@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/recover-49e09de0.js

@@ -0,0 +1 @@
+import{i as t,d as e,M as s,a as r,z as i,A as a,B as o,h as n,C as l,D as p,r as c,m as d,E as m,F as u}from"./app-b369b169.js";import{T as h,N as f,g}from"./termsetting-33ea66f1.js";import{F as b,g as j,a as y,f as v}from"./FilterRxComp-701a1480.js";import{f as x}from"./FilterStateless-54c0b763.js";import{appInit as w}from"./app-3320ab6f.js";import{r as C}from"./table-29d5a973.js";import{_ as T}from"./tslib.es6-c3c2d88f.js";import{a as k}from"./genesearch-a4e19f0d.js";import{m as S}from"./checkbox-96437f4d.js";import{r as _}from"./rehydrateFilter-12d118cb.js";class I extends b{constructor(t){super(t);this.api={main:this.main.bind(this),getNormalRoot:()=>j(this.rawFilter),getPromise:t=>this.promises[t]};if(t.debug)this.api.Inner=this}async main(t,e={}){this.dom.controlsTip.hide();this.dom.treeTip.hide();const s="activeCohort"in e?e.activeCohort:this.activeCohort;const r=y(t,"filterUiRoot");if(r)delete r.tag;t.lst.push({tag:"filterUiRoot",type:"tvslst",join:"",lst:[]});t.join=t.lst.length>1?"and":"";const i=JSON.stringify(t);if(this.rawCopy==i&&JSON.stringify(this.activeCohort)==JSON.stringify(s))return;await super.main(i,e)}refresh(t){this.dom.controlsTip.hide();this.dom.treeTip.hide();const e=JSON.parse(JSON.stringify(this.rawFilter));const s=v(e,this.filter.$id);if(!s||this.rawFilter.$id===this.filter.$id){this.opts.callback(e)}else{const r=s.lst.findIndex((t=>t.$id==this.filter.$id));s.lst[r]=t;this.opts.callback(e)}const r=e.lst.findIndex((e=>e.$id===t.$id));e.lst.splice(r,1);this.main(e)}}const A=t(I);function P(t){if(!t.div||!t.text||!t.callback)throw new Error("Missing required parameters");return t.div.append("button").property("disabled",t.disabled||false).style("border","none").style("border-radius","20px").style("padding","10px 15px").text(t.text).on("click",(()=>{t.callback()}))}function D(t,s){const r=s.selectAll().data(t,(t=>t.value)).enter().append("div").style("margin","5px");const i=r.append("label").on("mousedown",(t=>{t.stopPropagation()}));const a=i.append("input").attr("type","radio").attr("name",(t=>t.label)).attr("value",(t=>t.value)).property("checked",(t=>t.checked)).on("input",(function(t,r){return T(this,void 0,void 0,(function*(){t.stopPropagation();a.property("disabled",true);a.property("checked",false);s.selectAll(".contentDiv").style("display","none");const i=e(this.parentNode).append("div").classed("contentDiv",true).style("padding-left","25px").style("display","block");yield r.callback(i);e(this).property("checked",true);a.property("disabled",false)}))}));a.filter((t=>t.checked)).property("checked",true);i.append("span").html((t=>"&nbsp;"+t.label));i.append("span").style("display","block").style("padding-left","25px").style("font-size","0.75em").html((t=>t.sublabel||""))}class B{constructor(t){this.params2Add=[];this.tip=t.tip;this.params=t.params;this.callback=t.callback;this.addOptionalParams=t.addOptionalParams;this.tip.d.style("padding","15px");this.render();for(const t of this.params2Add)this.addOptionalParams(t)}render(){for(const t of this.params){const e=this.addParameter(t.param,this.tip.d.append("div"));t.input=e}const t=P({div:this.tip.d.append("div").style("padding","20px").style("display","inline-block"),text:"Calculate genes",callback:()=>T(this,void 0,void 0,(function*(){t.property("disabled",true).text("Loading...");yield this.callback();this.tip.hide()}))})}addParameter(t,e){var s;let r;if(t.type=="boolean"){if((s=t===null||t===void 0?void 0:t.options)===null||s===void 0?void 0:s.length){const s=e.append("div").style("margin","10px 0px").on("mousedown",(t=>{t.stopPropagation()}));r=s.append("input").attr("type","checkbox").attr("id",t.id);this.addLabels(s,"label",t);const i=e.append("div").style("padding-left","20px");for(const e of t.options){const t=this.addParameter(e,i.append("div"));this.params2Add.push({param:e,input:t})}if(t.value){r.property("checked",t.value);i.style("display","block")}else i.style("display","none");r.on("change",(()=>{i.style("display",r.property("checked")?"block":"none")}))}else{r=e.append("input").style("padding","2px").attr("type","checkbox").attr("id",t.id);if(t.value)r.property("checked",t.value);this.addLabels(e,"label",t)}}else if(t.type=="string"&&t.value){r=S({holder:e,id:t.id,checked:true,labeltext:t.label,callback:()=>{}})}else if(t.type=="number"){r=e.append("input").attr("type","number").style("width","50px").style("padding","5px").attr("id",t.id);if(t.value)r.attr("value",t.value);this.addLabels(e,"span",t)}else if(t.type=="radio"){const s=t.options.find((t=>t.checked));if(!s)t.options[0].checked=true;r=e.append("div").attr("id",t.id);r.append("p").style("font-size","0.8em").style("opacity",.75).text(t.label);D(t.options,r)}return r}addLabels(t,e,s){if(!s.sublabel)t.append(e).html(s.label).attr("for",s.id);else{const r=t.append("div").style("display","inline-block").style("vertical-align","middle");r.append(e).style("display","block").style("padding-top","3px").html(s.label).attr("for",s.id);r.append("span").style("display","block").style("font-size","0.75em").html(s.sublabel)}}}class G{constructor(t){var e,r,i;this.holder=t.holder;this.genome=t.genome;this.callback=t.callback;this.vocabApi=t.vocabApi;this.customInputs=t.customInputs;this.geneList=structuredClone(t.geneList||[]);this.tip2=new s({padding:"0px",parent_menu:t.holder.node(),test:"test"});this.minNumGenes=t.minNumGenes||0;if("mode"in t)this.mode=t.mode;if("titleText"in t)this.titleText=t.titleText;this.origLst=structuredClone(this.geneList);this.origNames=JSON.stringify(this.geneList.map((t=>t.gene)).sort());this.holder.selectAll("*").remove();const a=this.holder.append("div").style("padding","5px");if(this.titleText){a.append("div").style("margin-bottom","10px").html(this.titleText)}const o=a.append("div");const n=o.append("label");n.append("span").html("Search");const l=n.append("div").style("display","inline-flex").style("align-items","center").style("margin","8px 0px -5px 0px");const p=o.append("div").style("display","inline-flex").style("align-items","center").style("float","right").style("gap","5px");const c=this.addGene.bind(this);this.geneSearch=k({tip:this.tip2,genome:this.genome,row:l,searchOnly:"gene",callback:c,hideHelp:true,focusOff:true});this.menuList=[];this.api={dom:{holder:a,textControlDiv:p.append("div"),clearBtn:P({div:p,text:"Clear",disabled:!((e=this.geneList)===null||e===void 0?void 0:e.length),callback:()=>{this.geneList=[];this.renderGenes()}}),restoreBtn:((r=this.geneList)===null||r===void 0?void 0:r.length)?P({div:p,disabled:true,text:"Restore",callback:()=>{this.geneList=this.origLst;this.renderGenes()}}):null,geneHoldingDiv:this.renderGeneHoldingDiv(a),statLegendDiv:a.append("div"),submitBtn:P({div:a.append("div").style("margin-top","10px"),text:"Submit",disabled:!((i=this.geneList)===null||i===void 0?void 0:i.length),callback:()=>{this.callback({geneList:this.geneList})}})},topMutatedGenesParams:[],topVariablyExpressedGenesParams:[],statColor2label:new Map,destroy(){t.holder.remove()}};this.getParams();this.createMenuList();this.renderTextControls(this.api.dom.textControlDiv);this.renderGenes()}getParams(){var t,e,s,i;if(this.mode==h.GENE_VARIANT&&((e=(t=this.vocabApi.termdbConfig)===null||t===void 0?void 0:t.queries)===null||e===void 0?void 0:e.topMutatedGenes)){if(this.vocabApi.termdbConfig.queries.topMutatedGenes.arguments){for(const t of this.vocabApi.termdbConfig.queries.topMutatedGenes.arguments)this.api.topMutatedGenesParams.push({param:t})}}if(this.mode==h.GENE_EXPRESSION&&((i=(s=this.vocabApi.termdbConfig)===null||s===void 0?void 0:s.queries)===null||i===void 0?void 0:i.topVariablyExpressedGenes)){if(this.vocabApi.termdbConfig.queries.topVariablyExpressedGenes.arguments){for(const t of this.vocabApi.termdbConfig.queries.topVariablyExpressedGenes.arguments){if(t.type=="radio"){if(!t.options||t.options.length==0)throw"Radio button must have options";for(const e of t.options){if(e.type=="tree"){e.callback=s=>T(this,void 0,void 0,(function*(){const r=yield import("./app-3320ab6f.js");const i=s.append("div");yield r.appInit({holder:i,state:{dslabel:e.value,genome:this.genome.name,nav:{header_mode:"search_only"}},tree:{click_term:r=>{s.append("div").classed("ts_pill sja_filter_tag_btn sja_tree_click_term termlabel",true).style("margin","5px").text(`${r.id}`);t.value={type:e.value,geneList:r._geneset.map((t=>t.symbol))};i.selectAll("*").remove()}}})}))}if(e.type=="text"){e.callback=s=>T(this,void 0,void 0,(function*(){s.append("span").style("display","block").style("font-size","0.8em").style("opacity",.75).text("Enter genes separated by spaces or commas");s.append("textarea").style("display","block").on("keyup",r.debounce((function(){const s=this.value.split(/[\s,]+/).map((t=>t.trim())).filter((t=>t!==""));t.value={type:e.value,geneList:s}})),500)}))}if(e.type=="boolean"){e.callback=()=>{t.value={type:e.value,geneList:null}}}}}this.api.topVariablyExpressedGenesParams.push({param:t})}}}}baseGeneMenuArgs(t){t=this.removeDuplicates(t);return{tip:this.tip2,params:t,addOptionalParams:({param:e,input:s})=>{t.push({param:e,input:s})}}}removeDuplicates(t){var e;for(const s of t){if((e=s.param)===null||e===void 0?void 0:e.options){s.param.options.forEach((e=>{if(!e.id)return;const s=t.findIndex((t=>t.param.id==e.id));if(s!=-1)t.splice(s,1)}))}}return t}createMenuList(){var t,e,s,r;if(((t=this.api)===null||t===void 0?void 0:t.topMutatedGenesParams.length)>0){this.menuList.push({label:"Top mutated genes",callback:t=>T(this,void 0,void 0,(function*(){this.tip2.clear().showunder(t.target);const e=()=>T(this,void 0,void 0,(function*(){const t={filter0:this.vocabApi.state.termfilter.filter0};for(const{param:e,input:s}of this.api.topMutatedGenesParams){const r=s.attr("id");t[r]=this.getInputValue({param:e,input:s})}const e=yield this.vocabApi.getTopMutatedGenes(t);this.geneList=[];this.geneList.push(...e.genes);this.renderGenes()}));const s=Object.assign(this.baseGeneMenuArgs(this.api.topMutatedGenesParams),{callback:e});new B(s)}))})}if(((e=this.api)===null||e===void 0?void 0:e.topVariablyExpressedGenesParams.length)>0){this.menuList.push({label:"Top variably expressed genes",callback:t=>{this.api.topVariablyExpressedGenesParams.filter((t=>{var e;return t.param.type=="radio"&&((e=t.param)===null||e===void 0?void 0:e.options)})).forEach((t=>{if(typeof t.param.options[0].value==="string"){t.param.value={type:t.param.options[0].value,value:null}}else{console.error(`Unexpected radio button value type: ${typeof t.param.options[0].value}`)}}));this.tip2.clear().showunder(t.target);const e=()=>T(this,void 0,void 0,(function*(){const t={genome:this.vocabApi.state.vocab.genome,dslabel:this.vocabApi.state.vocab.dslabel};if(this.vocabApi.state.termfilter){if(this.vocabApi.state.termfilter.filter)t.filter=this.vocabApi.state.termfilter.filter;if(this.vocabApi.state.termfilter.filter0)t.filter0=this.vocabApi.state.termfilter.filter0}for(const{param:e,input:s}of this.api.topVariablyExpressedGenesParams){const r=s.attr("id");t[r]=this.getInputValue({param:e,input:s})}const e=yield this.vocabApi.getTopVariablyExpressedGenes(t);this.geneList=[];if(e.genes){for(const t of e.genes)this.geneList.push({gene:t})}this.renderGenes()}));const s=Object.assign(this.baseGeneMenuArgs(this.api.topVariablyExpressedGenesParams),{callback:e});new B(s)}})}if((r=(s=this.genome)===null||s===void 0?void 0:s.termdbs)===null||r===void 0?void 0:r.msigdb){for(const