheight/2;if(e.closelabel){e.label_loss.attr("y",a-(l+t.labelfontsize)/2);e.closelabel.attr("y",a+(l+t.labelfontsize)/2)}else{e.label_loss.attr("y",a)}const o=[];e.tklabel.each((function(){o.push(this.getBBox().width)}));e.label_gain.each((function(){o.push(this.getBBox().width)}));e.label_loss.each((function(){o.push(this.getBBox().width)}));if(e.subhierarchylabel){e.subhierarchylabel.each((function(){o.push(this.getBBox().width)}))}e.leftLabelMaxwidth=Math.max(...o);t.setllabel()}function m(e,t,l){t.cohortFilter.holderTable.selectAll("*").remove();if(e.attributeSummary){b(e.attributeSummary,t,l)}if(e.hierarchySummary){if(!t.cohortFilter.hierarchies){t.cohortFilter.hierarchies={keys:{}};for(const l in e.hierarchySummary){t.cohortFilter.hierarchies.keys[l]={opennodeids:new Set}}}n({hash:e.hierarchySummary,tk:t,block:l,makenodelabel:(e,l)=>{g(e,l,t);const a=e.isleaf?"#858585":"inherit";l.append("span").style("margin-right","5px").style("color",a).text(e.label||e.name);if(e.totalCount){if(e.gain){l.append("span").style("font-size",".7em").style("color",t.gain.color).text(Math.ceil(100*e.gain/e.totalCount)+"%")}if(e.loss){l.append("span").style("font-size",".7em").style("color",t.loss.color).text((e.gain?", ":"")+Math.ceil(100*e.loss/e.totalCount)+"%")}}},clicknode:(e,a)=>{i(t,l,{hierarchyname:a,levelidx:e.depth-1,valuekey:e.name,valuelabel:e.label,nodeid:e.id})}})}}function b(e,t,l){for(const a of e){const e=t.cohortFilter.holderTable.append("tr").style("border-spacing","5px").style("border-collapse","separate");e.append("td").text(a.label).style("color","#858585");const o=e.append("td");for(const e of a.values){const n=o.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{f(t,l,a,e,n)}));if(e.label){n.property("title",e.label)}g(e,n,t);n.append("span").text(e.name)}if(t.cohortFilter.hiddenAttr[a.key]){for(const e in t.cohortFilter.hiddenAttr[a.key]){const n=o.append("div").style("display","inline-block").style("padding","8px").style("color","#858585").attr("class","sja_clb").style("text-decoration","line-through").text(e).on("click",(()=>{f(t,l,a,{name:e},n)}))}}}for(const a in t.cohortFilter.hiddenAttr){if(e.findIndex((e=>e.key==a))!=-1){continue}const o=t.cohortFilter.holderTable.append("tr").style("border-spacing","5px").style("border-collapse","separate");o.append("td").text(a).style("color","#858585");const n=o.append("td");for(const e in t.cohortFilter.hiddenAttr[a]){const o=n.append("div").style("display","inline-block").style("padding","8px").style("color","#858585").attr("class","sja_clb").style("text-decoration","line-through").text(e).on("click",(()=>{f(t,l,{key:a},{name:e},o)}))}}}function g(e,t,l){const a=t.append("div").style("display","inline-block").style("margin-right","5px");if(e.gain){a.append("span").style("padding","1px 3px").style("background",l.gain.color).style("color","white").style("font-size",".8em").text(e.gain)}if(e.loss){a.append("span").style("padding","1px 3px").style("background",l.loss.color).style("color","white").style("font-size",".8em").text(e.loss)}}function f(e,t,l,a,o){const n=e.legendMenu;n.clear().showunder(o.node());if(a.gain){n.d.append("div").html('<span style="color:white;background:'+e.gain.color+'">&nbsp;'+a.gain+"&nbsp;</span> sample"+(a.gain>1?"s":"")+" with copy number gain").style("margin","10px").style("font-size",".8em").style("color","#858585")}if(a.loss){n.d.append("div").html('<span style="color:white;background:'+e.loss.color+'">&nbsp;'+a.loss+"&nbsp;</span> sample"+(a.loss>1?"s":"")+" with copy number loss").style("margin","10px").style("font-size",".8em").style("color","#858585")}n.d.append("div").text((a.label||a.name)+(a.totalCount?", "+a.totalCount+" total":"")).style("margin","10px").style("font-size",".8em").style("color","#858585");if(e.cohortFilter.hiddenAttr[l.key]&&e.cohortFilter.hiddenAttr[l.key][a.name]){n.d.append("div").attr("class","sja_menuoption").text("Show").on("click",(()=>{n.hide();o.text("Loading ...");delete e.cohortFilter.hiddenAttr[l.key][a.name];c(e,t)}))}else{n.d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{n.hide();o.text("Loading ...");if(!e.cohortFilter.hiddenAttr[l.key]){e.cohortFilter.hiddenAttr[l.key]={}}e.cohortFilter.hiddenAttr[l.key][a.name]=1;c(e,t)}))}n.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{n.hide();o.text("Loading ...");if(!e.cohortFilter.hiddenAttr[l.key]){e.cohortFilter.hiddenAttr[l.key]={}}for(const t of l.values){e.cohortFilter.hiddenAttr[l.key][t.name]=1}delete e.cohortFilter.hiddenAttr[l.key][a.name];c(e,t)}));if(e.cohortFilter.hiddenAttr[l.key]){let a=0;for(const t in e.cohortFilter.hiddenAttr[l.key]){a++}if(a){n.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{n.hide();o.text("Loading ...");delete e.cohortFilter.hiddenAttr[l.key];c(e,t)}))}}}function u(e,t){if(e.permanentHierarchy){e.subhierarchylabel=t.maketklefthandle(e).text(e.permanentHierarchy.hierarchyname+": "+e.permanentHierarchy.valuelabel).attr("class",null).attr("fill","#858585")}e.label_gain=t.maketklefthandle(e).on("click",(()=>{}));e.label_loss=t.maketklefthandle(e).on("click",(()=>{}));if(e.permanentHierarchy){e.closelabel=r(e,t)}e.config_handle=t.maketkconfighandle(e).on("click",(()=>{y(e,t)}));if(e.parentTk);else{e.legendMenu=new a({padding:"0px"});const[l,n]=o(t,e.name);e.tr_legend=l;e.td_legend=n;e.cohortFilter={holderTable:e.td_legend.append("table"),hiddenAttr:{}};if(e.mds.cohortHiddenAttr){for(const t in e.mds.cohortHiddenAttr){e.cohortFilter.hiddenAttr[t]={};for(const l in e.mds.cohortHiddenAttr[t]){e.cohortFilter.hiddenAttr[t][l]=1}}}}}function y(e,t){e.tkconfigtip.clear().showunder(e.config_handle.node());const l=e.tkconfigtip.d;{const a=l.append("div").style("margin-bottom","15px");a.append("span").html(e.valueLabel+" cutoff&nbsp;");a.append("input").property("value",e.valueCutoff||0).attr("type","number").style("width","50px").on("keyup",(l=>{if(l.code!="Enter"&&l.code!="NumpadEnter")return;let a=l.target.value;if(!a||a<0){a=0}if(a==0){if(e.valueCutoff){e.valueCutoff=0;c(e,t)}return}if(e.valueCutoff){if(e.valueCutoff==a);else{e.valueCutoff=a;c(e,t)}}else{e.valueCutoff=a;c(e,t)}}));a.append("div").style("font-size",".7em").style("color","#858585").html("Only shows CNV events with absolute "+e.valueLabel+" no less than cutoff.<br>Set to 0 to cancel.")}{const a=l.append("div").style("margin-bottom","15px");a.append("span").html("CNV segment size limit&nbsp;");a.append("input").property("value",e.bplengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(l=>{if(l.code!="Enter"&&l.code!="NumpadEnter")return;let a=l.target.value;if(!a||a<0){a=0}if(a==0){if(e.bplengthUpperLimit){e.bplengthUpperLimit=0;c(e,t)}return}if(e.bplengthUpperLimit){if(e.bplengthUpperLimit==a);else{e.bplengthUpperLimit=a;c(e,t)}}else{e.bplengthUpperLimit=a;c(e,t)}}));a.append("span").text("bp");a.append("div").style("font-size",".7em").style("color","#858585").html("Limit the CNV segment length to show only focal events.<br>Set to 0 to cancel.")}{const a=l.append("div").style("margin-bottom","15px");a.append("span").text("Track height");a.append("button").html("&nbsp;&nbsp;+&nbsp;&nbsp;").style("margin-left","10px").on("click",(()=>{e.gain.barheight+=10;e.loss.barheight+=10;c(e,t);t.block_setheight()}));a.append("button").html("&nbsp;&nbsp;-&nbsp;&nbsp;").style("margin-left","5px").on("click",(()=>{if(e.gain.barheight<=60)return;e.gain.barheight-=10;e.loss.barheight-=10;c(e,t);t.block_setheight()}))}{const a=l.append("div").style("margin-bottom","1px");a.append("span").html("Copy number gain&nbsp;");a.append("input").attr("type","color").property("value",e.gain.color).on("change",(l=>{e.gain.color=l.target.value;c(e,t)}));a.append("span").html("&nbsp;&nbsp;loss&nbsp;");a.append("input").attr("type","color").property("value",e.loss.color).on("change",(l=>{e.loss.color=l.target.value;c(e,t)}))}}export{c as loadTk};

package/dist/{block.mds.expressionrank-7e3b208c.js → block.mds.expressionrank-96bf864b.js}

@@ -1 +1 @@
-import{q as t,r as e,c0 as a,a9 as s,Z as n,ag as r,I as o,b as i}from"./app-b369b169.js";import{m as l,a as c,s as p,i as d}from"./block.mds.expressionstat-f2d31c86.js";import{b as f}from"./axis-747c801e.js";async function h(e,a){a.tkcloakon(e);a.block_setheight();if(e.uninitialized){b(e,a);delete e.uninitialized}const s=[];for(let t=a.startidx;t<=a.stopidx;t++){const e=a.rglst[t];s.push({chr:e.chr,start:e.start,stop:e.stop,width:e.width})}if(a.subpanels.length==e.subpanels.length){for(const[t,e]of a.subpanels.entries()){s.push({chr:e.chr,start:e.start,stop:e.stop,width:e.width,exonsf:e.exonsf,subpanelidx:t})}}e.regions=s;const n=[];for(const r of s){const s={jwt:a.jwt,genome:a.genome.name,rglst:[{chr:r.chr,start:r.start,stop:r.stop}],sample:e.sample};if(e.iscustom){s.iscustom=1;s.file=e.file;s.url=e.url;s.indexURL=e.indexURL}else{s.dslabel=e.mds.label;s.querykey=e.querykey;s.attributes=e.attributes}n.push(t("/mdsexpressionrank",s).then((t=>{if(t.error)throw{message:t.error};if(t.result&&t.result.length>0){r.items=t.result}e.totalsamples=t.samplecount;return})))}Promise.all(n).then((()=>{if(!e.regions.find((t=>t.items)))throw{message:"no data in view range"}})).catch((t=>{if(t.stack){console.log(t.stack)}return t.message})).then((t=>{g(e,a);a.tkcloakoff(e,{error:t})}))}function g(t,i){t.glider.selectAll("*").remove();for(const e of t.subpanels){e.glider.attr("transform","translate(0,0)").selectAll("*").remove()}let d=null,h;if(t.showrank){d=0;h=100}else{for(const e of t.regions){if(!e.items)continue;for(const t of e.items){if(d==null){d=h=t.thisvalue}else{d=Math.min(d,t.thisvalue);h=Math.max(h,t.thisvalue)}}}if(d>0)d=0;else if(h<0)h=0}const g=u(d,h,t.barheight);for(const r of t.regions){if(!r.items)continue;const o=r.subpanelidx!