@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/hierCluster-26e14090.js

@@ -0,0 +1 @@
+import{Matrix as e}from"./matrix-00bb50ff.js";import{F as t,b as r,I as s,bR as i,h as a}from"./app-b369b169.js";import{r as o}from"./hierCluster.renderers-74a64cf5.js";import{c as l,d as n,i as c}from"./hierCluster.interactivity-e56f6542.js";import{k as d}from"./termsetting-33ea66f1.js";import{g as m,c as h}from"./FilterRxComp-701a1480.js";export{getPlotConfig}from"./hierCluster.config-98e82dff.js";import"./matrix.dom-4e10bbe9.js";import"./matrix.interactivity-84169b43.js";import"./table-29d5a973.js";import"./tslib.es6-c3c2d88f.js";import"./pointer-c7475677.js";import"./matrix.renderers-78010275.js";import"./matrix.cluster-783ceab0.js";import"./matrix.controls-7b2a6f95.js";import"./controls.config-28d6d6a8.js";import"path";import"./matrix.sorterUi-9bf7e6f9.js";import"./radiobutton-09bff425.js";import"./checkbox-96437f4d.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./genesearch-a4e19f0d.js";import"./rehydrateFilter-12d118cb.js";import"./svg.legend-8d490df2.js";import"./matrix.data-dac4f1b7.js";import"./matrix.layout-dd5a44fd.js";import"./axis-747c801e.js";import"./matrix.serieses-9b4fd744.js";import"./matrix.cells-914dd0c6.js";import"./matrix.legend-ac6d45e6.js";import"./legacy-d3-polyfill-bdb2d792.js";import"./matrix.groups-b9fca14a.js";import"./filter-b3d3964e.js";import"./matrix.sort-014d798d.js";import"./matrix.config-6ce74dfe.js";function p(e,t){let r;let s;if(t===undefined){for(const t of e){if(t!=null){if(r===undefined){if(t>=t)r=s=t}else{if(r>t)r=t;if(s<t)s=t}}}}else{let i=-1;for(let a of e){if((a=t(a,++i,e))!=null){if(r===undefined){if(a>=a)r=s=a}else{if(r>a)r=a;if(s<a)s=a}}}}return[r,s]}class f extends e{constructor(e){super(e);this.type="hierCluster";this.chartType="hierCluster"}async init(e){await super.init(e);this.maySetSandboxHeader();this.hcClipId=this.seriesClipId+"-hc";this.dom.hcClipRect=this.dom.svg.select("defs").append("clipPath").attr("id",this.hcClipId).attr("clipPathUnits","userSpaceOnUse").append("rect").attr("display","block");this.dom.topDendrogram=this.dom.svg.insert("g","g").attr("clip-path",`url(#${this.hcClipId})`).append("g").attr("class","sjpp-matrix-dendrogram").attr("data-testid","hierCluster_top_dendrogram").on("click",(e=>{const t=this.getClusterFromTopDendrogram(e);if(t){this.clickedClusterIds=this.getAllChildrenClusterIds(t);this.clickedClusterIds.push(t);const r=this.hierClusterData.clustering.col.mergedClusters.get(t);const s=r.children.map((e=>e.name));this.addSelectedSamplesOptions(s,e)}else{delete this.clickedClusterIds}if(this.clickedLeftClusterIds){delete this.clickedLeftClusterIds;this.plotDendrogramHclust()}else this.plotDendrogramHclust("top")}));this.dom.leftDendrogram=this.dom.svg.insert("g","g").attr("class","sjpp-matrix-dendrogram").attr("data-testid","hierCluster_left_dendrogram").on("click",(e=>{const t=this.getClusterFromLeftDendrogram(e);if(t){this.clickedLeftClusterIds=this.getAllChildrenClusterIds(t,true);this.clickedLeftClusterIds.push(t);const r=this.hierClusterData.clustering.row.mergedClusters.get(t);const s=r.children.map((e=>e.name));this.addSelectedRowsOptions(s,e)}else{delete