t in this.genome.termdbs){const e=this.genome.termdbs[t];this.menuList.push({label:`${e.label} gene set`,callback:()=>T(this,void 0,void 0,(function*(){this.tip2.clear().showunder(this.api.dom.textControlDiv.node());const e=yield import("./app-3320ab6f.js");e.appInit({holder:this.tip2.d,state:{dslabel:t,genome:this.genome.name,nav:{header_mode:"search_only"}},tree:{click_term:t=>{this.geneList=[];const e=t._geneset;if(e){for(const t of e)this.geneList.push({gene:t.symbol});this.renderGenes()}this.tip2.hide();this.api.dom.submitBtn.node().focus()}}})}))})}}if(this.customInputs){for(const t of this.customInputs){this.menuList.push({label:t.label,callback:()=>{t.showInput({callback:({geneList:t})=>{this.geneList=t;this.renderGenes()}})},tagName:"button"})}}}renderTextControls(t){for(const e of this.menuList){if(e.tagName=="button")P({div:t,text:e.label,callback:e.callback});else t.append("a").style("text-decoration","underline").style("padding","0px 10px").style("color","black").html(`${e.label} &#9660;`).on("click",(t=>T(this,void 0,void 0,(function*(){yield e.callback(t)}))))}}getInputValue({param:t,input:e}){if(t.type=="radio")return t.value;const s=e.node().value;if(e.attr("type")=="number")return Number(s);if(e.attr("type")=="checkbox"){if(t.type=="string")return e.node().checked?t.value:"";if(t.type=="boolean")return e.node().checked?1:0}}renderGeneHoldingDiv(t){return t.append("div").append("div").style("display","flex").style("flex-wrap","wrap").style("gap","5px").style("min-height","20px").style("border","solid 1px #aaa").style("margin","15px 0px").style("padding","6px 2px").style("min-height","30px")}renderStatLegend(){if(!this.api.statColor2label||this.api.statColor2label.size==0){this.api.dom.statLegendDiv.style("display","none");return}this.api.dom.statLegendDiv.style("display","block").selectAll("*").remove();for(const[t,e]of this.api.statColor2label){this.api.dom.statLegendDiv.append("div").style("display","inline-block").style("width","12px").style("height","12px").style("background-color",t);this.api.dom.statLegendDiv.append("span").html(` ${e} &nbsp;&nbsp;`)}return this.api.dom.statLegendDiv}addGene(){const t=this.geneSearch.geneSymbol;for(const e of this.geneList){if(e.gene==t){window.alert(`The gene ${t} has already been added`);return}}if(t)this.geneList.push({gene:t});this.renderGenes()}renderGenes(){var t,s,r,i;const a=this.geneList.some((t=>t.mutationStat));if(!a)this.geneList.sort(((t,e)=>{if(t.gene<e.gene)return-1;if(t.gene>e.gene)return 1;return 0}));this.api.dom.geneHoldingDiv.selectAll("*").remove();const o=this.renderGene.bind(this);const n=this.deleteGene.bind(this);this.api.dom.geneHoldingDiv.selectAll("div").data(this.geneList||[]).enter().append("div").attr("aria-label","Click to delete").attr("class","sja_menuoption").attr("tabindex",0).style("position","relative").style("display","inline-block").style("padding","5px 16px 5px 9px").style("margin-left","5px").each((function(t){const s=e(this).style("border-radius","5px");o(s,t);s.on("click",(()=>n(t)))})).on("mouseover",(function(t){const s=e(t.target);s.append("div").style("margin-left","4px").classed("sjpp_deletebt",true).style("display","inline-block").style("position","absolute").style("right","0px").style("top","0px").style("transform","scale(0.6)").style("pointer-events","none").html(`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-x-lg" viewBox="0 0 16 16">\n                <path stroke='#f00' d="M2.146 2.854a.5.5 0 1 1 .708-.708L8 7.293l5.146-5.147a.5.5 0 0 1 .708.708L8.707 8l5.147 5.146a.5.5 0 0 1-.708.708L8 8.707l-5.146 5.147a.5.5 0 0 1-.708-.708L7.293 8 2.146 2.854Z"/>\n                </svg>`)})).on("mouseout",(function(t){e(t.target).select(".sjpp_deletebt").remove()})).on("focus",(t=>{t.target.dispatchEvent(new PointerEvent("mouseover"))})).on("blur",(t=>{t.target.dispatchEvent(new PointerEvent("mouseout"))})).on("keyup",(t=>{if(t.key=="Enter")t.target.click()}));this.renderStatLegend();this.api.dom.clearBtn.property("disabled",!((t=this.geneList)===null||t===void 0?void 0:t.length));const l=this.origNames!==JSON.stringify(this.geneList.map((t=>t.gene)).sort());(s=this.api.dom.restoreBtn)===null||s===void 0?void 0:s.property("disabled",!l);this.api.dom.submitBtn.property("disabled",!l||((r=this.geneList)===null||r===void 0?void 0:r.length)<this.minNumGenes||!((i=this.geneList)===null||i===void 0?void 0:i.length));if(l)this.api.dom.submitBtn.node().focus()}renderGene(t,e){if(e.mutationStat){t.html(`${e.gene}&nbsp;&nbsp;`);for(const s of e.mutationStat){let e;let r="black";if("class"in s){if(!i[s.class])throw"invalid stat class";e=i[s.class].color;this.api.statColor2label.set(e,i[s.class].label)}else if("dt"in s){if(!a[s["dt"]])throw"invalid stat dt";e=a[s["dt"]];r="white";this.api.statColor2label.set(e,o[s["dt"]])}else{throw"stat missing dt/class"}t.insert("span").style("font-size",".7em").style("background-color",e).style("padding","1px 2px").style("color",r).text(s.count)}}else{t.insert("div").style("display","inline-block").html(e.gene)}}deleteGene(t){const e=this.geneList.findIndex((e=>e.gene===t.gene));if(e!=-1){this.geneList.splice(e,1);this.renderGenes()}}}function L(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-95bad59a.js");case"../plots/Disco.js":return import("./Disco-a6e921a0.js");case"../plots/DziViewer.js":return import("./DziViewer-354a790d.js");case"../plots/WSIViewer.js":return import("./WSIViewer-dc7f8eb0.js");case"../plots/barchart.data.js":return import("./FilterRxComp-701a1480.js").then((function(t){return t.j}));case"../plots/barchart.events.js":return import("./barchart.events-da29c90d.js");case"../plots/barchart.js":return import("./barchart-8277ed43.js");case"../plots/bars.renderer.js":return import("./bars.renderer-dcfdd59b.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-e17a17b7.js");case"../plots/brainImaging.js":return import("./brainImaging-bf2ceee9.js");case"../plots/controls.btns.js":return import("./controls.btns-79b805dd.js");case"../plots/controls.config.js":return import("./controls.config-28d6d6a8.js");case"../plots/controls.js":return import("./controls-287e6efa.js");case"../plots/cuminc.js":return import("./cuminc-9e275854.js");case"../plots/dataDownload.js":return import("./dataDownload-3a3d4f33.js");case"../plots/dictionary.js":return import("./dictionary-c5a19d90.js");case"../plots/facet.js":return import("./facet-a9b44ef3.js");case"../plots/geneExpression.js":return import("./geneExpression-589f485b.js");case"../plots/geneORA.js":return import("./geneORA-903a780f.js");case"../plots/geneset.js":return import("./geneset-108a39d2.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-d5067811.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-12f86a36.js");case"../plots/gsea.js":return import("./gsea-543dab25.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-98e82dff.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-e56f6542.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-26e14090.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-74a64cf5.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-b9eae4ae.js");case"../plots/matrix.cells.js":return import("./matrix.cells-914dd0c6.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-783ceab0.js");case"../plots/matrix.config.js":return import("./matrix.config-6ce74dfe.js");case"../plots/matrix.controls.js":return import("./matrix.controls-7b2a6f95.js");case"../plots/matrix.data.js":return import("./matrix.data-dac4f1b7.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-4e10bbe9.js");case"../plots/matrix.groups.js":return import("./matrix.groups-b9fca14a.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-84169b43.js");case"../plots/matrix.js":return import("./matrix-00bb50ff.js");case"../plots/matrix.layout.js":return import("./matrix.layout-dd5a44fd.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-ac6d45e6.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-78010275.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-9b4fd744.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-014d798d.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-9bf7e6f9.js");case"../plots/plot.app.js":return import("./plot.app-30c4b8e5.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-2ceb6023.js");case"../plots/plot.disco.js":return import("./plot.disco-6011f87f.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-5581dc56.js");case"../plots/profileBarchart.js":return import("./profileBarchart-0476f1f8.js");case"../plots/profilePlot.js":return import("./profilePlot-c7e099e8.js");case"../plots/profilePolar.js":return import("./profilePolar-6b981e63.js");case"../plots/profileRadar.js":return import("./profileRadar-bca1cc03.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-bbb1ecd8.js");case"../plots/profileSummary.js":return import("./profileSummary-b114204f.js");case"../plots/regression.inputs.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-5929d25a.js");case"../plots/regression.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-69bc42d0.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.b}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-0b12ac61.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-484ab133.js");case"../plots/scatter.js":return import("./scatter-205e013f.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-73b2738f.js");case"../plots/stattable.js":return import("./stattable-7c5ecc2f.js");case"../plots/summary.js":return import("./summary-5ec455d3.js");case"../plots/survival.js":return import("./survival-92250664.js");case"../plots/table.js":return import("./table-ad744310.js");case"../plots/variantBrowser.js":return import("./variantBrowser-7c540224.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-4da6d7a9.js");case"../plots/violin.js":return import("./violin-2ba509eb.js");case"../plots/violin.renderer.js":return import("./violin.renderer-ce024265.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class E{constructor(t={}){this.type="charts";q(this)}async init(t){this.dom={holder:this.opts.holder,tip:new s({padding:"0px"})};this.makeButtons(t)}getState(t){const e=N(t);const s=JSON.parse(JSON.stringify(t.termdbConfig?.supportedChartTypes||{}));const r={vocab:t.vocab,activeCohort:t.activeCohort,termfilter:t.termfilter,supportedChartTypes:s[e]||["summary"],termdbConfig:t.termdbConfig};if(t?.termfilter?.filter){r.filter=j(t.termfilter.filter)}if(!r.supportedChartTypes.includes("dictionary")&&!r.termdbConfig.hiddenChartTypes?.includes("dictionary")){if(r.vocab.dslabel=="ProfileFull"||r.vocab.dslabel=="ProfileAbbrev")r.supportedChartTypes.push(...t.termdbConfig.allowedChartTypes);r.supportedChartTypes.push("dictionary");r.supportedChartTypes.push("facet")}return r}main(){this.dom.btns.style("display",(t=>this.state.supportedChartTypes.includes(t.chartType)?"":"none"))}}const R=n(E);function N(t){if(t?.termdbConfig?.selectCohort?.values){if(!Number.isInteger(t.activeCohort))throw"appState.activeCohort is not integer array index";const e=t.termdbConfig.selectCohort.values[t.activeCohort];if(!e)throw"appState.activeCohort array index out of bound";return[...e.keys].sort().join(",")}return""}function M(t,e){const s=[{label:"Data 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l;const p=n.append("input").style("margin","2px 5px").style("width","210px").attr("placeholder","Group Name").on("input",(()=>{l=p.property("value")}));const c={index:0,name:l,label:l,lst:[],status:"new"};new G({holder:a.append("div"),genome:r.opts.genome,geneList:s,mode:"geneExpression",vocabApi:r.vocabApi,callback:async({geneList:t,groupName:e})=>{if(!c)throw`missing selectedGroup`;i.hide();const s={name:e||l,lst:[],type:"hierCluster"};const o=s.lst.filter((t=>t.term.type!