=undefined?t.subpanels[r.subpanelidx].glider:t.glider;for(const d of r.items){const f=Math.max(r.start,d.start);const h=Math.min(r.stop,d.stop);let u,m;if(r.subpanelidx!=undefined){u=(f-r.start)*r.exonsf;m=(h-r.start)*r.exonsf}else{const t=i.seekcoord(r.chr,f)[0];const e=i.seekcoord(r.chr,h)[0];if(!t||!e)continue;u=Math.min(t.x,e.x);m=Math.max(t.x,e.x)}const[b,k]=g(t.showrank?d.rank:d.thisvalue);l(d,t.gecfg);const x=c(d,t.gecfg);const y=e(x);const w="rgba("+y.r+","+y.g+","+y.b+",.2)";const v=o.append("g").attr("transform","translate("+u+",0)");v.append("line").attr("x2",Math.max(2,m-u)).attr("stroke",x).attr("stroke-width",1).attr("shape-rendering","crispEdges").attr("y1",d.rank>0?b:b+k).attr("y2",d.rank>0?b:b+k);v.append("rect").attr("y",b).attr("width",Math.max(2,m-u)).attr("height",k).attr("fill",w).attr("shape-rendering","crispEdges").on("mouseover",(e=>{e.target.setAttribute("stroke",x);t.tktip.clear().show(e.clientX,e.clientY);const n=[{k:"gene",v:d.gene},{k:"rank",v:a(d.rank)},{k:t.gecfg.datatype||"actual value",v:d.thisvalue}];const r=s(t.tktip.d,n).style("margin","0px");{const t=r.append("tr");const e=t.append("td").attr("colspan",3);e.text(d.chr+":"+d.start+"-"+d.stop)}p(d,t.gecfg,r)})).on("mouseout",(e=>{t.tktip.hide();e.target.setAttribute("stroke","")})).on("click",(e=>{const a=n({x:e.clientX,y:e.clientY});a.header.text(d.gene+" "+t.gecfg.datatype);const s={gene:d.gene,chr:d.chr,start:d.start,stop:d.stop,holder:a.body,genome:i.genome,jwt:i.jwt,hostURL:i.hostURL,sample:{name:t.sample,value:d.thisvalue}};if(t.iscustom){s.file=t.file;s.url=t.url;s.indexURL=t.indexURL}else{s.dslabel=t.mds.label;s.querykey=t.querykey}import("./block.mds.geneboxplot-f0fbaf12.js").then((t=>{t.init(s)}))}))}}t.rankaxis.label.text(t.showrank?"Rank":t.gecfg.datatype||"actual value");r({axis:t.rankaxis.g.call(f().scale(o().domain([d,h]).range([t.barheight,0])).tickValues([d,h])),showline:true});m(t,i)}function u(t,e,a){return s=>{if(t<0){if(e<=0){return[0,Math.max(1,a*s/t)]}const n=a/(e-t);if(s>0)return[n*(e-s),Math.max(1,n*s)];return[n*e,Math.max(1,n*-s)]}const n=a/e;return[n*(e-s),Math.max(1,n*s)]}}function m(t,e){t.tklabel.attr("y",t.barheight/2-e.labelfontsize/2);t.rankaxis.label.attr("y",t.barheight/2+e.labelfontsize/2);t.height_main=t.toppad+t.barheight+t.bottompad;e.block_setheight()}async function b(t,e){if(!t.sample)throw"sample name missing";if(t.dslabel){delete t.iscustom}if(t.iscustom){if(!t.file&&!t.url)throw"file or url missing for custom tk";if(!t.gecfg)t.gecfg={}}else{if(!t.dslabel)throw"dslabel missing for native track";if(!t.querykey)throw"querykey missing for native track";t.mds=e.genome.datasets[t.dslabel];if(!t.mds)throw"dataset not found: invalid value for dslabel";if(t.mds.mdsIsUninitiated){const a=await i(`getDataset?genome=${e.genome.name}&dsname=${t.dslabel}`);if(a.error)throw a.error;if(!a.ds)throw"ds missing";Object.assign(t.mds,a.ds);delete t.mds.mdsIsUninitiated}delete t.dslabel;t.gecfg=t.mds.queries[t.querykey];if(!t.gecfg)throw"expression query not found: invalid value for querykey"}if(t.datatype){t.gecfg.datatype=t.datatype;delete t.datatype}if(!t.barheight)t.barheight=60;if(!("showrank"in t))t.showrank=true;if(!t.gecfg.itemcolor){t.gecfg.itemcolor="green"}d(t.gecfg);t.rankaxis={g:t.gleft.append("g"),label:e.maketklefthandle(t).attr("class",null)};t.config_handle=e.maketkconfighandle(t).attr("y",10+e.labelfontsize).on("click",(a=>{k(t,e)}))}function k(t,e){t.tkconfigtip.clear().showunder(t.config_handle.node());{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Height&nbsp;&nbsp;");a.append("input").attr("size",5).property("value",t.barheight).on("keyup",(a=>{if(a.key!="Enter")return;const s=a.target.value;if(s=="")return;const n=Number.parseInt(s);if(Number.isNaN(n)||n<=1){alert("track height must be positive integer");return}t.barheight=n;g(t,e)}))}{const a=t.tkconfigtip.d.append("table").style("margin-bottom","15px").style("border-spacing","5px");const n=Math.random();let r,o;{const s=a.append("tr");s.append("td").text("Show");const r=s.append("td");o=r.append("input").attr("type","radio").attr("name",n).attr("id",n+2).on("change",(a=>{t.showrank=false;g(t,e)}));r.append("label").html("&nbsp;"+(t.gecfg.datatype||"actual value")).attr("for",n+2).attr("class","sja_clbtext")}{const o=a.append("tr");o.append("td");const i=o.append("td");r=i.append("input").attr("type","radio").attr("name",n).attr("id",n+1).on("change",(a=>{t.showrank=true;g(t,e)}));i.append("label").html("&nbsp;Rank of a group of samples").attr("for",n+1).attr("class","sja_clbtext").style("margin-right","10px");const l=[];if(t.attributes){for(const e of t.attributes){l.push({k:e.label||e.k,v:e.fullvalue||e.kvalue})}}if(t.totalsamples){l.push({k:"Total number of samples",v:t.totalsamples+1})}if(l.length){s(i,l)}}if(t.showrank){r.property("checked",1)}else{o.property("checked",1)}}}export{h as loadTk};
+import{q as t,r as e,c0 as a,a9 as s,Z as n,ag as r,I as o,b as i}from"./app-2cd97738.js";import{m as l,a as c,s as p,i as d}from"./block.mds.expressionstat-dcab3fd1.js";import{b as f}from"./axis-747c801e.js";async function h(e,a){a.tkcloakon(e);a.block_setheight();if(e.uninitialized){b(e,a);delete e.uninitialized}const s=[];for(let t=a.startidx;t<=a.stopidx;t++){const e=a.rglst[t];s.push({chr:e.chr,start:e.start,stop:e.stop,width:e.width})}if(a.subpanels.length==e.subpanels.length){for(const[t,e]of a.subpanels.entries()){s.push({chr:e.chr,start:e.start,stop:e.stop,width:e.width,exonsf:e.exonsf,subpanelidx:t})}}e.regions=s;const n=[];for(const r of s){const s={jwt:a.jwt,genome:a.genome.name,rglst:[{chr:r.chr,start:r.start,stop:r.stop}],sample:e.sample};if(e.iscustom){s.iscustom=1;s.file=e.file;s.url=e.url;s.indexURL=e.indexURL}else{s.dslabel=e.mds.label;s.querykey=e.querykey;s.attributes=e.attributes}n.push(t("/mdsexpressionrank",s).then((t=>{if(t.error)throw{message:t.error};if(t.result&&t.result.length>0){r.items=t.result}e.totalsamples=t.samplecount;return})))}Promise.all(n).then((()=>{if(!e.regions.find((t=>t.items)))throw{message:"no data in view range"}})).catch((t=>{if(t.stack){console.log(t.stack)}return t.message})).then((t=>{g(e,a);a.tkcloakoff(e,{error:t})}))}function g(t,i){t.glider.selectAll("*").remove();for(const e of t.subpanels){e.glider.attr("transform","translate(0,0)").selectAll("*").remove()}let d=null,h;if(t.showrank){d=0;h=100}else{for(const e of t.regions){if(!e.items)continue;for(const t of e.items){if(d==null){d=h=t.thisvalue}else{d=Math.min(d,t.thisvalue);h=Math.max(h,t.thisvalue)}}}if(d>0)d=0;else if(h<0)h=0}const g=u(d,h,t.barheight);for(const r of t.regions){if(!r.items)continue;const o=r.subpanelidx!=undefined?t.subpanels[r.subpanelidx].glider:t.glider;for(const d of r.items){const f=Math.max(r.start,d.start);const h=Math.min(r.stop,d.stop);let u,m;if(r.subpanelidx!=undefined){u=(f-r.start)*r.exonsf;m=(h-r.start)*r.exonsf}else{const t=i.seekcoord(r.chr,f)[0];const e=i.seekcoord(r.chr,h)[0];if(!t||!e)continue;u=Math.min(t.x,e.x);m=Math.max(t.x,e.x)}const[b,k]=g(t.showrank?d.rank:d.thisvalue);l(d,t.gecfg);const x=c(d,t.gecfg);const y=e(x);const w="rgba("+y.r+","+y.g+","+y.b+",.2)";const v=o.append("g").attr("transform","translate("+u+",0)");v.append("line").attr("x2",Math.max(2,m-u)).attr("stroke",x).attr("stroke-width",1).attr("shape-rendering","crispEdges").attr("y1",d.rank>0?b:b+k).attr("y2",d.rank>0?b:b+k);v.append("rect").attr("y",b).attr("width",Math.max(2,m-u)).attr("height",k).attr("fill",w).attr("shape-rendering","crispEdges").on("mouseover",(e=>{e.target.setAttribute("stroke",x);t.tktip.clear().show(e.clientX,e.clientY);const n=[{k:"gene",v:d.gene},{k:"rank",v:a(d.rank)},{k:t.gecfg.datatype||"actual value",v:d.thisvalue}];const r=s(t.tktip.d,n).style("margin","0px");{const t=r.append("tr");const e=t.append("td").attr("colspan",3);e.text(d.chr+":"+d.start+"-"+d.stop)}p(d,t.gecfg,r)})).on("mouseout",(e=>{t.tktip.hide();e.target.setAttribute("stroke","")})).on("click",(e=>{const a=n({x:e.clientX,y:e.clientY});a.header.text(d.gene+" "+t.gecfg.datatype);const s={gene:d.gene,chr:d.chr,start:d.start,stop:d.stop,holder:a.body,genome:i.genome,jwt:i.jwt,hostURL:i.hostURL,sample:{name:t.sample,value:d.thisvalue}};if(t.iscustom){s.file=t.file;s.url=t.url;s.indexURL=t.indexURL}else{s.dslabel=t.mds.label;s.querykey=t.querykey}import("./block.mds.geneboxplot-e5b2a4ce.js").then((t=>{t.init(s)}))}))}}t.rankaxis.label.text(t.showrank?"Rank":t.gecfg.datatype||"actual value");r({axis:t.rankaxis.g.call(f().scale(o().domain([d,h]).range([t.barheight,0])).tickValues([d,h])),showline:true});m(t,i)}function u(t,e,a){return s=>{if(t<0){if(e<=0){return[0,Math.max(1,a*s/t)]}const n=a/(e-t);if(s>0)return[n*(e-s),Math.max(1,n*s)];return[n*e,Math.max(1,n*-s)]}const n=a/e;return[n*(e-s),Math.max(1,n*s)]}}function m(t,e){t.tklabel.attr("y",t.barheight/2-e.labelfontsize/2);t.rankaxis.label.attr("y",t.barheight/2+e.labelfontsize/2);t.height_main=t.toppad+t.barheight+t.bottompad;e.block_setheight()}async function b(t,e){if(!t.sample)throw"sample name missing";if(t.dslabel){delete t.iscustom}if(t.iscustom){if(!t.file&&!t.url)throw"file or url missing for custom tk";if(!t.gecfg)t.gecfg={}}else{if(!t.dslabel)throw"dslabel missing for native track";if(!t.querykey)throw"querykey missing for native track";t.mds=e.genome.datasets[t.dslabel];if(!t.mds)throw"dataset not found: invalid value for dslabel";if(t.mds.mdsIsUninitiated){const a=await i(`getDataset?genome=${e.genome.name}&dsname=${t.dslabel}`);if(a.error)throw a.error;if(!a.ds)throw"ds missing";Object.assign(t.mds,a.ds);delete t.mds.mdsIsUninitiated}delete t.dslabel;t.gecfg=t.mds.queries[t.querykey];if(!t.gecfg)throw"expression query not found: invalid value for querykey"}if(t.datatype){t.gecfg.datatype=t.datatype;delete t.datatype}if(!t.barheight)t.barheight=60;if(!