="geneVariant"));const n=await Promise.all(t.map((async t=>{const e={gene:t.symbol||t.gene,name:t.symbol||t.gene,type:"geneExpression"};let r=s.lst.find((e=>e.term.name==t.symbol||e.term.name==t.gene));if(!r){r={term:e,q:{}}}return r})));if(n.length==1){const t=n[0];r.dispatch({type:"plot_create",config:{chartType:"summary",term:t}});return}if(n.length==2){const t=n[0];const 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X(this)}getMassFilter(){if(!this.state.termfilter.filter||this.state.termfilter.filter.lst.length==0){return{type:"tvslst",in:true,join:"",lst:[]}}const t=j(structuredClone(this.state.termfilter.filter));return t}async groups2samplelst(t){const e=[];const s=new Set,r=[];for(const i of t){const t=await this.app.vocabApi.getFilteredSampleList(i.filter);const a=[];for(const i of t){const t={sampleId:i.id};if("name"in i){t.sample=i.name}if(!s.has(i.id))a.push(t);else{for(const t of e){const e=t.items.findIndex((t=>t.sampleId===i.id));if(e!==-1)r.push(...t.items.splice(e,1))}}s.add(t.sampleId)}if(a.length)e.push({name:i.name,items:a,color:i.color})}if(r.length){const t=confirm('Overlap detected: 1 or more samples belong to >1 groups. 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this.state.termdbConfig.scatterplots){if(t.colorTW)i.append("div").attr("class","sja_menuoption sja_sharp_border").text(`Open ${t.name}`).on("click",(()=>{let e={chartType:"sampleScatter",name:t.name};if(t.sampleCategory)e.sampleCategory={tw:structuredClone(t.sampleCategory.tw),order:t.sampleCategory.order,defaultValue:t.sampleCategory.defaultValue};if(t.sampleType)e.sampleType=t.sampleType;e.colorTW=structuredClone(r);if(t.settings)e.settings=structuredClone(t.settings);this.app.dispatch({type:"plot_create",config:e});this.tip.hide()}))}this.tip.showunder(t.target)}}const z=n(U);function J(t,e,s,r,i){t.append("div").attr("class","sja_menuoption sja_sharp_border").text("Differential expression").on("click",(t=>{const i=[];for(const t of r.q.groups){if(t.values&&t.values.length>0){i.push(t)}else{throw"group does not contain samples for DE analysis"}}const a={chartType:"DEanalysis",state:s,samplelst:{groups:i}};e.tip.hide();e.app.dispatch({type:"plot_create",config:a})}))}function W(t){t.dom.filterTableDiv=t.dom.holder.append("div").style("margin-bottom","10px");const e=t.dom.holder.append("div");t.dom.addNewGroupBtnHolder=e.append("span").style("margin-right","20px");t.dom.newTermSpan=e.append("span");t.dom.newTermSpan.append("span").style("padding-left","15px").text("Add variable:");t.dom.newTermNameInput=t.dom.newTermSpan.append("input").attr("type","text");t.dom.launchButton=t.dom.newTermSpan.append("span").attr("class","sja_menuoption").on("click",(()=>Q(t)));t.dom.noGroupSelected=e.append("span").text("No groups selected").style("opacity",.5);t.dom.customTermDiv=t.dom.holder.append("div").style("margin","20px").style("border-left","solid 1px black").style("padding","10px");t.dom.holder.on("click",(t=>{if(tt)tt.hide()}))}async function X(t){if(!t.filterPrompt)t.filterPrompt=await A({holder:t.dom.addNewGroupBtnHolder,vocabApi:t.app.vocabApi,emptyLabel:"Add 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t.app.vocabApi.getFilteredSampleCount(r.filter)},{}])}t.selectedGroupsIdx.clear();if(e.length==1){t.selectedGroupsIdx.add(0)}else{s.noButtonCallback=(e,s)=>{if(s.checked)t.selectedGroupsIdx.add(e);else t.selectedGroupsIdx.delete(e);t.updateLaunchButton()};s.selectedRows=[];for(let r=0;r<e.length;r++){s.selectedRows.push(r);t.selectedGroupsIdx.add(r)}}C(s);for(const[r,i]of s.rows.entries()){const s=e[r];x({holder:i[3].__td,vocabApi:t.app.vocabApi,termdbConfig:t.state.termdbConfig,callback:r=>{if(!r||r.lst.length==0){const t=e.findIndex((t=>t.name==s.name));e.splice(t,1)}else{s.filter=r}t.app.dispatch({type:"app_refresh",state:{groups:e}})}}).main(s.filter)}t.updateLaunchButton();t.displayCustomTerms()}async function Q(t){const e=[];for(const s of t.selectedGroupsIdx){const r=t.state.groups[s];if(r)e.push(r)}if(e.length==0)throw"No groups, should not happen";const s=t.dom.newTermNameInput.property("value");const r=await 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import("./matrix.cells-914dd0c6.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-783ceab0.js");case"../plots/matrix.config.js":return import("./matrix.config-6ce74dfe.js");case"../plots/matrix.controls.js":return import("./matrix.controls-7b2a6f95.js");case"../plots/matrix.data.js":return import("./matrix.data-dac4f1b7.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-4e10bbe9.js");case"../plots/matrix.groups.js":return import("./matrix.groups-b9fca14a.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-84169b43.js");case"../plots/matrix.js":return import("./matrix-00bb50ff.js");case"../plots/matrix.layout.js":return import("./matrix.layout-dd5a44fd.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-ac6d45e6.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-78010275.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-9b4fd744.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-014d798d.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-9bf7e6f9.js");case"../plots/plot.app.js":return import("./plot.app-30c4b8e5.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-2ceb6023.js");case"../plots/plot.disco.js":return import("./plot.disco-6011f87f.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-5581dc56.js");case"../plots/profileBarchart.js":return import("./profileBarchart-0476f1f8.js");case"../plots/profilePlot.js":return import("./profilePlot-c7e099e8.js");case"../plots/profilePolar.js":return import("./profilePolar-6b981e63.js");case"../plots/profileRadar.js":return import("./profileRadar-bca1cc03.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-bbb1ecd8.js");case"../plots/profileSummary.js":return import("./profileSummary-b114204f.js");case"../plots/regression.inputs.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-5929d25a.js");case"../plots/regression.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-69bc42d0.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.b}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-0b12ac61.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-484ab133.js");case"../plots/scatter.js":return import("./scatter-205e013f.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-73b2738f.js");case"../plots/stattable.js":return import("./stattable-7c5ecc2f.js");case"../plots/summary.js":return import("./summary-5ec455d3.js");case"../plots/survival.js":return import("./survival-92250664.js");case"../plots/table.js":return import("./table-ad744310.js");case"../plots/variantBrowser.js":return import("./variantBrowser-7c540224.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-4da6d7a9.js");case"../plots/violin.js":return import("./violin-2ba509eb.js");case"../plots/violin.renderer.js":return import("./violin.renderer-ce024265.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}const mt="_MASS_AUTOID_"+Math.random().toString().slice(-6);let ut=(+new Date).toString().slice(-8);function ht(){return mt+"_"+ut++}const ft=new Set(["with_tabs","hidden","search_only","hide_search","only_buttons","with_cohortHtmlSelect"]);const gt={nav:{header_mode:"with_tabs",activeTab:0},activeCohort:0,search:{isVisible:true},plots:[],termfilter:{filter:{type:"tvslst",in:true,join:"",lst:[]}},reuse:{customTermQ:{byId:{},byName:{}}},groups:[],customTerms:[],autoSave:true};class bt{constructor(t){this.type="store";this.defaultState=gt;this.prevGeneratedId=0}validateOpts(t){const e=t.state;if(e.vocab.dslabel){if(!e.vocab.genome)throw".state[.vocab].genome missing"}else{if(!Array.isArray(e.vocab.terms))throw"vocab.terms must be an array of objects"}}validateState(){if(!ft.has(this.state.nav.header_mode))throw"invalid state.nav.header_mode"}async init(){try{this.state.termdbConfig=await this.app.vocabApi.getTermdbConfig();await this.setTermfilter();await this.rehydrateGroups();await this.app.vocabApi.main({termfilter:JSON.parse(JSON.stringify(this.state.termfilter)),termdbConfig:this.state.termdbConfig});const t=[];for(const[e,s]of this.state.plots.entries()){let r;try{const t=await dt(`../plots/${s.chartType}.js`);r=await t.getPlotConfig(s,this.app)}catch(t){this.app.printError(t);console.error(`getPlotConfig() failed: ${t}`)}if(!r){t.push(e);continue}this.state.plots[e]=r;if(!("id"in r))r.id=`_AUTOID_${ut++}_${e}`;if(r.mayAdjustConfig)r.mayAdjustConfig(r)}if(t.length){for(const e of t){this.state.plots.splice(e,1)}}}catch(t){throw t}}setId(t){t.$id=this.prevGeneratedId++;if(t.$lst){for(const e of t.$lst){this.setId(e)}}}async setTermfilter(){let t=y(this.state.termfilter.filter,"filterUiRoot");if(!t){this.state.termfilter.filter.tag="filterUiRoot";t=this.state.termfilter.filter}await Promise.all(_(this.state.termfilter.filter,this.app.vocabApi));if(!this.state.termdbConfig.selectCohort){this.state.activeCohort=-1;if(this.state.activeTab===0)this.state.activeTab=1;if(this.state.nav.header_mode==="with_cohortHtmlSelect"){console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);this.state.nav.header_mode="search_only"}}else{let e=y(this.state.termfilter.filter,"cohortFilter");if(!e){e={tag:"cohortFilter",type:"tvs",tvs:{term:JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),values:this.state.activeCohort==-1?[]:this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((t=>({key:t,label:t})))}};this.state.termfilter.filter={type:"tvslst",in:true,join:"and",lst:[e,t]}}else{const t=(t,e)=>t<e?-1:1;e.tvs.values.sort(((t,e)=>t.key<e.key?-1:1));const s=JSON.stringify(e.tvs.values.map((t=>t.key)).sort(t));const r=this.state.termdbConfig.selectCohort.values.findIndex((e=>s==JSON.stringify(e.keys.sort(t))));if(this.state.activeCohort!==-1&&this.state.activeCohort!==0&&r!==this.state.activeCohort){console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch")}this.state.activeCohort=r}}}async rehydrateGroups(){const t=[];for(const e of this.state.groups){t.push(..._(e.filter,this.app.vocabApi))}await Promise.all(t)}}bt.prototype.actions={app_refresh(t={}){this.state=this.copyMerge(this.toJson(this.state),t.state||{});const e=new Set;if(t.subactions){for(const s of t.subactions){this.actions[s.type].call(this,s);if(s.type.startsWith("plot_"))e.add(s.id)}}for(const s in this.state.plots){if(s.mayAdjustConfig&&!e.has(s.id)){s.mayAdjustConfig(s,t.config)}}},tab_set(t){this.state.nav.activeTab=t.activeTab},cohort_set(t){this.state.activeCohort=t.activeCohort;const e=this.state.termdbConfig.selectCohort.values[t.activeCohort];const s=y(this.state.termfilter.filter,"cohortFilter");if(!s)throw`No item tagged with 'cohortFilter'`;s.tvs.values=e.keys.map((t=>({key:t,label:t})))},async plot_prep(t){const e={id:"id"in t?t.id:ht()};if(!t.config)throw".config{} missing for plot_prep";if(t.config.chartType&&Object.keys(t.config).length==1){const e=await ct(`../plots/${t.config.chartType}.js`);const s=await e.getPlotConfig(t.config,this.app);t.config=Object.assign(s,t.config)}Object.assign(e,t.config);this.state.plots.push(e)},async plot_create(t){const e=await pt(`../plots/${t.config.chartType}.js`);const s=await e.getPlotConfig(t.config,this.app);if(!