("showrank"in t))t.showrank=true;if(!t.gecfg.itemcolor){t.gecfg.itemcolor="green"}d(t.gecfg);t.rankaxis={g:t.gleft.append("g"),label:e.maketklefthandle(t).attr("class",null)};t.config_handle=e.maketkconfighandle(t).attr("y",10+e.labelfontsize).on("click",(a=>{k(t,e)}))}function k(t,e){t.tkconfigtip.clear().showunder(t.config_handle.node());{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Height&nbsp;&nbsp;");a.append("input").attr("size",5).property("value",t.barheight).on("keyup",(a=>{if(a.key!="Enter")return;const s=a.target.value;if(s=="")return;const n=Number.parseInt(s);if(Number.isNaN(n)||n<=1){alert("track height must be positive integer");return}t.barheight=n;g(t,e)}))}{const a=t.tkconfigtip.d.append("table").style("margin-bottom","15px").style("border-spacing","5px");const n=Math.random();let r,o;{const s=a.append("tr");s.append("td").text("Show");const r=s.append("td");o=r.append("input").attr("type","radio").attr("name",n).attr("id",n+2).on("change",(a=>{t.showrank=false;g(t,e)}));r.append("label").html("&nbsp;"+(t.gecfg.datatype||"actual value")).attr("for",n+2).attr("class","sja_clbtext")}{const o=a.append("tr");o.append("td");const i=o.append("td");r=i.append("input").attr("type","radio").attr("name",n).attr("id",n+1).on("change",(a=>{t.showrank=true;g(t,e)}));i.append("label").html("&nbsp;Rank of a group of samples").attr("for",n+1).attr("class","sja_clbtext").style("margin-right","10px");const l=[];if(t.attributes){for(const e of t.attributes){l.push({k:e.label||e.k,v:e.fullvalue||e.kvalue})}}if(t.totalsamples){l.push({k:"Total number of samples",v:t.totalsamples+1})}if(l.length){s(i,l)}}if(t.showrank){r.property("checked",1)}else{o.property("checked",1)}}}export{h as loadTk};

package/dist/{block.mds.expressionstat-f2d31c86.js → block.mds.expressionstat-dcab3fd1.js}

@@ -1 +1 @@
-import{a9 as e,aN as t}from"./app-b369b169.js";const a="#858585";function l(e){if(!e.datatype)e.datatype="FPKM";if(!e.itemcolor)e.itemcolor="green";if(!e.ase)e.ase={};if(e.ase.qvalue==undefined)e.ase.qvalue=.05;if(e.ase.meandelta_monoallelic==undefined)e.ase.meandelta_monoallelic=.3;if(e.ase.asemarkernumber_biallelic==undefined)e.ase.asemarkernumber_biallelic=0;if(!e.ase.color_noinfo)e.ase.color_noinfo=a;if(!e.ase.color_uncertain)e.ase.color_uncertain="#A8E0B5";if(!e.ase.color_biallelic)e.ase.color_biallelic="#40859C";if(!e.ase.color_monoallelic)e.ase.color_monoallelic="#d95f02";if(!e.outlier)e.outlier={};if(e.outlier.pvalue_cutoff==undefined)e.outlier.pvalue_cutoff=.05;if(e.outlier.rank_asehigh_cutoff==undefined)e.outlier.rank_asehigh_cutoff=.1;if(!e.outlier.color_outlier)e.outlier.color_outlier="#FF8875";if(!e.outlier.color_outlier_asehigh)e.outlier.color_outlier_asehigh="blue"}function i(e,t){if(!t)return;e.estat={};if(e.ase&&t.ase){const a=e.ase.qvalue||e.ase.geometricmean;if(a==undefined){e.estat.ase_noinfo=true}else if(a<=t.ase.qvalue){if(e.ase.mean_delta>=t.ase.meandelta_monoallelic){e.estat.ase_monoallelic=true}else{e.estat.ase_uncertain=true}}else{if(e.ase.ase_markers==t.ase.asemarkernumber_biallelic){e.estat.ase_biallelic=true}else{e.estat.ase_uncertain=true}}}else{e.estat.ase_noinfo=true}if(e.outlier&&t.outlier){if(e.outlier.test_whitelist){if(e.outlier.test_whitelist.pvalue<=t.outlier.pvalue_cutoff){e.estat.outlier=true}else{if(e.estat.ase_monoallelic){if(Number.isInteger(e.outlier.test_whitelist.rank)&&Number.isInteger(e.outlier.test_whitelist.size)&&e.outlier.test_whitelist.rank/e.outlier.test_whitelist.size<=t.outlier.rank_asehigh_cutoff){e.estat.outlier_asehigh=true;e.outlier.test_whitelist.asehigh=true}}}}else if(e.outlier.test_biallelic){if(e.outlier.test_biallelic.pvalue<=t.outlier.pvalue_cutoff){e.estat.outlier=true}else{if(e.estat.ase_monoallelic){if(Number.isInteger(e.outlier.test_biallelic.rank)&&Number.isInteger(e.outlier.test_biallelic.size)&&e.outlier.test_biallelic.rank/e.outlier.test_biallelic.size<=t.outlier.rank_asehigh_cutoff){e.estat.outlier_asehigh=true;e.outlier.test_biallelic.asehigh=true}}}}else if(e.outlier.test_entirecohort){if(e.outlier.test_entirecohort.pvalue<=t.outlier.pvalue_cutoff){e.estat.outlier=true}else{if(e.estat.ase_monoallelic){if(Number.isInteger(e.outlier.test_entirecohort.rank)&&Number.isInteger(e.outlier.test_entirecohort.size)&&e.outlier.test_entirecohort.rank/e.outlier.test_entirecohort.size<=t.outlier.rank_asehigh_cutoff){e.estat.outlier_asehigh=true;e.outlier.test_entirecohort.asehigh=true}}}}}}function r(a,l,i){if(!a.estat)return;if(l.no_ase)return;if(a.ase){const t=i.append("tr");t.append("td").attr("colspan",2).style("background",s(a,l)).style("color","white").html((a.estat.ase_monoallelic?"Mono-allelic":a.estat.ase_biallelic?"Bi-allelic":"ASE uncertain")+"<br>(allele-specific expression)");const r=[{k:"#SNPs heterozygous in DNA",v:a.ase.markers},{k:"#SNPs showing ASE in RNA",v:a.ase.ase_markers},{k:"Mean delta of ASE SNPs",v:a.ase.mean_delta}];if(a.ase.qvalue){r.push({k:"Q-value",v:a.ase.qvalue})}else if(a.ase.geometricmean){r.push({k:"Geometric mean of binomial P-values of ASE SNPs",v:a.ase.geometricmean})}const o=t.append("td");e(o,r)}else{const e=i.append("tr");e.append("td").attr("colspan",3).style("background",l.ase.color_noinfo).style("color","white").text("No info on allele-specific expression")}if(a.snps&&a.snps.length>0){const e=a.snps.filter((e=>e.dnacount&&e.dnacount.ishet));if(e.length>0){const a=[];for(const l of e){a.push("<tr>"+"<td>"+l.chr+":"+(l.pos+1)+" "+l.ref+">"+l.alt+"</td>"+"<td>"+t(null,{f:l.dnacount.f})+" "+l.dnacount.ref+"/"+l.dnacount.alt+"</td>"+"<td>"+(l.rnacount.nocoverage?'<span style="font-size:.8em;opacity:.5">No coverage</span>':t(null,{f:l.rnacount.f})+" "+l.rnacount.ref+"/"+l.rnacount.alt)+"</td>"+"<td>"+(l.rnacount.pvalue||"-")+"</td>"+"</tr>")}i.append("tr").append("td").attr("colspan",3).html('<table style="margin-top:10px;border:solid 1px #ededed;border-spacing:5px;">'+'<tr style="opacity:.5"><td>SNP</td><td>DNA</td><td>RNA</td><td>Binomial test P-value</td></tr>'+a.join("")+"</table>")}}if(a.outlier){if(a.outlier.test_whitelist){const t=i.append("tr");t.append("td").attr("colspan",2).text("Outlier (white list)");const r=[];for(const e in a.outlier.test_whitelist){r.push({k:e,v:a.outlier.test_whitelist[e]})}const s=t.append("td");e(s,r);if(a.outlier.test_whitelist.asehigh){s.append("div").style("background",l.outlier.color_outlier_asehigh).style("padding","2px 10px").style("color","white").text("ASE high")}}if(a.outlier.test_biallelic){const t=i.append("tr");t.append("td").attr("colspan",2).text("Outlier (biallelic)");const r=[];for(const e in a.outlier.test_biallelic){r.push({k:e,v:a.outlier.test_biallelic[e]})}const s=t.append("td");e(s,r);if(a.outlier.test_biallelic.asehigh){s.append("div").style("background",l.outlier.color_outlier_asehigh).style("padding","2px 10px").style("color","white").text("ASE high")}}if(a.outlier.test_entirecohort){const t=i.append("tr");t.append("td").attr("colspan",2).text("Outlier (all samples)");const r=[];for(const e in a.outlier.test_entirecohort){r.push({k:e,v:a.outlier.test_entirecohort[e]})}const s=t.append("td");e(s,r);if(a.outlier.test_entirecohort.asehigh){s.append("div").style("background",l.outlier.color_outlier_asehigh).style("padding","2px 10px").style("color","white").text("ASE high")}}}}function s(e,t){if(t.no_ase)return a;if(!t.ase)return a;if(!e.estat)return t.ase.color_noinfo;if(e.estat.ase_monoallelic)return t.ase.color_monoallelic;if(e.estat.ase_biallelic)return t.ase.color_biallelic;if(e.estat.ase_uncertain)return t.ase.color_uncertain;return t.ase.color_noinfo}function o(e,t,a,l){const i=30;{const i=e.append("div").style("margin-bottom","5px");i.append("span").html("If "+(a.checkrnabam?"p-value geometric mean":"Q-VALUE")+" &le;&nbsp;");i.append("input").attr("type","number").style("width","50px").property("value",t.ase.qvalue).on("keyup",(e=>{if(e.code!="Enter"&&e.code!="NumpadEnter")return;let a=Number.parseFloat(e.target.value);if(!a||a<=0){return}if(t.ase.qvalue==a){return}t.ase.qvalue=a;l()}));i.append("span").html("&nbsp;:")}{const a=e.append("div").style("margin","0px 5px 5px "+i+"px");a.append("span").html("If MEAN_DELTA &ge;&nbsp;");a.append("input").attr("type","number").style("width","50px").property("value",t.ase.meandelta_monoallelic).on("keyup",(e=>{if(e.code!="Enter"&&e.code!="NumpadEnter")return;let a=Number.parseFloat(e.target.value);if(!a||a<=0){return}if(t.ase.meandelta_monoallelic==a){return}t.ase.meandelta_monoallelic=a;l()}));a.append("span").html("&nbsp;:&nbsp;")}e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_monoallelic+';padding:1px 5px;color:white;">mono-allelic expression</span>');e.append("div").style("margin","0px 5px 5px "+i+"px").html("Else:");e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_uncertain+';padding:1px 5px;color:white;">ASE uncertain</span>');e.append("div").style("margin","0px 5px 5px 0px").html("Else:");{const a=e.append("div").style("margin","0px 5px 5px "+i+"px");a.append("span").html("If number of ASE markers &le;&nbsp;");a.append("input").attr("type","number").style("width","50px").property("value",t.ase.asemarkernumber_biallelic).on("keyup",(e=>{if(e.code!="Enter"&&e.code!="NumpadEnter")return;let a=Number.parseInt(e.target.value);if(a<0){return}if(t.ase.asemarkernumber_biallelic==a){return}t.ase.asemarkernumber_biallelic=a;l()}));a.append("span").html("&nbsp;:&nbsp;")}e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_biallelic+';padding:1px 5px;color:white;">bi-allelic expression</span>');e.append("div").style("margin","0px 5px 5px "+i+"px").html("Else:");e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_uncertain+';padding:1px 5px;color:white;">ASE uncertain</span>');e.append("div").style("margin","10px").append("button").text("Default ASE parameters").on("click",(()=>{t.ase.qvalue=.05;t.ase.meandelta_monoallelic=.3;t.ase.asemarkernumber_biallelic=0;l()}))}export{s as a,l as i,i as m,r as s,o as u};