("id"in t))t.id=ht();s.id=t.id;if(s.mayAdjustConfig){s.mayAdjustConfig(s,t.config)}this.state.plots.push(s)},plot_edit(t){const e=this.state.plots.find((e=>e.id===t.id));if(!e)throw`missing plot id='${t.id}' in store.plot_edit()`;this.copyMerge(e,t.config,t.opts?t.opts:{});if(e.mayAdjustConfig){e.mayAdjustConfig(e,t.config)}if(t.config&&"cutoff"in t.config){e.cutoff=t.config.cutoff}else{delete e.cutoff}},plot_delete(t){const e=this.state.plots.findIndex((e=>e.id===t.id));if(e!==-1)this.state.plots.splice(e,1)},plot_nestedEdits(t){const e=this.state.plots.find((e=>e.id===t.id));if(!e)throw`missing plot id='${t.id}' in store.plot_edit_nested`;for(const s of t.edits){const t=s.nestedKeys.pop();const r=s.nestedKeys.reduce(((t,e)=>t[e]),e);r[t]=s.value}},async plot_splice(t){for(const e of t.subactions){await this.actions[e.type].call(this,e)}},filter_replace(t){if("filter0"in t){this.state.termfilter.filter0=t.filter0;return}const e=t.filter?t.filter:{type:"tvslst",join:"",in:1,lst:[]};if(!t.filter.tag){this.state.termfilter.filter=e}else{const s=y(this.state.termfilter.filter,t.filter.tag);if(!s)throw`cannot replace missing filter with tag '${t.filter.tag}'`;const r=v(this.state.termfilter.filter,s.$id);if(r==s){this.state.termfilter.filter=e}else{const t=r.lst.indexOf(s);r.lst[t]=e}}},cache_termq({termId:t,q:e}){if(!t)throw`missing termId for caching custom term.q`;if(!e?.reuseId)throw`missing or empty tw.q.reuseId as cache identifier for term='${t}'`;const s=this.state.reuse.customTermQ.byId;if(!s[t])s[t]={};s[t][e.reuseId]=e;for(const t of this.state.plots){if(!(t.chartType in yt))continue;const s=yt[t.chartType](t);for(const t of s){if(t?.q?.reuseId===e.reuseId)t.q=e}}},uncache_termq({term:t,q:e}){if(!t.id)throw`missing term.id for uncaching custom term.q`;if(!e.reuseId)throw`missing qname as uncache identifier for term.id='${t.id}'`;const s=this.state.reuse.customTermQ.byId[t.id];if(!s)throw`missing term.q cache for term.id='${t.id}`;if(!(e.reuseId in s))console.warn(`q.reuseId='${e.cacheid}' not cached for term.id='${t.id}'`);else{delete s[e.reuseId];for(const t of this.state.plots){if(!(t.chartType in yt))continue;const s=yt[t.chartType](t);for(const t of s){if(t.q.reuseId===e.reuseId){delete t.q.reuseId;delete t.q.name}}}}},add_customTerm(t){this.state.customTerms.push(t.obj)},delete_customTerm({name:t}){const e=this.state.customTerms.findIndex((e=>e.name==t));if(e!=-1)this.state.customTerms.splice(e,1)},add_group(t){if(this.state.nav.header_mode!="hidden"){const e=t.obj;const s=`Group ${this.state.groups.length+1}`;const r=lt([e]);const i={name:s,filter:ot(r),plotId:e.plotId};this.state.groups.push(i);this.state.nav.activeTab=1}else if("plotId"in t.obj){const e=this.state.plots.find((e=>e.id==t.obj.plotId));if(e.groups){t.obj.index=e.groups.length;t.obj.name=`Group ${e.groups.length+1}`;e.groups.push(t.obj)}}},rename_group(t){const e=t.index;const s=t.newName;if(this.state.nav.header_mode!="hidden"){this.state.groups[e].name=s}else{for(const t of this.state.plots){if(t?.groups){t.groups[e].name=s}}}},change_color_group(t){const e=t.index;const s=t.newColor;if(this.state.nav.header_mode!="hidden"){this.state.groups[e].color=s}else{for(const t of this.state.plots){if(t?.groups){t.groups[e].color=s}}}},delete_group({name:t}){if(this.state.nav.header_mode!="hidden"){const e=this.state.groups.findIndex((e=>e.name==t));if(e!=-1)this.state.groups.splice(e,1)}else{for(const e of this.state.plots){if(e?.groups){const s=e.groups.findIndex((e=>e.name==t));if(s!=-1)e.groups.splice(s,1)}}}}};const jt=t=>[t.term0,t.term,t.term2].filter((t=>!!t));const yt={summary:jt,survival:jt,cuminc:jt,regression:t=>[t.outcome,...t.independent].filter((t=>!!t)),matrix:t=>t.termgroups.reduce(((t,e)=>{t.push(...e.lst);return t}),[])};const vt=d(bt);class xt{constructor(t={}){this.type="recover";this.initialHolderDisplay=t.holder.style("display");this.dom={holder:t.holder,btnDiv:t.holder.append("div").style("position","sticky").style("top","12px").style("right","20px").style("margin",t.margin?t.margin:"10px").style("text-align","right")};this.hasStatePreMain=true;this.reactsTo=t.reactsTo||(()=>true);this.getState=t.getState||(t=>t);this.debouncedTrack=()=>{this.trackPending=true;this.trackState();this.render()};this.wait="wait"in t?t.wait:800;this.maxHistoryLen=t.maxHistoryLen||10}preApiFreeze(t){t.replaceLastState=t=>{if(this.isRecovering)return;this.state=this.getState(t);if(!this.trackPending)this.history[this.currIndex]=this.state}}init(){this.app.register(this.api);this.currIndex=-1;this.history=[];this.isActive=!isNaN(this.maxHistoryLen)&&+this.maxHistoryLen>0;if(this.isActive){Ct(this);this.initUi()}this.eventTypes=["postInit","postRender"]}async main(){if(!this.isActive)return;if(this.opts.hide?.(this.state)){this.dom.holder.style("display","none");return}this.dom.holder.style("display",this.initialHolderDisplay||"");if(!this.timedTrack){this.trackState();this.trackPending=true;this.timedTrack=setTimeout((()=>{}),this.wait);return}clearTimeout(this.timedTrack);this.trackPending=true;this.timedTrack=setTimeout(this.debouncedTrack,this.wait)}trackState(){if(this.isRecovering){this.isRecovering=false;return}if(this.state._scope_=="none")return;this.isRecovering=false;const t=this.opts.adjustTrackedState?this.opts.adjustTrackedState(this.state):this.state;if(!t){console.error("no state to track");return}if(!Object.isFrozen(t))m(t);if(this.currIndex==-1)this.origState=t;if(this.currIndex<this.history.length-1){this.history.splice(this.currIndex,this.history.length-(this.currIndex+1))}if(u(t,this.history[this.history.length-1]))return;this.history.push(t);this.currIndex+=1;if(this.history.length>this.maxHistoryLen){this.history.splice(1,1);this.currIndex+=-1}this.trackPending=false}goto(t){if(t<0&&this.currIndex+t>-1)this.currIndex+=t;else if(t>0&&this.currIndex+t<this.history.length)this.currIndex+=t;else return;this.isRecovering=true;const e=this.history[this.currIndex];this.render();if(this.opts.plot_id){const t=structuredClone(e);this.app.dispatch({type:"plot_edit",id:this.opts.plot_id,config:t.config,_scope_:t._scope_})}else{this.app.dispatch({type:"app_refresh",state:e})}}reset(){this.currIndex=0;this.isRecovering=true;const t=this.origState;if(this.opts.plot_id){const e=t.plots.find((t=>t.id===this.opts.plot_id));this.app.dispatch({type:"plot_edit",id:this.opts.plot_id,config:structuredClone(e)})}else this.app.dispatch({type:"app_refresh",state:t})}}const wt=n(xt);function Ct(t){t.initUi=function(){t.dom.undoBtn=t.dom.btnDiv.append("button").attr("aria-label","undo the previous action").property("disabled",true).style("margin","0 0 0 4px").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.undoHtml||`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-arrow-counterclockwise" viewBox="0 0 16 16" style='vertical-align: middle'>\n\t\t\t  <path stroke='#000' stroke-width='0.25' fill-rule="evenodd" d="M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z"/>\n\t\t\t  <path d="M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z"/>\n\t\t\t</svg>`).on("click",(()=>t.goto(-1)));t.dom.redoBtn=t.dom.btnDiv.append("button").attr("aria-label","redo a subsequent action").property("disabled",true).style("margin",t.opts.resetHtml?"0":"0 4px 0 0").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.redoHtml||`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-arrow-clockwise" viewBox="0 0 16 16" style='vertical-align: middle'>\n\t\t\t  <path stroke='#000' stroke-width='0.25' fill-rule="evenodd" d="M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z"/>\n\t\t\t  <path d="M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z"/>\n\t\t\t</svg>`).on("click",(()=>t.goto(1)));if(t.opts.resetHtml)t.dom.resetBtn=t.dom.btnDiv.append("button").attr("aria-label","Restore the initial rendered state").property("disabled",true).style("margin","0 4px 0 0").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.resetHtml).on("click",(()=>t.reset()))};t.render=function(){if(t.dom.undoBtn)t.dom.undoBtn.property("disabled",t.currIndex<1||t.history.length===1);if(t.dom.redoBtn)t.dom.redoBtn.property("disabled",t.history.length<2||t.currIndex>=t.history.length-1);if(t.dom.resetBtn)t.dom.resetBtn.property("disabled",t.currIndex===0)}}export{G,lt as a,ot as b,R as c,at as d,it as e,st as f,z as g,et as h,N as i,Y as j,nt as k,Z as o,wt as r,vt as s};

package/dist/regression.inputs-a761f40d.js

@@ -0,0 +1 @@
+import{f as t,h as e,b as i}from"./termsetting-33ea66f1.js";import{h as s,P as n,y as r,M as o,d as a}from"./app-b369b169.js";import"./FilterRxComp-701a1480.js";import{g as p}from"./termdb.bins-8b656cc3.js";import{InputValuesTable as c}from"./regression.inputs.values.table-5929d25a.js";import{mayRunSnplstTask as d}from"./snplst.sampleSum-e47d05f0.js";import{R as l}from"./regression.results-69bc42d0.js";class m{constructor(t){this.type="regression";this.genomeObj=t.app.opts.genome}async init(t){this.dom={header:this.opts.header,errordiv:this.opts.holder.append("div"),inputs:this.opts.holder.append("div").style("margin","20px 10px"),results:this.opts.holder.append("div").style("margin-left","40px")};const e=t.plots.find((t=>t.id===this.id));this.inputs=new O({app:this.app,parent:this,id:this.id,holder:this.dom.inputs,regressionType:e.regressionType});this.results=new l({app:this.app,parent:this,id:this.id,holder:this.dom.results,regressionType:e.regressionType})}getState(t,e){const i=t.plots.find((t=>t.id===this.id));if(!i){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}if(!i.regressionType)throw"regressionType is required";return{vocab:t.vocab,formIsComplete:i.outcome&&i.independent.length,activeCohort:t.activeCohort,termfilter:t.termfilter,config:i,allowedTermTypes:t.termdbConfig.allowedTermTypes,minTimeSinceDx:t.termdbConfig.minTimeSinceDx}}async main(){try{this.config=JSON.parse(JSON.stringify(this.state.config));this.mayUpdateSandboxHeader();this.getFilter();await this.inputs.main();await this.results.main();this.inputs.resetSubmitButton()}catch(t){if(this.inputs.hasError){this.results.main()}r(this.dom.errordiv,"Error: "+(t.error||t));if(t.stack)console.log(t.stack)}}mayUpdateSandboxHeader(){if(!this.dom.header)return;const t=this.config.outcome;this.dom.header.html((t?t.term.name:"")+'<span style="opacity:.6;font-size:.7em;margin-left:10px;">'+this.config.regressionType.toUpperCase()+" REGRESSION</span>")}getFilter(){const t=[];if(this.state.termfilter?.filter)t.push(this.state.termfilter.filter);const e=[this.config.outcome,...this.config.independent];const i=e.filter((t=>t?.q.restrictAncestry));if(i.length){if(i.length>1){const t=new Set(i.map((t=>t.q.restrictAncestry.name)));if(t.size>1)throw"samples cannot be restricted to more than 1 ancestry"}const e=i[0];t.push({type:"tvs",tvs:e.q.restrictAncestry.tvs});this.inputs.dom.submitMsg.style("display","block").text(`restricting analysis to samples of ${e.q.restrictAncestry.name}`)}else{this.inputs.dom.submitMsg.style("display","none")}this.filter={type:"tvslst",join:"and",lst:t}}}const u=s(m);const f=u;let h=1;async function g(e,i){if(!e.outcome)e.outcome={};{await t(e.outcome,i.vocabApi,y(e.regressionType,"outcome"))}const s="id"in e?e.id:`_REGRESSION_${h++}`;const r={id:s};r.outcome=e.outcome;if(e.independent){if(!Array.isArray(e.independent))throw".independent[] is not array";for(const s of e.independent){const e=!s.q?.mode?{numeric:{mode:"continuous"}}:undefined;await t(s,i.vocabApi,e)}r.independent=e.independent}else{r.independent=[]}return n(r,e)}function y(t,e=""){const i={};i["numeric"]=t=="logistic"&&e=="outcome"?