+import{a9 as e,aN as t}from"./app-2cd97738.js";const a="#858585";function l(e){if(!e.datatype)e.datatype="FPKM";if(!e.itemcolor)e.itemcolor="green";if(!e.ase)e.ase={};if(e.ase.qvalue==undefined)e.ase.qvalue=.05;if(e.ase.meandelta_monoallelic==undefined)e.ase.meandelta_monoallelic=.3;if(e.ase.asemarkernumber_biallelic==undefined)e.ase.asemarkernumber_biallelic=0;if(!e.ase.color_noinfo)e.ase.color_noinfo=a;if(!e.ase.color_uncertain)e.ase.color_uncertain="#A8E0B5";if(!e.ase.color_biallelic)e.ase.color_biallelic="#40859C";if(!e.ase.color_monoallelic)e.ase.color_monoallelic="#d95f02";if(!e.outlier)e.outlier={};if(e.outlier.pvalue_cutoff==undefined)e.outlier.pvalue_cutoff=.05;if(e.outlier.rank_asehigh_cutoff==undefined)e.outlier.rank_asehigh_cutoff=.1;if(!e.outlier.color_outlier)e.outlier.color_outlier="#FF8875";if(!e.outlier.color_outlier_asehigh)e.outlier.color_outlier_asehigh="blue"}function i(e,t){if(!t)return;e.estat={};if(e.ase&&t.ase){const a=e.ase.qvalue||e.ase.geometricmean;if(a==undefined){e.estat.ase_noinfo=true}else if(a<=t.ase.qvalue){if(e.ase.mean_delta>=t.ase.meandelta_monoallelic){e.estat.ase_monoallelic=true}else{e.estat.ase_uncertain=true}}else{if(e.ase.ase_markers==t.ase.asemarkernumber_biallelic){e.estat.ase_biallelic=true}else{e.estat.ase_uncertain=true}}}else{e.estat.ase_noinfo=true}if(e.outlier&&t.outlier){if(e.outlier.test_whitelist){if(e.outlier.test_whitelist.pvalue<=t.outlier.pvalue_cutoff){e.estat.outlier=true}else{if(e.estat.ase_monoallelic){if(Number.isInteger(e.outlier.test_whitelist.rank)&&Number.isInteger(e.outlier.test_whitelist.size)&&e.outlier.test_whitelist.rank/e.outlier.test_whitelist.size<=t.outlier.rank_asehigh_cutoff){e.estat.outlier_asehigh=true;e.outlier.test_whitelist.asehigh=true}}}}else if(e.outlier.test_biallelic){if(e.outlier.test_biallelic.pvalue<=t.outlier.pvalue_cutoff){e.estat.outlier=true}else{if(e.estat.ase_monoallelic){if(Number.isInteger(e.outlier.test_biallelic.rank)&&Number.isInteger(e.outlier.test_biallelic.size)&&e.outlier.test_biallelic.rank/e.outlier.test_biallelic.size<=t.outlier.rank_asehigh_cutoff){e.estat.outlier_asehigh=true;e.outlier.test_biallelic.asehigh=true}}}}else if(e.outlier.test_entirecohort){if(e.outlier.test_entirecohort.pvalue<=t.outlier.pvalue_cutoff){e.estat.outlier=true}else{if(e.estat.ase_monoallelic){if(Number.isInteger(e.outlier.test_entirecohort.rank)&&Number.isInteger(e.outlier.test_entirecohort.size)&&e.outlier.test_entirecohort.rank/e.outlier.test_entirecohort.size<=t.outlier.rank_asehigh_cutoff){e.estat.outlier_asehigh=true;e.outlier.test_entirecohort.asehigh=true}}}}}}function r(a,l,i){if(!a.estat)return;if(l.no_ase)return;if(a.ase){const t=i.append("tr");t.append("td").attr("colspan",2).style("background",s(a,l)).style("color","white").html((a.estat.ase_monoallelic?"Mono-allelic":a.estat.ase_biallelic?"Bi-allelic":"ASE uncertain")+"<br>(allele-specific expression)");const r=[{k:"#SNPs heterozygous in DNA",v:a.ase.markers},{k:"#SNPs showing ASE in RNA",v:a.ase.ase_markers},{k:"Mean delta of ASE SNPs",v:a.ase.mean_delta}];if(a.ase.qvalue){r.push({k:"Q-value",v:a.ase.qvalue})}else if(a.ase.geometricmean){r.push({k:"Geometric mean of binomial P-values of ASE SNPs",v:a.ase.geometricmean})}const o=t.append("td");e(o,r)}else{const e=i.append("tr");e.append("td").attr("colspan",3).style("background",l.ase.color_noinfo).style("color","white").text("No info on allele-specific expression")}if(a.snps&&a.snps.length>0){const e=a.snps.filter((e=>e.dnacount&&e.dnacount.ishet));if(e.length>0){const a=[];for(const l of e){a.push("<tr>"+"<td>"+l.chr+":"+(l.pos+1)+" "+l.ref+">"+l.alt+"</td>"+"<td>"+t(null,{f:l.dnacount.f})+" "+l.dnacount.ref+"/"+l.dnacount.alt+"</td>"+"<td>"+(l.rnacount.nocoverage?'<span style="font-size:.8em;opacity:.5">No coverage</span>':t(null,{f:l.rnacount.f})+" "+l.rnacount.ref+"/"+l.rnacount.alt)+"</td>"+"<td>"+(l.rnacount.pvalue||"-")+"</td>"+"</tr>")}i.append("tr").append("td").attr("colspan",3).html('<table style="margin-top:10px;border:solid 1px #ededed;border-spacing:5px;">'+'<tr style="opacity:.5"><td>SNP</td><td>DNA</td><td>RNA</td><td>Binomial test P-value</td></tr>'+a.join("")+"</table>")}}if(a.outlier){if(a.outlier.test_whitelist){const t=i.append("tr");t.append("td").attr("colspan",2).text("Outlier (white list)");const r=[];for(const e in a.outlier.test_whitelist){r.push({k:e,v:a.outlier.test_whitelist[e]})}const s=t.append("td");e(s,r);if(a.outlier.test_whitelist.asehigh){s.append("div").style("background",l.outlier.color_outlier_asehigh).style("padding","2px 10px").style("color","white").text("ASE high")}}if(a.outlier.test_biallelic){const t=i.append("tr");t.append("td").attr("colspan",2).text("Outlier (biallelic)");const r=[];for(const e in a.outlier.test_biallelic){r.push({k:e,v:a.outlier.test_biallelic[e]})}const s=t.append("td");e(s,r);if(a.outlier.test_biallelic.asehigh){s.append("div").style("background",l.outlier.color_outlier_asehigh).style("padding","2px 10px").style("color","white").text("ASE high")}}if(a.outlier.test_entirecohort){const t=i.append("tr");t.append("td").attr("colspan",2).text("Outlier (all samples)");const r=[];for(const e in a.outlier.test_entirecohort){r.push({k:e,v:a.outlier.test_entirecohort[e]})}const s=t.append("td");e(s,r);if(a.outlier.test_entirecohort.asehigh){s.append("div").style("background",l.outlier.color_outlier_asehigh).style("padding","2px 10px").style("color","white").text("ASE high")}}}}function s(e,t){if(t.no_ase)return a;if(!t.ase)return a;if(!e.estat)return t.ase.color_noinfo;if(e.estat.ase_monoallelic)return t.ase.color_monoallelic;if(e.estat.ase_biallelic)return t.ase.color_biallelic;if(e.estat.ase_uncertain)return t.ase.color_uncertain;return t.ase.color_noinfo}function o(e,t,a,l){const i=30;{const i=e.append("div").style("margin-bottom","5px");i.append("span").html("If "+(a.checkrnabam?"p-value geometric mean":"Q-VALUE")+" &le;&nbsp;");i.append("input").attr("type","number").style("width","50px").property("value",t.ase.qvalue).on("keyup",(e=>{if(e.code!="Enter"&&e.code!="NumpadEnter")return;let a=Number.parseFloat(e.target.value);if(!a||a<=0){return}if(t.ase.qvalue==a){return}t.ase.qvalue=a;l()}));i.append("span").html("&nbsp;:")}{const a=e.append("div").style("margin","0px 5px 5px "+i+"px");a.append("span").html("If MEAN_DELTA &ge;&nbsp;");a.append("input").attr("type","number").style("width","50px").property("value",t.ase.meandelta_monoallelic).on("keyup",(e=>{if(e.code!="Enter"&&e.code!="NumpadEnter")return;let a=Number.parseFloat(e.target.value);if(!a||a<=0){return}if(t.ase.meandelta_monoallelic==a){return}t.ase.meandelta_monoallelic=a;l()}));a.append("span").html("&nbsp;:&nbsp;")}e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_monoallelic+';padding:1px 5px;color:white;">mono-allelic expression</span>');e.append("div").style("margin","0px 5px 5px "+i+"px").html("Else:");e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_uncertain+';padding:1px 5px;color:white;">ASE uncertain</span>');e.append("div").style("margin","0px 5px 5px 0px").html("Else:");{const a=e.append("div").style("margin","0px 5px 5px "+i+"px");a.append("span").html("If number of ASE markers &le;&nbsp;");a.append("input").attr("type","number").style("width","50px").property("value",t.ase.asemarkernumber_biallelic).on("keyup",(e=>{if(e.code!="Enter"&&e.code!="NumpadEnter")return;let a=Number.parseInt(e.target.value);if(a<0){return}if(t.ase.asemarkernumber_biallelic==a){return}t.ase.asemarkernumber_biallelic=a;l()}));a.append("span").html("&nbsp;:&nbsp;")}e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_biallelic+';padding:1px 5px;color:white;">bi-allelic expression</span>');e.append("div").style("margin","0px 5px 5px "+i+"px").html("Else:");e.append("div").style("margin","0px 5px 5px "+i*2+"px").html('Is <span style="background:'+t.ase.color_uncertain+';padding:1px 5px;color:white;">ASE uncertain</span>');e.append("div").style("margin","10px").append("button").text("Default ASE parameters").on("click",(()=>{t.ase.qvalue=.05;t.ase.meandelta_monoallelic=.3;t.ase.asemarkernumber_biallelic=0;l()}))}export{s as a,l as i,i as m,r as s,o as u};

package/dist/{block.mds.geneboxplot-f0fbaf12.js → block.mds.geneboxplot-e5b2a4ce.js}

@@ -1 +1 @@