{mode:"binary"}:{mode:"discrete"};i["categorical"]=t=="logistic"&&e=="outcome"?{mode:"binary"}:{mode:"discrete"};if(e=="outcome"){if(t=="cox"){i.condition={mode:"cox"}}if(t=="logistic"){i.condition={mode:"binary"}}}return i}function b(t,e){const i=[{label:"Linear",type:"linear"},{label:"Logistic",type:"logistic"},{label:"Cox",type:"cox"}];for(const{label:s,type:n}of i){t.append("div").attr("class","sja_menuoption sja_sharp_border").text(s).on("click",(()=>{e.dom.tip.hide();e.prepPlot({config:{chartType:"regression",regressionType:n,independent:[]}})}))}}var v=Object.freeze({__proto__:null,regressionInit:u,componentInit:f,getPlotConfig:g,get_defaultQ4fillTW:y,makeChartBtnMenu:b});class x{constructor(t){this.opts=t;this.section=t.section;this.term=t.term;this.parent=t.parent}async init(t){const i=t.append("div");const s=i.append("span").style("display","inline-block");const n=i.append("span").style("margin-left","20px");this.dom={holder:t,termRow:i,pillDiv:s,interactionDiv:n,err_div:t.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),infoDiv:t.append("div"),tip:new o};try{const{app:t,config:i,state:s,disable_terms:n}=this.parent;const r={placeholder:this.section.selectPrompt,placeholderIcon:this.section.placeholderIcon,holder:this.dom.pillDiv,vocabApi:t.vocabApi,noTermPromptOptions:this.opts.noTermPromptOptions,activeCohort:s.activeCohort,debug:t.opts.debug,menuOptions:this.section.configKey=="outcome"?"{edit,reuse,replace}":"{edit,reuse,remove}",usecase:{target:"regression",detail:this.section.configKey,regressionType:i.regressionType},disable_terms:n,abbrCutoff:50,genomeObj:this.parent.parent.genomeObj,defaultQ4fillTW:y(i.regressionType,this.section.configKey),callback:t=>{this.parent.editConfig(this,t)}};this.furbishTsConstructorArg(r);this.pill=await e(r);if(this.section.configKey=="outcome"){this.setQ=S(i.regressionType)}this.valuesTable=new c({holder:this.dom.infoDiv,input:this,callback:t=>{this.parent.editConfig(this,t)}})}catch(t){this.displayError([t])}}furbishTsConstructorArg(t){const e=this.parent.config.regressionType;if(this.section.configKey=="outcome"){if(e=="logistic"){t.numericEditMenuVersion=["binary"];return}if(e=="linear"){t.numericEditMenuVersion=["continuous"];return}if(e=="cox"){return}throw"unknown regressionType"}if(this.section.configKey=="independent"){t.numericEditMenuVersion=["continuous","discrete","spline"];t.defaultQ4fillTW["geneVariant"]={type:"predefined-groupset"};t.geneVariantEditMenuOnlyGrp=true;return}throw"unknown section.configKey: "+this.section.configKey}displayError(t){this.hasError=true;this.dom.err_div.selectAll("*").remove();this.dom.err_div.style("display","block").selectAll("div").data(Array.isArray(t)?t:[t]).enter().append("div").text((t=>t));this.parent.handleError();console.error(t)}async main(){const t=this.term;if(t){delete t.error}this.dom.err_div.style("display","none").text("");this.hasError=false;const e=[];try{if(t&&this.setQ){const{app:e,state:i}=this.parent;await this.setQ[t.term.type](t,e.vocabApi,this.parent.parent.filter,i)}try{await this.updateTerm()}catch(t){e.push(t)}await this.pill.main(this.getPillArgs());this.renderInteractionPrompt();await this.valuesTable.main();const i=t&&t.error||this.pill.error;if(i)e.push(i);if(e.length)throw e}catch(e){this.displayError(e)}}async updateTerm(){const t=this.term;if(!t)return;if(!t.q)throw".term.q missing on this input";if(!t.q.mode&&i(t.term.type)){if(t.term.type=="categorical"||t.term.type=="condition"||t.term.type=="survival"||t.term.type=="samplelst")t.q.mode="discrete";else t.q.mode="continuous"}const e=t.term.type=="snplst"||t.term.type=="snplocus"?{cacheid:t.q.cacheid}:{term1_q:t.q};const s=await this.parent.app.vocabApi.getCategories(t.term,this.parent.parent.filter,e);if(!s)throw`no data for term.id='${t.term.id}'`;if(s.error)throw s.error;d(t,s);this.termStatus={topInfoStatus:[],bottomSummaryStatus:undefined,sampleCounts:undefined,excludeCounts:undefined,allowToSelectRefGrp:false};if(t.q.numOfSampleWithAnyValidGT){const e=t.term.snps.reduce(((t,e)=>t+(e.invalid?1:0)),0);this.termStatus.topInfoStatus.push(`${t.q.numOfSampleWithAnyValidGT} samples with valid genotypes`+(e>0?` ${e} invalid SNP${e>1?"s":""}.`:""))}if("geneticModel"in t.q){this.termStatus.topInfoStatus.push("Genetic model: "+(t.q.geneticModel==0?"Additive":t.q.geneticModel==1?"Dominant":t.q.geneticModel==2?"Recessive":"By genotype"))}if(t.q.restrictAncestry){this.termStatus.topInfoStatus.push("Analyzing "+t.q.restrictAncestry.name);if(t.q.restrictAncestry.PCcount){this.termStatus.topInfoStatus.push(`Adjusting for top ${t.q.restrictAncestry.PCcount} ancestry principal components`)}}if(t.term.reachedVariantLimit){this.termStatus.topInfoStatus.push(`<span class=sja_mcdot style="background:#aaa;font-size:1em">\n\t\t\t\t&nbsp;&#9888; Restricted to first ${t.term.snps.length}\n\t\t\t\tvariants of this region.&nbsp;</span> Try zooming in.`)}this.orderedLabels=s.orderedLabels;if(s.lst){this.summarizeSample(t,s.lst);if(t.term.type=="float"||t.term.type=="integer"){if(t.q.mode!="continuous"&&t.q.mode!="spline"){this.termStatus.allowToSelectRefGrp=true}if(t.q.scale&&t.q.scale!=1)this.termStatus.topInfoStatus.push(`Scale: Per ${t.q.scale}`);if(t.q.mode=="discrete"){this.termStatus.topInfoStatus.push(`Discrete variable with ${this.termStatus.sampleCounts.length} bins`)}if(t.q.mode=="spline"){this.termStatus.topInfoStatus.push(`Cubic spline variable with ${t.q.knots.length} knots: ${t.q.knots.map((t=>Number(t.value))).sort(((t,e)=>t-e)).join(", ")}`)}}else if(t.term.type=="categorical"||t.term.type=="geneVariant"||t.term.type=="samplelst"){this.termStatus.allowToSelectRefGrp=true}else if(t.term.type=="condition"){if(this.section.configKey=="outcome"&&this.parent.opts.regressionType=="logistic"){this.termStatus.allowToSelectRefGrp=true}if(this.section.configKey=="outcome"&&this.parent.opts.regressionType=="cox"){if(!["age","time"].includes(t.q.timeScale))throw"invalid q.timeScale";const e=this.parent.app.vocabApi.termdbConfig;this.termStatus.topInfoStatus.push(`Time axis: ${t.q.timeScale=="time"?e.timeUnit:"age"}`);this.termStatus.topInfoStatus.push(`<span style="padding-left: 10px;">-start: ${t.q.timeScale=="time"?" ":"age at "}entry into the cohort (i.e., ${e.cohortStartTimeMsg})</span>`);this.termStatus.topInfoStatus.push(`<span style="padding-left: 10px;">-end: ${t.q.timeScale=="time"?" ":"age at "}event or censoring/death</span>`);const i=Object.keys(t.term.values).map(Number);const s=Math.max(...i);this.termStatus.topInfoStatus.push(`<div style="padding-top: 8px;">Event: first occurrence of grade ${t.q.breaks[0]===s?t.q.breaks[0]:`${t.q.breaks[0]}-${s}</div>`}`)}}this.maySet_refGrp(t)}}summarizeSample(t,e){const i=new Set;if(t.term.values){for(const e in t.term.values){if(t.term.values[e].uncomputable)i.add(t.term.values[e].label)}}if(t.q.mode=="cox"){const t=e.find((t=>t.key==-1));if(t)i.add(t.label)}const s=this.termStatus.sampleCounts=e.filter((t=>!i.has(t.label)));const n=this.termStatus.excludeCounts=e.filter((t=>i.has(t.label)));const r={included:0,excluded:0,total:0};s.forEach((t=>r.included+=t.samplecount));n.forEach((t=>r.excluded+=t.samplecount));r.total=r.included+r.excluded;if(t.term.type=="condition"&&r.total){r.excluded=r.total-r.included}this.termStatus.bottomSummaryStatus=`${r.included} samples included`+(r.excluded?`. ${r.excluded} samples excluded:`:"");if(t&&t.q.mode!=="continuous"&&s.length<2)throw`there should be two or more discrete values with samples for variable='${t.term.name}'`}maySet_refGrp(t){if(this.section.configKey=="outcome"&&this.parent.config.regressionType=="cox"){return}if(t.q.mode=="continuous"){t.refGrp="NA";return}const e=this.termStatus.sampleCounts;if(!("refGrp"in t)||!e.find((e=>e.key==t.refGrp))){const i=this.orderedLabels;if(i&&i.length)e.sort(((t,e)=>i.indexOf(t.key)-i.indexOf(e.key)));else e.sort(((t,e)=>t.samplecount<e.samplecount?1:-1));t.refGrp=e[0].key}}getPillArgs(){const t=this.section;const{config:e,state:i,disable_terms:s}=this.parent;const n=Object.assign({activeCohort:i.activeCohort,disable_terms:s,usecase:{target:"regression",detail:t.configKey,regressionType:e.regressionType}},this.term);n.filter=this.parent.parent.filter;return n}remove(){this.dom.termRow.transition().duration(500).style("opacity",0).remove();for(const t in this.dom){delete this.dom[t]}}renderInteractionPrompt(){this.dom.interactionDiv.style("display","none");if(!this.term)return;if(this.section.configKey!="independent")return;if(this.term.q.mode=="spline")return;if(this.parent.app.vocabApi.termdbConfig.neuroOncRegression)return;{let t=0;for(const e of this.section.inputLst){if(e.term&&e.term.q.mode!="spline"){t++}}if(t<2)return}const t=this.term.interactions.length;this.dom.interactionDiv.style("display","inline").html(t==0?"Add interactions":`${t} interaction${t>1?"s":""}`).style("padding","5px").style("background-color",t==0?null:"#ececec").style("border-radius",t==0?null:"6px").style("color",t==0?"rgb(153, 153, 153)":"#000").style("font-size",t==0?"0.8em":"").style("cursor","pointer").on("click",(()=>this.renderInteractionOptions()))}renderInteractionOptions(){const t=this;t.dom.tip.clear().showunder(t.dom.interactionDiv.node());t.dom.tip.d.append("div").style("padding","5px").style("font-size","0.8em").style("color","rgb(153, 153, 153)").html(`Selected variables will each form pairwise interaction with ${this.term.term.name}`);t.dom.tip.d.append("div").selectAll("div").data(t.parent.config.independent.filter((e=>e&&e.term.id!==t.term.term.id&&e.term.name!==t.term.term.name&&e.q.mode!="spline"))).enter().append("div").style("margin","5px").each((function(e){const i=a(this).append("label");i.append("input").attr("type","checkbox").property("checked",t.term.interactions.includes(e.term.id||e.term.name));i.append("span").text(" "+e.term.name)}));t.dom.tip.d.append("button").text("Apply").style("margin","5px").on("click",(()=>{t.dom.tip.hide();t.term.interactions=[];t.dom.tip.d.selectAll("input").each((function(e){if(a(this).property("checked"))t.term.interactions.push(e.term.id||e.term.name)}));for(const e of t.parent.config.independent){const i=e.interactions.indexOf(t.term.term.id||t.term.term.name);if(t.term.interactions.includes(e.term.id||e.term.name)){if(i==-1)e.interactions.push(t.term.term.id||t.term.term.name)}else if(i!=-1){e.interactions.splice(i,1)}}t.parent.editConfig(t,t.term)}))}}function S(t){return{integer:t=="logistic"?T:k,float:t=="logistic"?T:k,geneExpression:t=="logistic"?T:k,categorical:q,condition:w,survival:w}}async function T(t,e,i,s){if(t.q.mode=="binary"&&t.q.lst&&t.q.lst.length==2){t.q.mode="binary";return}const n=await e.getPercentile(t.term.id,[50],i);if(n.error||!n.values.length||!Number.isFinite(n.values[0]))throw"cannot get median value: "+(n.error||"no data");const r=t.term.type=="integer"?Math.round(n.values[0]):Number(n.values[0].toFixed(2));t.q={mode:"binary",type:"custom-bin",lst:[{startunbounded:true,stopinclusive:true,stop:r},{stopunbounded:true,startinclusive:false,start:r}]};t.q.lst.forEach((e=>{e.label=p(e,t.q)}));t.refGrp=t.q.lst[0].label}function w(t,e,i,s){if(s.config.regressionType=="logistic"){if(!t.refGrp)t.refGrp=t.q.groups[0].name}if(s.config.regressionType=="cox"){if(!t.q.timeScale)t.q.timeScale="time"}}async function q(t,e,i,s){const{term:n,q:r}=t;if(r.mode=="binary"){if(r.type=="values"&&Object.keys(n.values).length==2)return;if(r.type=="predefined-groupset"){const t=r.predefined_groupset_idx;const e=n.groupsetting;if(e[t]&&Object.keys(e[t]).length==2)return}if(r.type=="custom-groupset"){const t=r.customset;if(t.groups.length==2)return}}const o=await e.getCategories(n,i);if(o.error)throw"cannot get categories: "+o.error;const a=new Map;const p=[];for(const t of o.lst){a.set(t.key,t.samplecount);if(n.values&&n.values[t.key]&&n.values[t.key].uncomputable)continue;p.push(t.key)}if(p.length<2){r.type="values";t.error="less than 2 categories/grades - cannot create separate groups";return}if(p.length==2){r.type="values";return}const c=n.groupsetting;if(r.customset&&r.customset.groups&&r.customset.groups.length==2&&_(r.customset,a)){r.type="custom-groupset";return}if(c&&c.lst){if(r.predefined_groupset_idx>=0&&c.lst[r.predefined_groupset_idx]&&c.lst[r.predefined_groupset_idx].groups.length==2&&_(c.lst[r.predefined_groupset_idx],a)){r.type="predefined-groupset";return}const t=c.lst.findIndex((t=>t.groups.length==2));if(t!