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Set to 0 to cancel.")}{const t=e.append("div");t.append("span").html("CNV segment size limit&nbsp;");t.append("input").property("value",i.svcnv.bplengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(t=>{if(t.code!="Enter"&&t.code!="NumpadEnter")return;let e=Number.parseInt(t.target.value);if(!e||e<0){e=0}if(e==0){if(i.svcnv.bplengthUpperLimit){i.svcnv.bplengthUpperLimit=0;_(i)}return}if(i.svcnv.bplengthUpperLimit){if(i.svcnv.bplengthUpperLimit==e);else{i.svcnv.bplengthUpperLimit=e;_(i)}}else{i.svcnv.bplengthUpperLimit=e;_(i)}}));t.append("span").html("&nbsp;bp");t.append("div").style("font-size",".7em").style("color","#858585").html("CNV segment longer than cutoff will not be considered. Set to 0 to cancel.")}}{const t=c.append("div");const e=Math.random().toString();t.append("input").attr("type","checkbox").property("checked",false).attr("id",e).on("change",(t=>{i.svcnv.usesv=t.target.checked;i.svconfig.div.style("display",i.svcnv.usesv?"block":"none");_(i)}));t.append("label").attr("for",e).attr("class","sja_clbtext").html("&nbsp;Add boxplot for samples with structural variation over "+i.gene).style("color",i.color.sv)}{const t=c.append("div").style("display","none");i.svconfig.div=t;const e=t.append("div").style("display","inline-block").style("margin","5px 10px 10px 30px").style("border","solid 1px #ededed").style("padding","10px");{const t=e.append("div");t.append("span").html("Include SV from flanking region of length:&nbsp;");t.append("input").property("value",0).attr("type","number").style("width","80px").on("keyup",(t=>{if(t.code!="Enter"&&t.code!="NumpadEnter")return;let e=Number.parseInt(t.target.value);if(!e||e<0){e=0}if(e==0){if(i.svcnv.svflank){i.svcnv.svflank=0;_(i)}return}if(i.svcnv.svflank){if(i.svcnv.svflank==e);else{i.svcnv.svflank=e;_(i)}}else{i.svcnv.svflank=e;_(i)}}));t.append("span").html("&nbsp;bp");t.append("div").style("font-size",".7em").style("color","#858585").html("Set to 0 to cancel.")}}}i.buttonholder_boxplot=p.append("span");i.buttonholder_sampleexpdata=p.append("span");p.append("button").text("SVG").on("click",(()=>{n(i.svg.node(),"Expression")}));i.svg=i.holder.append("svg");const g=i.svg.append("g");i.g0=i.svg.append("g");const f=50;const u=10;const y=500;const h=16;const b=10;const v=2;const w=30;const k=14;const z=2;i.place=()=>{i.axislabel.attr("x",y/2);let t=0;let e=0;const a=(i.uselog?m():s()).domain([i.data.min==0?.001:i.data.min,i.data.max]).range([0,y]);const n=t=>{if(i.uselog){if(t==0)return 0}return a(t)};o({axis:g.transition().call(x().scale(a)),showline:1});let l=b;if(i.data.lst){t=20;e=20;for(const t of 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e.out){n.circle=s.g.append("circle").attr("stroke",a).attr("fill","white").attr("fill-opacity",0).on("mouseover",(e=>{t.tip.clear().d.append("div").style("margin","10px").html(n.sample+"<br>"+n.value);t.tip.show(e.clientX,e.clientY)})).on("mouseout",(()=>{t.tip.hide()}));if(t.clicksample){n.circle.on("click",(()=>{t.clicksample(n,s,t)}))}}}}}if(t.sample){t.sample.g=t.g0.append("g");t.sample.svgtext=t.sample.g.append("text").text(t.sample.name).attr("font-family",i).attr("font-size",12).attr("text-anchor","middle").attr("dominant-baseline","hanging").attr("fill","blue");t.sample.line=t.sample.g.append("line").attr("shape-rendering","crispEdges").attr("stroke","blue")}t.place()}function z(t){t.buttonholder_boxplot.selectAll("*").remove();t.buttonholder_boxplot.append("button").text("Boxplots").on("click",(()=>{if(t.table_boxplotstats.style("display")=="block"){a(t.table_boxplotstats);return}t.table_boxplotstats.selectAll("*").remove();const n=t.table_boxplotstats.append("tr");n.append("td").text("Group").style("font-size",".8em").style("opacity",.5);n.append("td").text("1st quartile").style("font-size",".8em").style("opacity",.5);n.append("td").text("Median").style("font-size",".8em").style("opacity",.5);n.append("td").text("3rd quartile").style("font-size",".8em").style("opacity",.5);for(const[e,a]of t.data.groups.entries()){const n=t.table_boxplotstats.append("tr").style("background",e%2?"":"#f1f1f1");n.append("td").text(a.name);const s=a.boxplots?a.boxplots[0]:null;n.append("td").text(s?s.p25:"");n.append("td").text(s?s.p50:"");n.append("td").text(s?s.p75:"")}e(t.table_boxplotstats)}))}function L(t){t.buttonrow.append("button").text(t.gecfg.datatype).on("click",(()=>{const e=p({x:100,y:100});e.header.text(t.gene+" "+t.gecfg.datatype);const a=e.body.append("table").style("border-spacing","4px").style("border-collapse","separate");const n=a.append("tr");n.append("td").text("Sample").style("font-size",".8em").style("opacity",.5);n.append("td").text(t.gecfg.datatype).style("font-size",".8em").style("opacity",.5);for(const e of t.data.lst){const t=a.append("tr");t.append("td").text(e.sample);t.append("td").text(e.value)}}))}function S(t){t.buttonholder_sampleexpdata.selectAll("*").remove();t.buttonholder_sampleexpdata.append("button").text(t.gecfg.datatype).on("click",(async()=>{const e=p({x:100,y:100});e.header.text(t.gene+" "+t.gecfg.datatype);const a=e.body.append("div").style("margin","30px").text("Loading...");const n={genome:t.genome.name,gene:t.gene,chr:t.chr,start:t.start,stop:t.stop,getalllst:1};if(t.dslabel){n.dslabel=t.dslabel;n.querykey=t.querykey}else{n.iscustom=1;n.file=t.file;n.url=t.url;n.indexURL=t.indexURL}try{const s=await r("mdsgeneboxplot",{method:"POST",body:JSON.stringify(n)});if(s.error)throw s.error;a.remove();const o=e.body.append("table").style("border-spacing","4px").style("border-collapse","separate");const l=o.append("tr");l.append("td").text("Sample").style("font-size",".8em").style("opacity",.5);l.append("td").text(t.gecfg.datatype).style("font-size",".8em").style("opacity",.5);for(const t of s.lst){const e=o.append("tr");e.append("td").text(t.sample);e.append("td").text(t.value)}}catch(t){a.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}))}function M(t,e,a,n){const l=p({x:t,y:e});l.header.text(a.gene+" "+a.gecfg.datatype+" in "+n.name);const r={_plot:a,holder:l.body,uselog:a.uselog};if(n.attributes){r.getgroup=n.attributes}else{r.getgroup=1;r.getgroup_unannotated=1}r.errdiv=r.holder.append("div").style("margin","10px");const c=r.holder.append("div").style("margin","10px");r.holder.append("div").style("margin","10px").style("border","solid 1px #ededed").style("padding","10px").style("display","none");c.append("button").text("Log10").on("click",(t=>{r.uselog=!r.uselog;t.target.innerHTML=r.uselog?"Linear":"Log10";r.place()}));c.append("button").text("Data").on("click",(()=>{const t=p({x:200,y:200});t.header.text(l.header.node().innerHTML);const e=t.body.append("table").style("border-spacing","2px").style("border-collapse","separate");const s=e.append("tr");s.append("td").text("Sample").style("font-size",".8em").style("opacity",.5);s.append("td").text(a.gecfg.datatype).style("font-size",".8em").style("opacity",.5);for(const[t,s]of r.data.lst.entries()){const t=e.append("tr");const o=t.append("td").text(s.sample);if(a.clicksample){o.attr("class","sja_clbtext").on("click",(()=>{a.clicksample(s,n,a)}))}t.append("td").text(s.value)}}));r.svg=r.holder.append("svg");r.g0=r.svg.append("g");const d=r.svg.append("g");const u=400;const k=6;const _=6;const z=14;const L=10;const S=5;const M=2;r.place=()=>{for(const t of r.statuscolumns){t.width=20;for(const e of r.data.lst){if(!e.status2cell)continue;const a=e.status2cell.get(t.name);if(!a)continue;if(a.label){a.label.attr("font-size",k*2-2).each((function(){t.width=Math.max(t.width,this.getBBox().width+2)}))}}}let t=0;for(const e of r.data.lst){if(e.samplelabel){e.samplelabel.attr("font-size",k*2-1).attr("x",-S).attr("y",k).each((function(){t=Math.max(t,this.getBBox().width)}))}}let e=0;let a=0;for(const t of r.statuscolumns){if(!t.g){t.g=r.g0.append("g");t.namelabel=t.g.append("text").attr("font-family",i).attr("dominant-baseline","central").attr("transform","rotate(-90)").text(t.name)}t.g.attr("transform","translate("+(a+t.width/2)+",0)");t.namelabel.attr("font-size",Math.min(15,t.width)).each((function(){e=Math.max(e,this.getBBox().width)}));a+=t.width+S}a+=k;const n=Math.max(e,_+z+20);r.g0.attr("transform","translate("+(t+S)+","+n+")");r.axislabel.attr("x",a+u/2);d.attr("transform","translate("+(t+S+a)+","+n+")");const l=(r.uselog?m():s()).domain([r.data.min==0?.001:r.data.min,r.data.max]).range([0,u]);const p=t=>{if(r.uselog){if(t==0)return 0}return l(t)};o({axis:d.transition().call(x().scale(l).tickSize(_)),showline:1});let c=L;for(const[t,e]of r.data.lst.entries()){e.rowg.attr("transform","translate(0,"+c+")");if(e.rowbg){e.rowbg.attr("width",a+u).attr("height",k*2)}e.circle.transition().attr("r",k).attr("cx",a+p(e.value)).attr("cy",k);if(e.samplelabel){if(t>0&&!r.data.lst[t-1].samplelabel){c+=k*2-M;e.rowg.attr("transform","translate(0,"+c+")")}if(e.status2cell){let t=0;for(const a of r.statuscolumns){const n=e.status2cell.get(a.name);if(n){n.g.attr("transform","translate("+(t+a.width/2)+","+k+")");n.rect.attr("x",-a.width/2).attr("y",-k).attr("width",a.width).attr("height",k*2)}t+=a.width+S}}c+=k*2}else{c+=M}}r.svg.attr("width",t+S+a+u+k).attr("height",n+L+c+k*2)};r.makegraph=()=>{const t=r._plot;r.axislabel=r.g0.append("text").attr("font-size",14).attr("font-family",i).attr("text-anchor","middle").attr("y",-25).text(t.gene+" "+t.gecfg.datatype);for(const e of r.data.lst){g(e,t.gecfg)}let e=false,a=false,s=false,o=false,l=false;for(const t of r.data.lst){if(t.gain)e=true;if(t.loss)a=true;if(t.sv)s=true;if(t.estat.ase_monoallelic||t.estat.ase_uncertain||t.estat.ase_biallelic)o=true;if(t.estat.outlier||t.estat.outlier_asehigh)l=true}r.statuscolumns=[];if(e){r.statuscolumns.push({name:y})}if(a){r.statuscolumns.push({name:h})}if(s){r.statuscolumns.push({name:b,width:20})}if(o){r.statuscolumns.push({name:v,width:20})}if(l){r.statuscolumns.push({name:w,width:20})}for(const