=-1&&_(c.lst[t],a)){r.predefined_groupset_idx=t;r.type="predefined-groupset";return}}const d={activeCohort:s.activeCohort,groups:[{name:"Group 1",type:"values",values:[]},{name:"Group 2",type:"values",values:[]}]};const l=Math.round(p.length/2);for(const[t,e]of p.entries()){if(t<l)d.groups[0].values.push({key:e});else d.groups[1].values.push({key:e})}r.customset=d;r.type="custom-groupset"}function k(t){if(!t.q.type){console.log("may not happen: why is input.term.q not yet set for numeric term at this point")}t.q.mode="continuous"}function _(t,e){for(const i of t.groups){let t=0;if(i.type=="values"){for(const s of i.values)t+=e.get(s.key)||0;if(t==0)return false}}return true}var A=Object.freeze({__proto__:null,InputTerm:x});const C=[{termtype:"snplst",html:"A list of variants"},{termtype:"snplocus",html:"Variants in a locus"},{termtype:"prs",text:"Polygenic risk score"}];class O{constructor(t){this.opts=t;this.app=t.app;this.parent=t.parent;E(this);I(this);this.createSectionConfigs();this.initUI()}createSectionConfigs(){this.outcome={heading:"Outcome variable",selectPrompt:this.opts.regressionType=="linear"?"Select continuous outcome variable":"Select outcome variable",placeholderIcon:"",configKey:"outcome",limit:1,usecase:{target:"regression",regressionType:this.opts.regressionType,detail:"outcome"},inputLst:[],dom:{}};this.independent={heading:"Independent variable(s)",selectPrompt:"Add independent variable",placeholderIcon:"",configKey:"independent",limit:10,usecase:{target:"regression",regressionType:this.opts.regressionType,detail:"independent"},inputLst:[],dom:{}};this.sections=[this.outcome,this.independent]}async main(){try{this.config=this.parent.config;this.state=this.parent.state;this.hasError=false;this.setDisableTerms();const t=[];for(const e of this.sections){await this.renderSection(e);for(const i of e.inputLst){i.dom.holder.style("border-left",i.term?"1px solid #bbb":"");t.push(i.main())}}await Promise.all(t);for(const t of this.sections){for(const e of t.inputLst){if(e.term&&e.term.error||e.hasError){this.hasError=true}}}}catch(t){this.hasError=true;throw t}}setDisableTerms(){this.disable_terms=[];if(this.config.outcome&&this.config.outcome.term)this.disable_terms.push(this.config.outcome.term);if(this.config.independent){for(const t of this.config.independent){this.disable_terms.push(t.term)}}}handleError(){this.hasError=true;this.dom.submitBtn.property("disabled",true)}getNoTermPromptOptions(t){if(t.configKey!="independent")return;const e=[];for(const i of C){if(!this.state.allowedTermTypes.includes(i.termtype)){continue}if(t.inputLst.find((t=>t.term&&t.term.term.type==i.termtype))){continue}e.push(i)}if(e.length){e.unshift({isDictionary:true,text:"Dictionary variable"})}return e}}function I(t){t.initUI=()=>{const e=t.opts.holder.append("div").style("display","block");t.dom={div:t.opts.holder,controls:e,body:e.append("div"),foot:e.append("div").style("margin","0px 20px").style("display","flex").style("align-items","center").style("gap","20px")};t.dom.submitBtn=t.dom.foot.append("div").append("button").style("display","none").style("padding","5px 15px").style("border-radius","15px").style("cursor","pointer").text("Run analysis").on("click",t.submit);t.dom.submitMsg=t.dom.foot.append("div").style("display","none").style("color","#cc0000").style("font-style","italic").style("font-size","0.8em");for(const e of t.sections){const i=t.dom.body.append("div");t.addSection(e,i)}};t.addSection=function(t,e){e.style("display","none").style("margin","3px 5px").style("padding","3px 5px");t.dom={holder:e,headingDiv:e.append("div").style("margin","3px 5px 20px 5px").style("font-size","17px").style("color","#bbb").text(t.heading),inputsDiv:e.append("div")}};t.renderSection=function(n){n.dom.holder.style("display",n.configKey=="outcome"||t.config.outcome?"block":"none");e(n);const r=n.dom.inputsDiv.selectAll(":scope > div").data(n.inputLst,(t=>t.term&&(t.term.term.id||t.term.term.name)));r.exit().each(s);r.enter().append("div").each(i)};function e(e){const i=t.config[e.configKey];const s=Array.isArray(i)?i:i?[i]:[];for(const n of s){if(e.configKey=="independent"){if(!n.interactions)n.interactions=[];for(const t of n.interactions){const e=i.find((e=>(e.term.id||e.term.name)==t));if(!e)throw"interacting partner not found in independents: "+t;if(!e.interactions)e.interactions=[];if(!e.interactions.includes(n.term.id||n.term.name))e.interactions.push(n.term.id||n.term.name)}}const s=e.inputLst.find((t=>t.term?.term.id==n.term.id||t.term?.term.name==n.term.name));if(!s){e.inputLst.push(new x({section:e,term:n,parent:t}))}else{s.term=n}}$(e,t)}async function i(t){await t.init(a(this).style("width","fit-content").style("margin","0px 15px 35px 25px").style("padding","0px 5px"))}function s(t){t.remove();for(const e in t.dom){delete t.dom[e]}const e=a(this);e.transition().duration(500).style("opacity",0).remove()}t.resetSubmitButton=()=>{t.dom.submitBtn.text("Run analysis").style("display",t.config.outcome&&t.config.independent.length?"block":"none").property("disabled",t.hasError)}}function E(t){t.editConfig=async(e,i)=>{if(!i){const t=e.section.inputLst.findIndex((t=>t===e));if(t==-1)throw`deleting an unknown input`;e.section.inputLst.splice(t,1);if(e.term){for(const t of e.section.inputLst){if(!t.term||!t.term.interactions)continue;const i=t.term.interactions.indexOf(e.term.term.id||e.term.term.name);if(i!=-1)t.term.interactions.splice(i,1)}}}else{const t=e.term;if(t&&i.term.id===t.term.id){for(const e in t){if(!(e in i))i[e]=t[e]}}e.term=i;if(i.q.mode=="spline"&&i.interactions){for(const t of e.section.inputLst){if(!t.term||!t.term.interactions)continue;const i=t.term.interactions.indexOf(e.term.term.id||e.term.term.name);if(i!=-1)t.term.interactions.splice(i,1)}i.interactions=[]}}const s=[];for(const t of e.section.inputLst){if(t.term)s.push(t.term)}const n=e.section.configKey;const r=Array.isArray(t.config[n])?s:s[0];t.app.dispatch({type:"plot_edit",id:t.parent.id,chartType:"regression",config:{hasUnsubmittedEdits:true,[n]:JSON.parse(JSON.stringify(r))}})};t.submit=()=>{t.dom.submitBtn.property("disabled",true);if(t.hasError){alert("Please fix the input variable errors (highlighted in red background).");return}const e=JSON.parse(JSON.stringify(t.config));e.hasUnsubmittedEdits=false;t.app.dispatch({type:"plot_edit",id:t.parent.id,chartType:"regression",config:e})}}function $(t,e){if(t.inputLst.length>=t.limit){return}const i=t.inputLst.find((t=>!t.term));if(i){const s=e.getNoTermPromptOptions(t);if(s){i.pill.main({noTermPromptOptions:s})}return}t.inputLst.push(new x({section:t,parent:e,noTermPromptOptions:e.getNoTermPromptOptions(t)}))}var P=Object.freeze({__proto__:null,RegressionInputs:O});export{A as a,P as b,v as r};

package/dist/regression.inputs.values.table-5929d25a.js

@@ -0,0 +1 @@
+import{getDefaultViolinSettings as t}from"./violin-2ba509eb.js";import{appInit as e}from"./plot.app-30c4b8e5.js";import{d as o}from"./app-b369b169.js";import"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./termsetting-33ea66f1.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./violin.renderer-ce024265.js";import"./brush-aa175142.js";import"./pointer-c7475677.js";import"./nodrag-16ad4b03.js";import"./table-29d5a973.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";import"./log-99af3443.js";import"./html.legend-a3f4ebfe.js";import"./violin.interactivity-4da6d7a9.js";import"./FilterRxComp-701a1480.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./niceNumLabels-238aabce.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";const i="#fff6dc";class l{constructor(t){this.opts=t;this.input=t.input;s(this);this.setDOM(t.holder)}main(){try{const t=this.input.term;if(!t||!this.input.termStatus){this.dom.holder.style("display","none");this.dom.loading_div.style("display","none");return}else if(t){this.dom.holder.style("display","block");this.dom.loading_div.style("display","block");this.updateValueCount();this.dom.loading_div.style("display","none");this.render();return}}catch(t){this.dom.loading_div.style("display","none");throw t}}updateValueCount(){const t=this.input;try{if(t.pill&&t.pill.validateQ){t.pill.validateQ({term:t.term.term,q:t.term.q,sampleCounts:t.termStatus.sampleCounts})}}catch(e){t.term.error=e}}}function s(l){l.setDOM=t=>{l.dom={holder:t.style("margin","10px").style("font-size",".8em").style("text-align","left").style("color","#999"),loading_div:t.append("div").text("Loading..").style("display","none"),top_info_div:t.append("div").style("padding-bottom","5px"),violin_div:t.append("div").style("color","black").style("padding-top","5px"),table_div:t.append("table").style("margin","5px 0px 15px 0px").style("border-collapse","collapse").style("color","black"),bottom_info_div:t.append("div"),excluded_div:t.append("table").style("display","none").style("margin","5px 10px").style("border-collapse","collapse")}};l.render=async()=>{const t=l.input;s(t);await n(t);p(t);a(t)};function s(t){if(t.termStatus.topInfoStatus?.length){l.dom.top_info_div.style("display","block").html(t.termStatus.topInfoStatus.join("<br>"))}else{l.dom.top_info_div.style("display","none")}}async function n(o){if(o.term.q.mode=="continuous"||o.term.q.mode=="spline"){l.dom.violin_div.style("display","block");l.dom.table_div.style("display","none");if(l.plotAppApi){const t={type:"app_refresh",state:{termfilter:{filter:l.input.parent.parent.filter}},subactions:[{type:"plot_edit",id:l.violinApi.id,config:{term:o.term}}]};l.plotAppApi.dispatch(t)}else{const i={holder:l.dom.violin_div,vocabApi:l.input.parent.app.vocabApi,state:{vocab:{genome:l.input.parent.app.vocabApi.genome,dslabel:l.input.parent.app.vocabApi.dslabel},termfilter:{filter:l.input.parent.parent.filter},plots:[{chartType:"violin",term:o.term,settings:{violin:t(null,{svgw:350,axisHeight:25,rightMargin:10,datasymbol:"rug",radius:3,plotThickness:100})}}]},violin:{mode:"minimal"}};l.plotAppApi=await e(i);const s=l.plotAppApi.getState().plots[0].id;l.violinApi=l.plotAppApi.getComponents(`plots.${s}`)}}else{l.dom.violin_div.style("display","none");const t=o.termStatus.sampleCounts;if(!t||!t.length){l.dom.table_div.style("display","none");return}l.dom.table_div.style("display","block");const e=l.input.orderedLabels;const i=e&&e.length?