e of r.data.lst){e.rowg=r.g0.append("g");if(e.gain||e.loss||e.sv||e.estat.ase_monoallelic||e.estat.ase_biallelic||e.estat.ase_uncertain){e.rowbg=e.rowg.append("rect").attr("class","sja_bgbox")}e.circle=e.rowg.append("circle").attr("fill","white").attr("fill-opacity",0).attr("stroke","#858585").on("mouseover",(a=>{N(e,t.tip.clear().d,r);t.tip.show(a.clientX,a.clientY)})).on("mouseout",(()=>{t.tip.hide()}));if(t.clicksample){e.circle.on("click",(()=>{t.clicksample(e,n,t)}))}const a=new Map;if(e.gain){const n={g:e.rowg.append("g")};n.rect=n.g.append("rect").attr("fill",t.color.cnvgain);a.set(y,n)}if(e.loss){const n={g:e.rowg.append("g")};n.rect=n.g.append("rect").attr("fill",t.color.cnvloss);a.set(h,n)}if(e.sv){const n={g:e.rowg.append("g")};n.rect=n.g.append("rect").attr("fill",t.color.sv);a.set(b,n)}if(e.estat.ase_monoallelic||e.estat.ase_biallelic||e.estat.ase_uncertain){const n={g:e.rowg.append("g")};n.rect=n.g.append("rect").attr("fill",f(e,t.gecfg)),n.label=n.g.append("text").text(e.estat.ase_monoallelic?"Mono":e.estat.ase_biallelic?"Bi":"?").attr("font-family",i).attr("dominant-baseline","central").attr("text-anchor","middle").attr("fill","white");a.set(v,n)}if(e.estat.outlier){const n={g:e.rowg.append("g")};n.rect=n.g.append("rect").attr("fill",t.gecfg.outlier.color_outlier);a.set(w,n)}else if(e.estat.outlier_asehigh){const n={g:e.rowg.append("g")};n.rect=n.g.append("rect").attr("fill",t.gecfg.outlier.color_outlier_asehigh);a.set(w,n)}if(a.size){e.status2cell=a;e.samplelabel=e.rowg.append("text").attr("font-family",i).attr("text-anchor","end").attr("dominant-baseline","central").text(e.sample)}}r.place()};C(r)}async function C(t){const e=t._plot;const a={genome:e.genome.name,gene:e.gene,chr:e.chr,start:e.start,stop:e.stop,getgroup:t.getgroup,getgroup_unannotated:t.getgroup_unannotated,svcnv:e.svcnv,sampleset:e.sampleset};if(e.dslabel){a.dslabel=e.dslabel;a.querykey=e.querykey}else{a.iscustom=1;a.file=e.file;a.url=e.url;a.indexURL=e.indexURL}t.g0.append("text").text("Loading ...").attr("font-size",20).attr("text-anchor","center").attr("dominant-baseline","central").attr("x",t.svg.attr("width")/2).attr("y",t.svg.attr("height")/2);try{const e=await r("mdsgeneboxplot",{method:"POST",body:JSON.stringify(a)});if(e.error)throw e.error;t.g0.selectAll("*").remove();t.data=e;t.makegraph()}catch(e){l(t.errdiv,"Error: "+(e.message||e));if(e.stack)console.log(e.stack)}}function N(t,e,a){const n=[{k:"sample",v:t.sample},{k:a._plot.gecfg.datatype,v:t.value}];if(t.gain||t.loss||t.sv){const e=[];if(t.gain){e.push('<span style="padding:0px 5px;color:white;background:'+a._plot.color.cnvgain+'">Copy number gain</span>')}if(t.loss){e.push('<span style="padding:0px 5px;color:white;background:'+a._plot.color.cnvloss+'">Copy number loss</span>')}if(t.sv){e.push('<span style="padding:0px 5px;color:white;background:'+a._plot.color.sv+'">SV</span>')}n.push({k:"Overlap",v:e.join(" ")})}const s=c(e,n);u(t,a._plot.gecfg,s)}function E(t){if(!t.boxplotgroupers)return;const e=t.buttonrow.append("select").on("change",(e=>{t.index_boxplotgroupers=e.target.selectedIndex;_(t)}));for(const[a,n]of t.boxplotgroupers.entries()){e.append("option").text(n)}}export{k as init};
+import{M as t,p as e,ac as a,U as n,I as s,ag as o,j as l,a7 as r,ah as i,Z as p,a9 as c}from"./app-2cd97738.js";import{i as d,m as g,a as f,s as u}from"./block.mds.expressionstat-dcab3fd1.js";import{l as m}from"./log-4d84c357.js";import{c as x}from"./axis-747c801e.js";const y="CNV gain";const h="CNV loss";const b="SV";const v="Allele-specific expression";const w="Outlier expression";async function k(r){if(!r.genome)return alert("cannot initiate plot: genome missing");const i=r;i.tip=new t({padding:"0px"});if(i.file||i.url){i.gecfg={}}else{if(!i.dslabel)return alert("dslabel missing");if(!i.querykey)return alert("querykey missing");const t=i.genome.datasets[i.dslabel];if(!t)return alert("invalid dataset label: "+i.dslabel);i.gecfg=t.queries[i.querykey];if(!i.gecfg)return alert("invalid query key: "+i.querykey)}d(i.gecfg);if(r.block&&r.block.debugmode){window.plot=i}i.errdiv=i.holder.append("div").style("margin","10px");const p=i.holder.append("div").style("margin","10px");i.buttonrow=p;E(i);const c=i.holder.append("div").style("margin","10px").style("border","solid 1px #ededed").style("padding","10px").style("display","none");i.table_boxplotstats=i.holder.append("table").style("margin","10px").style("border-spacing","4px").style("border-collapse","separate");p.append("button").text("Log10").on("click",(t=>{i.uselog=!i.uselog;t.target.innerHTML=i.uselog?"Linear":"Log10";i.place()}));if(i.sample){i.sample.shown=true;p.append("button").text(i.sample.name+" toggle").on("click",(()=>{i.sample.shown=!i.sample.shown;i.sample.line.attr("stroke-opacity",i.sample.shown?1:0);i.sample.svgtext.attr("fill-opacity",i.sample.shown?1:0)}))}if(i.svcnv){p.append("button").text("SV/CNV options").on("click",(()=>{if(c.style("display")=="none")e(c);else a(c)}));i.svcnv.useloss=true;i.svcnv.usegain=true;i.cnvconfig={};i.svconfig={};{const t=c.append("div");const e=Math.random().toString();t.append("input").attr("type","checkbox").property("checked",true).attr("id",e).on("change",(t=>{i.svcnv.usegain=t.target.checked;i.cnvconfig.div.style("display",i.svcnv.usegain||i.svcnv.useloss?"block":"none");_(i)}));t.append("label").attr("for",e).attr("class","sja_clbtext").html("&nbsp;Add boxplot for samples with copy number gain over "+i.gene).style("color",i.color.cnvgain)}{const t=c.append("div");const e=Math.random().toString();t.append("input").attr("type","checkbox").property("checked",true).attr("id",e).on("change",(t=>{i.svcnv.useloss=t.target.checked;i.cnvconfig.div.style("display",i.svcnv.usegain||i.svcnv.useloss?"block":"none");_(i)}));t.append("label").attr("for",e).attr("class","sja_clbtext").html("&nbsp;Add boxplot for samples with copy number loss over "+i.gene).style("color",i.color.cnvloss)}{const t=c.append("div");i.cnvconfig.div=t;const e=t.append("div").style("display","inline-block").style("margin","5px 10px 10px 30px").style("border","solid 1px #ededed").style("padding","10px");{const t=e.append("div").style("margin-bottom","15px");t.append("span").html("CNV log2(ratio) cutoff&nbsp;");t.append("input").property("value",i.svcnv.valueCutoff||0).attr("type","number").style("width","50px").on("keyup",(t=>{if(t.code!="Enter"&&t.code!="NumpadEnter")return;let e=Number.parseFloat(t.target.value);if(!e||e<0){e=0}if(e==0){if(i.svcnv.valueCutoff){i.svcnv.valueCutoff=0;_(i)}return}if(i.svcnv.valueCutoff){if(i.svcnv.valueCutoff==e);else{i.svcnv.valueCutoff=e;_(i)}}else{i.svcnv.valueCutoff=e;_(i)}}));t.append("div").style("font-size",".7em").style("color","#858585").html("CNV with absolute log2(ratio) lower than cutoff will not be considered. Set to 0 to cancel.")}{const t=e.append("div");t.append("span").html("CNV segment size limit&nbsp;");t.append("input").property("value",i.svcnv.bplengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(t=>{if(t.code!="Enter"&&t.code!="NumpadEnter")return;let e=Number.parseInt(t.target.value);if(!e||e<0){e=0}if(e==0){if(i.svcnv.bplengthUpperLimit){i.svcnv.bplengthUpperLimit=0;_(i)}return}if(i.svcnv.bplengthUpperLimit){if(i.svcnv.bplengthUpperLimit==e);else{i.svcnv.bplengthUpperLimit=e;_(i)}}else{i.svcnv.bplengthUpperLimit=e;_(i)}}));t.append("span").html("&nbsp;bp");t.append("div").style("font-size",".7em").style("color","#858585").html("CNV segment longer than cutoff will not be considered. Set to 0 to cancel.")}}{const t=c.append("div");const e=Math.random().toString();t.append("input").attr("type","checkbox").property("checked",false).attr("id",e).on("change",(t=>{i.svcnv.usesv=t.target.checked;i.svconfig.div.style("display",i.svcnv.usesv?"block":"none");_(i)}));t.append("label").attr("for",e).attr("class","sja_clbtext").html("&nbsp;Add boxplot for samples with structural variation over "+i.gene).style("color",i.color.sv)}{const t=c.append("div").style("display","none");i.svconfig.div=t;const e=t.append("div").style("display","inline-block").style("margin","5px 10px 10px 30px").style("border","solid 1px #ededed").style("padding","10px");{const t=e.append("div");t.append("span").html("Include SV from flanking region of length:&nbsp;");t.append("input").property("value",0).attr("type","number").style("width","80px").on("keyup",(t=>{if(t.code!="Enter"&&t.code!="NumpadEnter")return;let e=Number.parseInt(t.target.value);if(!e||e<0){e=0}if(e==0){if(i.svcnv.svflank){i.svcnv.svflank=0;_(i)}return}if(i.svcnv.svflank){if(i.svcnv.svflank==e);else{i.svcnv.svflank=e;_(i)}}else{i.svcnv.svflank=e;_(i)}}));t.append("span").html("&nbsp;bp");t.append("div").style("font-size",".7em").style("color","#858585").html("Set to 0 to cancel.")