(t,o)=>e.indexOf(t.label)-e.indexOf(o.label):(t,e)=>e.samplecount-t.samplecount;const s=t.sort(i);const n=Math.max(...s.map((t=>t.samplecount)),0);s.forEach((t=>t.bar_width_frac=Number((1-(n-t.samplecount)/n).toFixed(4))));l.dom.table_div.selectAll("tr").remove();const p=l.dom.table_div.selectAll("tr").data(s,(t=>t.key));p.enter().append("tr").each(r)}}function p(t){if(t.termStatus.bottomSummaryStatus){l.dom.bottom_info_div.style("display","block").html(t.termStatus.bottomSummaryStatus)}else{l.dom.bottom_info_div.style("display","none")}}function a(t){const e=t.termStatus.excludeCounts;if(!e||!e.length){l.dom.excluded_div.style("display","none");return}l.dom.excluded_div.style("display","block").selectAll("tr").remove();const o=l.dom.excluded_div.selectAll("tr").data(e,(t=>t.key));o.enter().append("tr").each(r);l.dom.excluded_div.selectAll("td").style("color","#999")}function r(t){const e=o(this);const i=this.parentNode.__data__;i.term;const l=150;e.style("text-align","left").style("cursor",i.termStatus.allowToSelectRefGrp?"pointer":"default");const s="1px 10px 1px 0px";e.append("td").style("padding",s).style("text-align","left").style("color","black").text(t.samplecount!==undefined?"n="+t.samplecount:"");e.append("td").style("padding",s).style("text-align","left").style("color","black").text(t.label);const n=e.append("td").style("padding",s);const p=l*t.bar_width_frac;n.append("div").style("margin",s).style("width",p+"px").style("height","15px").style("background-color","#ddd");d({input:i,item:t,tr:e,rendered:false})}function d({input:t,item:e,tr:s,rendered:n}){if(!e.bar_width_frac)return;const p=t.term;const a=t.termStatus.allowToSelectRefGrp;let r;if(n){s.style("background","white");r=o(s.node().lastChild).select("div").style("display",e.key===p.refGrp&&a?"inline-block":"none").style("border",e.key===p.refGrp&&a?"1px solid #bbb":"")}else if(t.term.q.mode!="cutoff"){const t=s.append("td").style("padding","1px 5px").style("text-align","left");r=t.append("div").style("display",e.key===p.refGrp&&a?"inline-block":"none").style("padding","2px 10px").style("border",e.key===p.refGrp&&a?"1px solid #bbb":"").style("border-radius","10px").style("color","#999").style("font-size",".7em").text("REFERENCE");if(a){s.on("mouseover",(()=>{if(p.refGrp!==e.key){s.style("background",i);r.style("display","inline-block").style("border","").text("Set as reference")}else s.style("background","white")})).on("mouseout",(()=>{s.style("background","white");if(p.refGrp!==e.key)r.style("display","none")})).on("click",(()=>{p.refGrp=e.key;r.style("border","1px solid #bbb").text("REFERENCE");l.opts.callback(p)}))}}}}export{l as InputValuesTable};

package/dist/regression.results-69bc42d0.js

@@ -0,0 +1 @@
+import{bL as e,y as t,I as n,f as s}from"./app-b369b169.js";import{a as r}from"./axisstyle-fac7f76b.js";import{C as o}from"./ColorScale-21cab8d2.js";import{a as i}from"./axis-747c801e.js";import{l as a}from"./log-99af3443.js";function p({bp:e,g:t,color:n,scale:s,rowheight:r,labpad:o}){if(e.label){t.append("text").attr("font-family","Arial").attr("text-anchor","end").attr("dominant-baseline","central").attr("fill",n).attr("x",-o).attr("y",r/2).attr("font-size",Math.min(15,r)).text(e.label)}if(e.w1!=undefined){const o=s(e.w1);const i=s(e.w2);const a=s(e.p25);const p=s(e.p50);const l=s(e.p75);e.hline=t.append("line").attr("stroke",n).attr("shape-rendering","crispEdges").attr("x1",o).attr("x2",i).attr("y1",r/2).attr("y2",r/2);e.linew1=t.append("line").attr("stroke",n).attr("shape-rendering","crispEdges").attr("x1",o).attr("x2",o).attr("y1",0).attr("y2",r);e.linew2=t.append("line").attr("stroke",n).attr("shape-rendering","crispEdges").attr("x1",i).attr("x2",i).attr("y1",0).attr("y2",r);e.box=t.append("rect").attr("fill","white").attr("stroke",n).attr("shape-rendering","crispEdges").attr("x",a).attr("y",0).attr("width",l-a).attr("height",r);e.linep50=t.append("line").attr("stroke",n).attr("shape-rendering","crispEdges").attr("x1",p).attr("x2",p).attr("y1",0).attr("y2",r)}for(const o of e.out){t.append("circle").attr("stroke",n).attr("fill","white").attr("fill-opacity",0).attr("cx",s(o.value)).attr("cy",r/2).attr("r",r/3)}}function l(e,t,n,s){const r=[];if(Array.isArray(e)){for(const o of e){if(o.namekey=="regulomedb"){if(typeof t.chr=="string"&&t.pos!==undefined&&Number.isInteger(t.pos)){const e=`${t.chr}%3A${t.pos}-${t.pos+1}`;r.push(`<a href="${o.base}regions=${e}&genome=${s=="hg38"?"GRCh38":s}" target="_blank">${o.linkText}</a>`)}continue}c(o,t,n,r)}}else{c(e,t,n,r)}return r}function c(e,t,n,s){const r=t[e.namekey];if(r==undefined)return;const o=e.base+r;if(e.shownSeparately){s.push(`<a href="${o}" target="_blank">${e.linkText||r}</a>`);return}n.html(`<a href="${o}" target="_blank">${n.html()}</a>`)}const d="NA";const f="#126e08";const m=f;class u{constructor(e){this.opts=e;this.app=e.app;this.parent=e.parent;this.type="regression";g(this);const t=this.opts.holder;t.append("div").style("margin-top","10px").style("padding-top","20px").style("font-size","1.2em").style("opacity",.3).html("Results");this.dom={holder:t,err_div:t.append("div"),snplocusBlockDiv:t.append("div"),oneSetResultDiv:t.append("div").style("margin","10px")}}async main(){try{this.parent.inputs.dom.submitBtn.text("Running...");this.config=this.parent.config;this.state=this.parent.state;if(!this.state.formIsComplete||this.parent.inputs.hasError||this.config.hasUnsubmittedEdits&&!this.hasUnsubmittedEdits_nullify_singleuse){this.dom.holder.style("display","none");return}delete this.hasUnsubmittedEdits_nullify_singleuse;if(this.snplocusBlock){this.snplocusBlock.cloakOn()}const e=await this.app.vocabApi.getRegressionData(this.getDataRequestOpts());if(e.error)throw e.error;this.dom.err_div.style("display","none");this.dom.oneSetResultDiv.selectAll("*").remove();this.dom.holder.style("display","block");await this.displayResult(e);const t=this.dom.holder.node().getBoundingClientRect().top+window.scrollY;const n=document.querySelector(".sjpp-nav").getBoundingClientRect().height;window.scroll({behavior:"smooth",top:t-n})}catch(e){this.hasError=true;this.dom.holder.style("display","block");this.dom.err_div.style("display","block");t(this.dom.err_div,"Error: "+(e.error||e));this.parent.inputs.dom.submitBtn.property("disabled",true);console.error(e)}}getDataRequestOpts(){const e=this.config;const t={regressionType:e.regressionType,outcome:e.outcome,independent:e.independent};t.filter=this.parent.filter;return t}getIndependentInput(e){for(const t of this.parent.inputs.independent.inputLst){if(!t.term)continue;if(t.term.term.id==e||t.term.term.name==e)return t;if(t.term.term&&t.term.term.snps){for(const n of t.term.term.snps){if(n.snpid==e){const s={id:e,q:{geneticModel:t.term.q.geneticModel},term:{id:e,name:e},effectAllele:t.term.q.snp2effAle[e]};if(t.term.q.snp2refGrp){s.refGrp=t.term.q.snp2refGrp[e]}if(n.mlst){const r=n.mlst.find((n=>n.alt==t.term.q.snp2effAle[e]));if(r){s.term.name=r.mname}else{s.term.name=n.mlst[0].mname}}return{term:s}}}}}return{term:{id:e,q:{},term:{name:e}}}}}function g(e){e.displayResult=async t=>{const n=e.parent.inputs.independent.inputLst.find((e=>e.term&&e.term.term.type=="snplocus"));if(n){if(!e.snplocusBlock){e.dom.snplocusBlockDiv.append("div").style("margin-top","30px").style("opacity",.3).text("Click on a variant within the browser to view its regression results");e.snplocusBlock=await v(e,n,t.resultLst)}else{await b(e,n,t.resultLst)}return}delete e.snplocusBlock;e.dom.snplocusBlockDiv.selectAll("*").remove();if(!t.resultLst[0]||!t.resultLst[0].data)throw"result is not [ {data:{}} ]";e.displayResult_oneset(t.resultLst[0].data)};e.displayResult_oneset=t=>{e.dom.oneSetResultDiv.selectAll("*").remove();e.dom.LDresultDiv=e.dom.oneSetResultDiv.append("div");e.mayshow_warn(t);if(t.sampleSize)e.newDiv("Sample size:",t.sampleSize);if(t.eventCnt)e.newDiv("Number of events:",t.eventCnt);e.mayshow_headerRow(t);e.mayshow_splinePlots(t);e.mayshow_residuals(t);e.mayshow_coefficients(t);e.mayshow_totalSnpEffect(t);e.mayshow_type3(t);e.mayshow_tests(t);e.mayshow_other(t);e.mayshow_fisher(t);e.mayshow_wilcoxon(t);e.mayshow_cuminc(t)};e.newDiv=(t,n,s)=>{const r=e.dom.oneSetResultDiv.append("div").style("margin","20px 0px 10px 0px").attr("name",t);const o=r.append("div");o.append("span").style("text-decoration","underline").text(t);if(n){o.append("span").html(n).style("margin-left","5px")}return s?o:r.append("div").style("margin-left","20px")};e.mayshow_warn=t=>{if(!t.warnings)return;const n=e.newDiv("Warnings");const s=new Set(t.warnings);for(const e of s){n.append("p").style("margin","5px").text(e)}};e.mayshow_headerRow=t=>{if(!t.headerRow)return;const n=t.headerRow.k;const s=t.headerRow.v;const r=e.parent.inputs.independent.inputLst.find((e=>e.term&&e.term.term.type=="snplocus"));if(r){const t=r.term.term.snps.find((e=>e.snpid==s.snpid));const o=t.mlst[0];o.chr=t.chr;const i=e.newDiv(n,null,true);const a=i.append("span").text(`${o.chr}:${o.pos+1} ${o.ref&&o.alt?o.ref+">"+o.alt:""}`).style("margin-left","5px");const p=e.app.vocabApi.termdbConfig.urlTemplates?.ssm||e.app.vocabApi.termdbConfig.queries?.snvindel?.ssmUrl;if(p){const t=l(p,o,a,e.parent.genomeObj.name);if(t?.length){i.append("span").style("margin-left","10px").html(t.join(" "))}}let c;const d=`Genotypes: ${s.gtcounts.join(", ")}`;if(s.monomorphic){c=[d]}else{const e=`Effect allele: ${s.effAle}`;const t=`Allele frequency: ${s.af}`;c=[e,t,d]}i.append("span").html(`&nbsp;&#65372;&nbsp;${c.join("&nbsp;&#65372;&nbsp;")}`)}else{e.newDiv(n,s)}};e.mayshow_splinePlots=t=>{if(!t.splinePlots)return;const n=e.newDiv("Cubic spline plots");for(const e of t.splinePlots){n.append("img").attr("src",e.src).style("width",e.size.width).style("height",e.size.height)}};e.mayshow_residuals=t=>{if(!t.residuals)return;const n=e.newDiv(t.residuals.label);const s=n.append("table").style("border-spacing","8px").attr("name","sjpp-residuals-table");const r=s.append("tr").style("opacity",.4);const o=s.append("tr");for(let e=0;e<t.residuals.header.length;e++){r.append("td").text(t.residuals.header[e]);o.append("td").text(t.residuals.rows[e])}};e.mayshow_cuminc=async t=>{if(!t.cuminc)return;const n=e.newDiv("Cumulative incidence test:");const s=await import("./cuminc-9e275854.js");const r=new s.Cuminc({holder:n,config:{term:e.config.outcome,term2:{term:{name:"Variant",values:{1:{key:1,label:"Has minor allele"},2:{key:2,label:"No minor allele"}}}}}});if(t.cuminc.ci_data){r.main(t.cuminc.ci_data)}else{n.append("div").style("margin","20px").text(t.cuminc.msg)}};e.mayshow_wilcoxon=t=>{if(!t.wilcoxon)return;const s=e.newDiv("Wilcoxon rank sum test:","p-value = "+t.wilcoxon.pvalue);if(t.wilcoxon.boxplots){const o=t.wilcoxon.boxplots;const a=20,l=400,c=160,d=40,f=20,u=10;const g=n().domain([o.minv,o.maxv]).range([0,l]);const h=s.append("svg").style("margin-top","10px").attr("width",c+f+l+10).attr("height",u*3+a*2+d);const y=h.append("g").attr("transform",`translate(${c+f},${u})`);p({g:y.append("g"),bp:o.hasEff,scale:g,rowheight:a,color:m,labpad:f});p({g:y.append("g").attr("transform",`translate(0,${a+u})`),bp:o.noEff,scale:g,rowheight:a,color:m,labpad:f});{const t=y.append("g").attr("transform",`translate(0,${a*2+u*2})`);const n=i().scale(g);r({axis:t.call(n),color:m,showline:true});t.append("text").text(e.config.outcome.term.name).attr("font-size",15).attr("x",l/2).attr("y",d-5).attr("text-anchor","middle").attr("fill",m)}}};e.mayshow_fisher=t=>{if(!t.fisher)return;const n=e.newDiv(t.fisher.isChi?"Chi-square test:":"Fisher's exact test:","p-value = "+t.fisher.pvalue);const s=n.append("table").style("margin","20px").style("border-spacing","5px").style("border-collapse","separate");for(const e of t.fisher.rows){const t=s.append("tr");for(const n of e){t.append("td").text(n)}}};e.mayshow_coefficients=t=>{if(!t.coefficients)return;const n=e.newDiv(t.coefficients.label);const s=n.append("table").style("border-spacing","0px").attr("data-testid","sjpp_regression_resultCoefficientTable");const r=e.config.regressionType=="cox"&&e.app.vocabApi.termdbConfig.neuroOncRegression;{const e=s.append("tr").style("opacity",.4);t.coefficients.header.forEach(((t,n)=>{if(r&&(n==2||n==3))return;e.append("td").text(t).style("padding","8px");if(n===1)e.append("td")}))}if(e.config.regressionType!="cox"){const e=s.append("tr").style("background","#eee");t.coefficients.intercept.forEach(((t,n)=>{e.append("td").text(t).style("padding","8px");if(n===1)e.append("td")}))}const o=e.getForestPlotter(t.coefficients.terms,t.coefficients.interactions,r);let i=e.config.regressionType=="cox"?1:0;for(const n in t.coefficients.terms){const a=t.coefficients.terms[n];const p=e.getIndependentInput(n).term;let l=s.append("tr").style("background",i++%2?"#eee":"none");const c=l.append("td").style("padding","8px");y(p,c);if(a.fields){const e=a.fields;{const e=l.append("td").style("padding","8px");N(e,p)}if(r){e.shift();e.shift()}o(l.append("td"),e);for(const t of e){l.append("td").text(t).style("padding","8px")}}else if(a.categories){const t=[];const d=e.getIndependentInput(n);if(d.orderedLabels){for(const e of d.orderedLabels){if(a.categories[e])t.push(e)}}for(const e in a.categories){if(!t.includes(e))t.push(e)}c.attr("rowspan",t.length).style("vertical-align","top");let f=true;for(const e of t){if(!f){l=s.append("tr").style("background",i++%2?"#eee":"none")}const t=a.categories[e];const n=l.append("td").style("padding","8px");N(n,p,e);if(r){const[e,s]=t.shift().split("/");const[r,o]=t.shift().split("/");if(f){const t=c.select(".sjpcb-regression-results-refGrp");t.append("div").html(`n = ${e}<br>events = ${r}`)}n.append("div").style("font-size",".8em").html(`n = ${s}<br>events = ${o}`)}o(l.append("td"),t);for(const e of t){l.append("td").text(e).style("padding","8px")}f=false}}else{l.append("td").text("ERROR: no .fields[] or .categories{}")}}for(const n of t.coefficients.interactions){const t=s.append("tr").style("background",i++%2?"#eee":"none");const r=e.getIndependentInput(n.term1).term;const a=e.getIndependentInput(n.term2).term;{const e=t.append("td").style("padding","8px");h(e.append("div"),r?r.term.name+" : ":n.term1+" : ");h(e.append("div"),a?a.term.name:n.term2)}{const e=t.append("td").style("padding","8px");N(e.append("div"),r,n.category1);N(e.append("div"),a,n.category2)}o(t.append("td"),n.lst);for(const e of n.lst){t.append("td").text(e).style("padding","8px")}}const a=s.append("tr");a.append("td");a.append("td");o(a.append("td"));for(const e of t.coefficients.header)a.append("td")};e.mayshow_totalSnpEffect=t=>{if(!t.totalSnpEffect)return;const n=e.newDiv(t.totalSnpEffect.label);const s=n.append("table").style("border-spacing","0px");{const e=s.append("tr").style("opacity",.4);for(const n of t.totalSnpEffect.header){e.append("td").text(n).style("padding","8px")}}const r=s.append("tr").style("background","#eee");for(const e of t.totalSnpEffect.lst){r.append("td").text(e).style("padding","8px")}const o=e.getIndependentInput(t.totalSnpEffect.snp).term;const i=t.totalSnpEffect.interactions.map((t=>({t1:e.getIndependentInput(t.term1).term,t2:e.getIndependentInput(t.term2).term})));const a=`Total: total effect of removing the snp (${o.term.name}) and its interactions (${i.map((e=>e.t1.term.name+" : "+e.t2.term.name)).join(" ; ")}) from the model`;n.append("div").style("margin","20px 0px 20px 10px").style("font-size",".8em").style("text-align","left").style("color","#999").text(a)};e.mayshow_type3=t=>{if(!t.type3||e.parent.app.vocabApi.termdbConfig.neuroOncRegression)return;const n=e.newDiv(t.type3.label);const s=n.append("table").style("border-spacing","0px");{const e=s.append("tr").style("opacity",.4);for(const n of t.type3.header){e.append("td").text(n).style("padding","8px")}}if(e.config.regressionType!="cox"){const e=s.append("tr").style("background","#eee");for(const n of t.type3.intercept){e.append("td").text(n).style("padding","8px")}}let r=e.config.regressionType=="cox"?1:0;for(const n in t.type3.terms){const o=t.type3.terms[n];const i=e.getIndependentInput(n).term;let a=s.append("tr").style("background",r++%2?"#eee":"none");const p=a.append("td").style("padding","8px");h(p,i.term.name);for(const e of o){a.append("td").text(e).style("padding","8px")}}for(const n of t.type3.interactions){const t=s.append("tr").style("background",r++%2?"#eee":"none");const o=e.getIndependentInput(n.term1).term;const i=e.getIndependentInput(n.term2).term;const a=t.append("td").style("padding","8px");h(a.append("div"),o.term.name+" : ");h(a.append("div"),i.term.name);for(const e of 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package/dist/{renderPvalueTable-895a72c2.js → renderPvalueTable-dc5d15f2.js}

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s=e(this);s.append("input").attr("type","checkbox").style("margin-right","5px");s.append("span").html(`${t.series1.id} vs ${t.series2.id}`)}));a.d.append("button").html("Show checked test(s)").on("click",(()=>{const t=[];i.filter((function(){return!e(this.firstChild).property("checked")})).each((e=>t.push(e)));c(t);a.hide()}));a.show(s.clientX,s.clientY)}))}}}export{o as a,r as g,l as r,n as s};
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o=i.style("fill","transparent").node();function a(t){const i=s(t,o);const n=i[0];const a=+l.xScale.invert(n).toFixed(l.decimals);const c=l.xScale(a);e.style("display","").attr("stroke","#aaa").attr("stroke-dasharray",4).attr("x1",c).attr("x2",c);const d=[];for(const t of l.serieses){const e=t.data;const s=e.map((t=>t.x));if(a>=Math.min(...s)&&a<=Math.max(...s)){const t=Math.max(...s.filter((t=>t<=a)));const i=e.find((e=>e.x==t));if(i)d.push(i.html)}}if(d.length){r.show(t.clientX,t.clientY).d.html(`${l.xTitleLabel}: ${a}<br>`+d.map((t=>t)).join(l.separator))}else{r.hide()}}i.on("mouseover",a).on("mousemove",a).on("mouseout",(()=>{e.style("display","none");r.hide()}));const l={separator:"<br>",decimals:1};return{update(t={}){Object.assign(l,t);const s=i.attr("x");const n=i.attr("y");e.attr("x1",s).attr("x2",s).attr("y1",n).attr("y2",i.attr("height")-n)},destroy(){i.on("mouseover",null).on("mousemove",null).on("mouseout",null)}}}function o({g:t,s:s,chart:i,term2values:n,term2toColor:r,onSerieClick:o}){const l={};const c=i.xTickValues.filter((t=>t>=i.xMin));for(const t of i.visibleSerieses){const e=[];let s=0,i=t.data[0],n=i,r=0;for(const o of c){while(i&&i.x<o){r+=i.ncensor;n=i;s++;i=t.data[s]}if(i&&i.x===o){e.push([o,i.nrisk,r])}else{e.push([o,n.nrisk-n.nevent-n.ncensor,r])}}l[t.seriesId]=e}const d=s.svgh-s.svgPadding.top-s.svgPadding.bottom+60;const p=i.serieses.map((t=>t.seriesId));if(n){p.sort(((t,e)=>{const s=n[t];const i=n[e];if(s&&i){if("order"in s&&"order"in i)return s.order-i.order;if(s.order)return s.order;if(i.order)return i.order;return 0}if(s)return s.order||0;if(i)return i.order||0;return 0}))}let h;t.selectAll(".sjpp-atrisk-title").remove();if(s.atRiskVisible){h=Object.keys(l).sort(((t,e)=>p.indexOf(t)-p.indexOf(e)));const e=i.serieses.length==1&&!i.serieses[0].seriesId;const n=t.append("text").attr("class","sjpp-atrisk-title").attr("transform",`translate(${s.atRiskLabelOffset}, 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h=i.serieses.find((e=>e.seriesId===t));p.append("text").attr("transform",`translate(${s.atRiskLabelOffset}, 0)`).attr("text-anchor","end").attr("font-size",`${s.axisTitleFontSize-4}px`).attr("cursor","pointer").datum({seriesId:t}).text(t&&t!="*"?h.seriesLabel||t:"");a(p.append("g"),i,c,s,t,l[t])}))}function a(t,s,i,n,r,o){const a=o.slice().reverse();const l=i.map((t=>{if(t===0)return{seriesId:r,tickVal:t,atRisk:o[0][1],nCensored:o[0][2]};const e=a.find((e=>e[0]<=t));return{seriesId:r,tickVal:t,atRisk:e[1],nCensored:e[2]}}));const c=t.selectAll("text").data(l);c.exit().remove();c.attr("transform",(t=>`translate(${s.xScale(t.tickVal)},0)`)).attr("text-anchor","middle").attr("font-size",`${n.axisTitleFontSize-4}px`).attr("cursor","pointer").each(d);c.enter().append("text").attr("transform",(t=>`translate(${s.xScale(t.tickVal)},0)`)).attr("text-anchor","middle").attr("font-size",`${n.axisTitleFontSize-4}px`).attr("cursor","pointer").each(d);function d(t){const s=e(this).selectAll("tspan").data([t.atRisk,`(${t.nCensored})`]);s.exit().remove();s.attr("y",((t,e)=>e===0?0:e*(n.axisTitleFontSize-4))).text((t=>t));s.enter().append("tspan").attr("x",0).attr("y",((t,e)=>e===0?0:e*(n.axisTitleFontSize-4))).text((t=>t))}}function l({title:t,holder:s,plot:i,tests:n,s:r,bins:o,tip:a,setActiveMenu:l,updateHiddenPvalues:c}){let d;if(r.axisTitleFontSize){d=r.axisTitleFontSize-2}else d=15;const p=10;s.selectAll("*").remove();if(!i){throw`plot type '${i}' not recognized`}s.append("div").style("padding-bottom","5px").style("font-size",d+"px").style("font-weight","bold").text(t);const h=s.append("div").style("border","1px solid #ccc");if(i=="violin"&&n.pvalues.length>p||n.length>p){h.style("overflow","auto").style("height","220px")}const f=r.hiddenPvalues?n.filter((t=>!r.hiddenPvalues.find((e=>e.series1.id===t.series1.id&&e.series2.id===t.series2.id)))):n;if(i=="violin"?f.pvalues.length:f.length){const t=o&&o.length>0?o.map((t=>t.label)):null;if(t){for(const e of f){const s=[e.series1.id,e.series2.id].sort(((e,s)=>t.indexOf(e)-t.indexOf(s)));if(e.series2.id==s[0]){e.series1_new=e.series2;e.series2_new=e.series1;e.series1=e.series1_new;e.series2=e.series2_new;delete e.series1_new;delete e.series2_new}}f.sort(((e,s)=>t.indexOf(e.series1.id)-t.indexOf(s.series1.id)||t.indexOf(e.series2.id)-t.indexOf(s.series2.id)))}const e=h.append("table").style("width","100%");e.append("thead").append("tr").selectAll("td").data(["Group 1","Group 2","P-value"]).enter().append("td").style("padding","1px 8px 1px 2px").style("color","#858585").style("position","sticky").style("top","0px").style("background","white").style("font-size",d+"px").text((t=>t));const n=e.append("tbody");const a=n.selectAll("tr").data(i=="violin"?f.pvalues:f).enter().append("tr").attr("class",`pp-${i}-chartLegends-pvalue`);if(i=="survival"){a.on("click",((t,e)=>{const s=r.hiddenPvalues.slice();s.push(e);c(s)}))}a.selectAll("td").data((t=>[t.series1,t.series2,t.pvalue])).enter().append("td").attr("aria-label",i?"Click to hide a p-value":"").style("color",i=="violin"?"black":t=>t.color).style("padding","1px 8px 1px 2px").style("font-size",d+"px").style("cursor",i=="survival"?"pointer":"auto").text((t=>i=="violin"?t:t.text));if(i=="cuminc"){if(f.find((t=>t.permutation))){s.append("div").style("margin-top","10px").style("font-size",d-2+"px").text("*computed by permutation of Gray's test statistic")}}}if(i=="survival"){const t=n.filter((t=>r.hiddenPvalues.find((e=>e.series1.id===t.series1.id&&e.series2.id===t.series2.id))));if(t.length){s.append("div").style("color","#aaa").style("cursor","pointer").html(`<span style='color:#aaa; font-weight:400'><span>Hidden tests (${t.length})</span>`).on("click",(s=>{a.clear();const i=a.d.append("div").selectAll("div").data(t).enter().append("div").each((function(t){l(true);const s=e(this);s.append("input").attr("type","checkbox").style("margin-right","5px");s.append("span").html(`${t.series1.id} vs ${t.series2.id}`)}));a.d.append("button").html("Show checked test(s)").on("click",(()=>{const t=[];i.filter((function(){return!e(this.firstChild).property("checked")})).each((e=>t.push(e)));c(t);a.hide()}));a.show(s.clientX,s.clientY)}))}}}export{o as a,r as g,l as r,n as s};