}}}i.buttonholder_boxplot=p.append("span");i.buttonholder_sampleexpdata=p.append("span");p.append("button").text("SVG").on("click",(()=>{n(i.svg.node(),"Expression")}));i.svg=i.holder.append("svg");const g=i.svg.append("g");i.g0=i.svg.append("g");const f=50;const u=10;const y=500;const h=16;const b=10;const v=2;const w=30;const k=14;const z=2;i.place=()=>{i.axislabel.attr("x",y/2);let t=0;let e=0;const a=(i.uselog?m():s()).domain([i.data.min==0?.001:i.data.min,i.data.max]).range([0,y]);const n=t=>{if(i.uselog){if(t==0)return 0}return a(t)};o({axis:g.transition().call(x().scale(a)),showline:1});let l=b;if(i.data.lst){t=20;e=20;for(const t of i.data.lst){t.circle.transition().attr("cx",n(t.value)).attr("cy",l).attr("r",h/2);l+=z}}else{for(const a of i.data.groups){a.g.attr("transform","translate(0,"+l+")");const s=h*(a.boxplots.length>1?.8:1);let o=0;for(const t of a.boxplots){if(t.label){t.label.attr("font-size",s).attr("x",y+5).attr("y",o+s/2).each((function(){e=Math.max(e,this.getBBox().width)}))}if(t.hline){const e=n(t.w1);const a=n(t.w2);const l=n(t.p25);const r=n(t.p50);const i=n(t.p75);t.hline.transition().attr("x1",e).attr("x2",a).attr("y1",o+s/2).attr("y2",o+s/2);t.linew1.transition().attr("x1",e).attr("x2",e).attr("y1",o).attr("y2",o+s);t.linew2.transition().attr("x1",a).attr("x2",a).attr("y1",o).attr("y2",o+s);t.box.transition().attr("x",l).attr("y",o).attr("width",i-l).attr("height",s);t.linep50.transition().attr("x1",r).attr("x2",r).attr("y1",o).attr("y2",o+s)}for(const e of t.out){e.circle.transition().attr("cx",n(e.value)).attr("cy",o+s/2).attr("r",s/3)}o+=s+v}const r=(s+v)*a.boxplots.length-v;a.label.attr("x",-u).attr("y",r/2).attr("font-size",k).each((function(){t=Math.max(t,this.getBBox().width)}));if(a.bg)a.bg.attr("y",-b/2).attr("width",y).attr("height",r+b);l+=r+b}}i.g0.attr("transform","translate("+(t+u)+","+f+")");g.attr("transform","translate("+(t+u)+","+f+")");if(i.sample){i.sample.g.transition().attr("transform","translate("+n(i.sample.value)+","+l+")");i.sample.line.attr("y1",-l)}i.svg.attr("width",t+u+y+w+e).attr("height",f+l+30)};try{await _(i)}catch(t){l(i.errdiv,"Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function _(t){const e={genome:t.genome.name,gene:t.gene,chr:t.chr,start:t.start,stop:t.stop,svcnv:t.svcnv,index_boxplotgroupers:t.index_boxplotgroupers,sampleset:t.sampleset};if(t.dslabel){e.dslabel=t.dslabel;e.querykey=t.querykey}else{e.iscustom=1;e.file=t.file;e.url=t.url;e.indexURL=t.indexURL}t.g0.append("text").text("Loading ...").attr("font-size",20).attr("text-anchor","center").attr("dominant-baseline","central").attr("x",t.svg.attr("width")/2).attr("y",t.svg.attr("height")/2);const a=await r("mdsgeneboxplot",{method:"POST",body:JSON.stringify(e)});if(a.error)throw a.error;t.g0.selectAll("*").remove();t.axislabel=t.g0.append("text").attr("font-size",14).attr("font-family",i).attr("text-anchor","middle").attr("y",-25).text(t.gene+" "+t.gecfg.datatype);t.data=a;const n="green";if(a.lst){L(t);for(const e of a.lst){e.circle=t.g0.append("circle").attr("fill","white").attr("fill-opacity",0).attr("stroke",n).attr("stroke-opacity",.8).on("mouseover",(a=>{t.tip.clear().d.append("div").style("margin","10px").html(e.sample+"<br>"+e.value);t.tip.show(a.clientX,a.clientY)})).on("mouseout",(()=>t.tip.hide()));if(t.clicksample){e.circle.on("click",(()=>{t.clicksample(e,null,t)}))}}}else{z(t);S(t);for(const[e,s]of 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style="padding:0px 5px;color:white;background:'+a._plot.color.cnvloss+'">Copy number loss</span>')}if(t.sv){e.push('<span style="padding:0px 5px;color:white;background:'+a._plot.color.sv+'">SV</span>')}n.push({k:"Overlap",v:e.join(" ")})}const s=c(e,n);u(t,a._plot.gecfg,s)}function E(t){if(!t.boxplotgroupers)return;const e=t.buttonrow.append("select").on("change",(e=>{t.index_boxplotgroupers=e.target.selectedIndex;_(t)}));for(const[a,n]of t.boxplotgroupers.entries()){e.append("option").text(n)}}export{k as init};

package/dist/{block.mds.junction-7f87f48f.js → block.mds.junction-534eef9b.js}

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height");o.append("button").html("&nbsp;&nbsp;+&nbsp;&nbsp;").style("margin-left","10px").on("click",(()=>{t.axisheight+=30;t.legheight=t.axisheight/4;lt(t,e);e.block_setheight()}));o.append("button").html("&nbsp;&nbsp;-&nbsp;&nbsp;").style("margin-left","5px").on("click",(()=>{if(t.axisheight<=90)return;t.axisheight-=30;t.legheight=t.axisheight/4;lt(t,e);e.block_setheight()}))}{const o=n.append("div").style("margin-bottom","1px");const a=Math.random();const i=o.append("input").attr("type","checkbox").style("margin-right","10px").attr("id",a).on("change",(()=>{t.yscaleUseLog=!t.yscaleUseLog;lt(t,e)}));if(t.yscaleUseLog){i.property("checked",1)}o.append("label").text("Use log10 for Y scale read count").attr("for",a)}}function At(t,e,n,o,a){const i=n.append("div").style("margin-bottom","5px").style("white-space","nowrap");{const n=rt(e);const o=t.info[n.key];if(o){const t=new Set;o.lst.forEach((e=>t.add(e.attrValue)));for(const e of t){const t=n.categories[e];i.append("span").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color",t?t.color:K).style("margin-right","5px").text(t?t.label:e)}}}{const e=i.append("div").style("display","inline-block").style("margin-right","10px");if(!t.sv||t.chr==t.sv.mate.chr){e.html(l(Math.abs(t.start-(t.sv?t.sv.mate.start:t.stop)))+' <span style="font-size:.8em;">'+t.chr+":"+(t.start+1)+"-"+((t.sv?t.sv.mate.start:t.stop)+1)+"</span>")}else{e.html('<span style="font-size:.8em;">'+t.chr+":"+(t.start+1)+"-"+t.sv.mate.chr+":"+(t.sv.mate.start+1)+"</span>")}}const s=n.append("div").style("white-space","nowrap");if(t.sampleCount==1){s.append("div").html(t.medianReadCount+' <span style="font-size:.8em;color:#858585">read count, single sample</span>')}else{s.append("div").style("display","inline-block").style("margin-right","10px").html(t.medianReadCount+' <span style="font-size:.8em;color:#858585">median read count</span>');s.append("div").style("display","inline-block").style("margin-right","10px").html(t.sampleCount+' <span style="font-size:.8em;color:#858585">samples</span>')}const r=[];const c=[];if(t.info&&t.info[et]){for(const e of t.info[et].lst){if(e.isskipexon||e.isaltexon){r.push(e)}else if(e.a5ss||e.a3ss){c.push(e)}}}const d=n.append("div");if(r.length+c.length>0){if(a){if(r.length){Nt(r,d,t,e,o)}if(c.length){Nt(c,d,t,e,o)}return}if(r.length){const n=f(r);const a=r[n];St(t,a,e,d,o)}if(c.length){const n=c[0];Ft(t,n,e,d,o)}}else{Ct(t,e,d)}}function Ct(t,e,n){if(!t.ongene){return}const o=new Map;if(t.ongene.exonleft)t.ongene.exonleft.forEach((t=>o.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.exonleftin)t.ongene.exonleftin.forEach((t=>o.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.intronleft)t.ongene.intronleft.forEach((t=>o.set(t.isoform,{gene:t.gene,strand:t.strand})));const a=new Map;if(t.ongene.exonright)t.ongene.exonright.forEach((t=>a.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.exonrightin)t.ongene.exonrightin.forEach((t=>a.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.intronright)t.ongene.intronright.forEach((t=>a.set(t.isoform,{gene:t.gene,strand:t.strand})));let i;let s;if(o.size){if(a.size){for(const[t,e]of o){if(a.has(t)){i=t;s=e.strand;break}}}else{const t=[...o][0];i=t[0];s=t[1].strand}}else if(a.size){const t=[...a][0];i=t[0];s=t[1].strand}if(i){if(s!="+"&&s!="-"){n.text("unknown strand for "+i);return}import("./spliceevent.noeventdiagram-ea97b0fb.js").then((e=>{e.samegene({isoform:i,reverse:s=="-",ongene:t.ongene,holder:n})}));return}import("./spliceevent.noeventdiagram-ea97b0fb.js").then((e=>{e.differentgenes({ongene:t.ongene,holder:n})}))}function Ft(t,e,n,o,a){const i={junctionB:{start:t.start,stop:t.stop,v:t.medianReadCount},a5ss:e.a5ss,a3ss:e.a3ss,altinintron:e.altinintron,altinexon:e.altinexon,frame:e.frame,exon5idx:e.exon5idx,strand:e.strand,sitedist:e.sitedist};if(e.junctionA){i.junctionA={start:e.junctionA.start,stop:e.junctionA.stop,v:"..."}}import("./spliceevent.a53ss.diagram-e2eab72b.js").then((s=>{const r=s.default({event:i,holder:o});if(!r)return;setTimeout((()=>{if(r.node().getBoundingClientRect().top==0)return;Mt(n,a,t,new Map([[e.junctionA.start+"."+e.junctionA.stop,r]]),[[e.junctionA.start,e.junctionA.stop]])}),1e3)}))}function St(t,e,n,o,a){const i={gm:{name:e.gene,isoform:e.isoform},junctionB:{data:[{v:t.medianReadCount}]},skippedexon:e.skippedexon,isskipexon:e.isskipexon,isaltexon:e.isaltexon,frame:e.frame,junctionAlst:[],color:"#99004d"};if(e.junctionAlst){for(const t of 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a=Math.random().toString();const s=t.gleft.append("defs");const r=s.append("linearGradient").attr("id",o);r.append("stop").attr("offset",0).attr("stop-color",n);r.append("stop").attr("offset",1).attr("stop-color","white");const l=s.append("linearGradient").attr("id",i);l.append("stop").attr("offset",0).attr("stop-color",e);l.append("stop").attr("offset",.5).attr("stop-color","white");l.append("stop").attr("offset",1).attr("stop-color",e);const c=s.append("linearGradient").attr("id",a);c.append("stop").attr("offset",0).attr("stop-color","white");c.append("stop").attr("offset",1).attr("stop-color",n);t.gradient4spanBackground={left:{id:o,gradient:r},mid:{id:i,gradient:l},right:{id:a,gradient:c}}}let n=tt+e.labelfontsize;if(t.permanentHierarchy){t.subhierarchylabel=e.maketklefthandle(t,n).text(t.permanentHierarchy.hierarchyname+": "+t.permanentHierarchy.valuelabel).attr("class",null).attr("fill","#858585");n+=tt+e.labelfontsize}{new r({padding:"none"});t.junctionCountLabel=e.maketklefthandle(t,n).on("click",(()=>{}))}n+=tt+e.labelfontsize;{new r({padding:"none"});t.sampleCountLabel=e.maketklefthandle(t,n).on("click",(()=>{}))}n+=tt+e.labelfontsize;if(t.permanentHierarchy){g(t,e,n)}t.config_handle=e.maketkconfighandle(t).on("click",(()=>{wt(t,e)}));if(t.parentTk);else{t.legendMenu=new r({padding:"0px"});const[n,o]=p(e,t.name);t.tr_legend=n;t.td_legend=o;t.infoFilter.holderTable=t.td_legend.append("table");t.infoFilter.useFilterIndex=0;for(const[n,o]of t.infoFilter.lst.entries()){const i=t.infoFilter.holderTable.append("tr");o.labelButton=i.append("td").text(o.label).attr("class",n==t.infoFilter.useFilterIndex?"sja_clb_selected":"sja_clb").on("click",(()=>{if(t.infoFilter.useFilterIndex==n){return}t.infoFilter.useFilterIndex=n;t.infoFilter.lst.forEach((t=>t.labelButton.attr("class","sja_clb")));o.labelButton.attr("class","sja_clb_selected");lt(t,e)}));o.holder=i.append("td")}t.cohortFilter={holderTable:t.td_legend.append("table"),hiddenAttr:{}};if(t.mds.cohortHiddenAttr){for(const e in t.mds.cohortHiddenAttr){t.cohortFilter.hiddenAttr[e]={};for(const n in t.mds.cohortHiddenAttr[e]){t.cohortFilter.hiddenAttr[e][n]=1}}}}}function wt(t,e){t.tkconfigtip.clear().showunder(t.config_handle.node());const n=t.tkconfigtip.d;{const o=n.append("div").style("margin-bottom","15px");o.append("span").html("Read count cutoff&nbsp;");o.append("input").property("value",t.readcountCutoff||0).attr("type","number").style("width","50px").on("keyup",(n=>{if(n.code!="Enter"&&n.code!="NumpadEnter")return;let o=n.target.value;if(!o||o<0){o=0}if(o==0){if(t.readcountCutoff){t.readcountCutoff=0;nt(t,e,true)}return}if(t.readcountCutoff){if(t.readcountCutoff==o);else{t.readcountCutoff=o;nt(t,e,true)}}else{t.readcountCutoff=o;nt(t,e,true)}}));o.append("div").style("font-size",".7em").style("color","#858585").text("For a junction, samples with read count lower than cutoff will not be shown.")}{const o=n.append("div").style("margin-bottom","15px");o.append("span").text("Track height");o.append("button").html("&nbsp;&nbsp;+&nbsp;&nbsp;").style("margin-left","10px").on("click",(()=>{t.axisheight+=30;t.legheight=t.axisheight/4;lt(t,e);e.block_setheight()}));o.append("button").html("&nbsp;&nbsp;-&nbsp;&nbsp;").style("margin-left","5px").on("click",(()=>{if(t.axisheight<=90)return;t.axisheight-=30;t.legheight=t.axisheight/4;lt(t,e);e.block_setheight()}))}{const o=n.append("div").style("margin-bottom","1px");const i=Math.random();const a=o.append("input").attr("type","checkbox").style("margin-right","10px").attr("id",i).on("change",(()=>{t.yscaleUseLog=!t.yscaleUseLog;lt(t,e)}));if(t.yscaleUseLog){a.property("checked",1)}o.append("label").text("Use log10 for Y scale read count").attr("for",i)}}function At(t,e,n,o,i){const a=n.append("div").style("margin-bottom","5px").style("white-space","nowrap");{const n=rt(e);const o=t.info[n.key];if(o){const t=new Set;o.lst.forEach((e=>t.add(e.attrValue)));for(const e of t){const t=n.categories[e];a.append("span").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color",t?t.color:K).style("margin-right","5px").text(t?t.label:e)}}}{const e=a.append("div").style("display","inline-block").style("margin-right","10px");if(!t.sv||t.chr==t.sv.mate.chr){e.html(l(Math.abs(t.start-(t.sv?t.sv.mate.start:t.stop)))+' <span style="font-size:.8em;">'+t.chr+":"+(t.start+1)+"-"+((t.sv?t.sv.mate.start:t.stop)+1)+"</span>")}else{e.html('<span style="font-size:.8em;">'+t.chr+":"+(t.start+1)+"-"+t.sv.mate.chr+":"+(t.sv.mate.start+1)+"</span>")}}const s=n.append("div").style("white-space","nowrap");if(t.sampleCount==1){s.append("div").html(t.medianReadCount+' <span style="font-size:.8em;color:#858585">read count, single sample</span>')}else{s.append("div").style("display","inline-block").style("margin-right","10px").html(t.medianReadCount+' <span style="font-size:.8em;color:#858585">median read count</span>');s.append("div").style("display","inline-block").style("margin-right","10px").html(t.sampleCount+' <span style="font-size:.8em;color:#858585">samples</span>')}const r=[];const c=[];if(t.info&&t.info[et]){for(const e of t.info[et].lst){if(e.isskipexon||e.isaltexon){r.push(e)}else if(e.a5ss||e.a3ss){c.push(e)}}}const d=n.append("div");if(r.length+c.length>0){if(i){if(r.length){Nt(r,d,t,e,o)}if(c.length){Nt(c,d,t,e,o)}return}if(r.length){const n=f(r);const i=r[n];St(t,i,e,d,o)}if(c.length){const n=c[0];Ft(t,n,e,d,o)}}else{Ct(t,e,d)}}function Ct(t,e,n){if(!t.ongene){return}const o=new Map;if(t.ongene.exonleft)t.ongene.exonleft.forEach((t=>o.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.exonleftin)t.ongene.exonleftin.forEach((t=>o.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.intronleft)t.ongene.intronleft.forEach((t=>o.set(t.isoform,{gene:t.gene,strand:t.strand})));const i=new Map;if(t.ongene.exonright)t.ongene.exonright.forEach((t=>i.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.exonrightin)t.ongene.exonrightin.forEach((t=>i.set(t.isoform,{gene:t.gene,strand:t.strand})));if(t.ongene.intronright)t.ongene.intronright.forEach((t=>i.set(t.isoform,{gene:t.gene,strand:t.strand})));let a;let s;if(o.size){if(i.size){for(const[t,e]of o){if(i.has(t)){a=t;s=e.strand;break}}}else{const t=[...o][0];a=t[0];s=t[1].strand}}else if(i.size){const t=[...i][0];a=t[0];s=t[1].strand}if(a){if(s!="+"&&s!="-"){n.text("unknown strand for "+a);return}import("./spliceevent.noeventdiagram-1d6d790d.js").then((e=>{e.samegene({isoform:a,reverse:s=="-",ongene:t.ongene,holder:n})}));return}import("./spliceevent.noeventdiagram-1d6d790d.js").then((e=>{e.differentgenes({ongene:t.ongene,holder:n})}))}function Ft(t,e,n,o,i){const a={junctionB:{start:t.start,stop:t.stop,v:t.medianReadCount},a5ss:e.a5ss,a3ss:e.a3ss,altinintron:e.altinintron,altinexon:e.altinexon,frame:e.frame,exon5idx:e.exon5idx,strand:e.strand,sitedist:e.sitedist};if(e.junctionA){a.junctionA={start:e.junctionA.start,stop:e.junctionA.stop,v:"..."}}import("./spliceevent.a53ss.diagram-1a84db58.js").then((s=>{const r=s.default({event:a,holder:o});if(!r)return;setTimeout((()=>{if(r.node().getBoundingClientRect().top==0)return;Mt(n,i,t,new Map([[e.junctionA.start+"."+e.junctionA.stop,r]]),[[e.junctionA.start,e.junctionA.stop]])}),1e3)}))}function St(t,e,n,o,i){const a={gm:{name:e.gene,isoform:e.isoform},junctionB:{data:[{v:t.medianReadCount}]},skippedexon:e.skippedexon,isskipexon:e.isskipexon,isaltexon:e.isaltexon,frame:e.frame,junctionAlst:[],color:"#99004d"};if(e.junctionAlst){for(const t of e.junctionAlst){if(t){t.data=[{v:"..."}];a.junctionAlst.push(t);continue}a.junctionAlst.push(null)}}if(e.up1junction){e.up1junction.data=[{v:"..."}];a.up1junction=e.up1junction}if(e.down1junction){e.down1junction.data=[{v:"..."}];a.down1junction=e.down1junction}import("./spliceevent.exonskip.diagram-da10648b.js").then((e=>{const[s,r]=e.default({event:a,holder:o,nophrase:true});setTimeout((()=>{for(const[t,e]of s){if(e.node().getBoundingClientRect().top==0){return}}Mt(n,i,t,s,r)}),1e3)}))}async function Mt(t,n,o,i,a){const s={genome:n.genome.name,dslabel:t.mds.label,querykey:t.querykey,readcountByjBsamples:true,junctionB:{chr:o.chr,start:o.start,stop:o.stop},junctionAposlst:a};ot(s,t);try{const t=await e("mdsjunction",{method:"POST",body:JSON.stringify(s)});if(t.error)throw t.error;if(!t.lst)throw".lst[] missing";for(const e of t.lst){const t=e.start+"."+e.stop;if(i.has(t)){i.get(t).text(e.v)}}}catch(t){console.error(t.message||t)}}function Nt(t,e,n,o,i){if(t.length==1){zt(t[0],e,n,o,i);return}const a=e.append("div").style("display","inline-block").style("font-size",".8em");for(const e of t){a.append("div").html(Bt(e)).attr("class","sja_menuoption").on("click",(t=>{o.tktip.clear().show(t.clientX+20,t.clientY-40);zt(e,o.tktip.d,n,o,i)}))}}function zt(t,e,n,o,i){const a=e.append("table").append("tr");const s=a.append("td");const r=s.append("p");if(t.isskipexon||t.isaltexon){r.html(Bt(t));St(n,t,o,s,i)}else{r.html(Bt(t));Ft(n,t,o,s,i)}a.append("td")}function Bt(t){if(t.isskipexon||t.isaltexon){return(t.isskipexon?"Exon skip":"Exon alt")+" "+t.gene+" "+t.isoform+" "+(t.frame==undefined?"":t.frame==c?"IN frame":"OUT of frame")}return(t.a5ss?"A5SS":"A3SS")+" "+t.gene+" "+t.isoform+" "+(t.frame==undefined?"":t.frame==c?"IN frame":"OUT of frame")}async function It(t,n,o,i){const a={genome:o.genome.name,dslabel:n.mds.label,querykey:n.querykey,junction:{chr:t.chr,start:t.start,stop:t.stop}};ot(a,n);const s=i.append("div").text("Loading ...");try{const t=await e("mdsjunction",{method:"POST",body:JSON.stringify(a)});if(t.error)throw t.error;s.remove();if(t.readcountboxplotpercohort){const e=i.append("div");for(const n of t.readcountboxplotpercohort){const t=e.append("div").style("margin","10px").style("display","inline-block").style("vertical-align","top");t.append("h3").text(n.label).style("text-align","center");const o=await import("./plot.boxplot-76229491.js");const i=o.default({holder:t,list:n.boxplots,axislabel:"Read count"});if(i){d(t,"Boxplot error: "+i)}}}else if(t.samples){if(t.sampletotalnumber){i.append("p").text("Displaying top "+t.samples.length+" samples").style("opacity",.5)}const e=i.append("div").style("margin-top","20px").style("display","grid").style("grid-template-columns","auto auto").style("gap-row-gap","1px").style("align-items","center").style("justify-items","left");const[o,a]=Et(e);o.text("Sample").style("opacity",.5).style("font-size",".7em");a.text("Read count").style("opacity",.5).style("font-size",".7em");for(const o of t.samples){const[t,i]=Et(e);t.text(o.sample_name?o.sample_name:n.samples[o.i]);i.text(o.readcount)}}}catch(t){if(t.stack)console.log(t.stack);s.text("Error: "+(t.message||t))}}function Et(t){return[t.append("div").style("width","100%").style("padding","5px 20px 5px 0px").style("border-bottom","solid 1px #ededed"),t.append("div").style("width","100%").style("border-bottom","solid 1px #ededed").style("padding","5px 20px 5px 0px")]}export{nt as loadTk};