this.clickedLeftClusterIds}if(this.clickedClusterIds){delete this.clickedClusterIds;this.plotDendrogramHclust()}else this.plotDendrogramHclust("left")}))}async setHierClusterData(e={}){this.prevServerData=this.currServerData;const r=new AbortController;const[s,i]=await this.api.detectStale((()=>this.requestData({signal:r.signal})),{abortCtrl:r});if(i)throw`stale sequenceId`;if(s.error)throw s.error;this.currServerData=structuredClone(s);if(!t(this.prevServerData,this.currServerData)){delete this.clickedClusterIds}const a=this.settings.hierCluster;const o=this.hcTermGroup.lst;if(!s.clustering){if(s.gene){throw`Cannot do clustering: data is only available for 1 gene (${s.gene}). Try again by adding more genes.`}}this.hierClusterData=s;const l=this.hierClusterData.clustering;this.setHierColorScale(l);this.settings.hierCluster.zScoreCap;const n={};for(const[e,t]of l.col.order.entries()){n[t.name]={sample:t.name};for(const[r,s]of l.row.order.entries()){const i=o.find((e=>e.term.name===s.name));const c=l.matrix[r][e];n[t.name][i.$id]={key:i.term.name,values:[{sample:t.name,dt:d[this.state.config.dataType],label:a.termGroupName,value:c}]}}}this.hcTermNameOrder=l.row.order.map((e=>e.name));this.hcTermSorter=(e,t)=>{const r=this.hcTermNameOrder.indexOf(e.tw.term.name);const s=this.hcTermNameOrder.indexOf(t.tw.term.name);if(r==-1&&s==-1)return 0;if(r==-1)return 1;if(s==-1)return-1;return r-s};this.hcSampleNameOrder=l.col.order.map((e=>e.name));this.hcSampleSorter=(e,t)=>{const r=this.hcSampleNameOrder.indexOf(e.sample);const s=this.hcSampleNameOrder.indexOf(t.sample);if(r==-1&&s==-1)return 0;if(r==-1)return 1;if(s==-1)return-1;return r-s};const c={};for(const e of o){if(s.byTermId[e.term.name])c[e.$id]=s.byTermId[e.term.name]}this.hierClusterSamples={refs:{byTermId:c,bySampleId:s.bySampleId},lst:l.col.order.map((e=>n[e.name])),samples:n}}async requestData({signal:e}){const t=this.currRequestOpts?.hierCluster||this.getHCRequestBody(this.state);const s=await r("termdb/cluster",{body:t,signal:e});return s}getHCRequestBody(e){this.hcTermGroup=this.config.termgroups.find((e=>e.type=="hierCluster"))||this.termOrder?.find((e=>e.grp.type=="hierCluster"))?.grp;const t=e.config.settings.hierCluster;const r={type:"tvslst",in:true,join:"and",lst:e.config.legendValueFilter.lst.filter((e=>!e.tvs.legendFilterType))};const s=this.getClusterRowTermsAsParameter();if(!s.length)throw"no data";if(!l.find((e=>e.value==t.clusterMethod)))throw"Invalid cluster method";if(!n.find((e=>e.value==t.distanceMethod)))throw"Invalid distance method";const i={genome:e.vocab.genome,dslabel:e.vocab.dslabel,dataType:e.config.dataType,clusterMethod:t.clusterMethod,distanceMethod:t.distanceMethod,terms:s,filter:m(h([e.filter,r])),filter0:e.filter0};return i}combineData(){if(!this.hierClusterSamples)return;const e=this.data;const t={};const r=[];for(const s in this.hierClusterSamples.samples){const i=this.hierClusterSamples.samples[s];t[s]=i;r.push(i);if(s in e.samples)Object.assign(i,e.samples[s]);const a=this.hierClusterSamples.refs.bySampleId[s]||{};if(!i._ref_)i._ref_=a;else Object.assign(i._ref_,a)}const s=this.hierClusterSamples.refs.byTermId;for(const t of Object.keys(s)){e.refs.byTermId[t]=Object.assign({},e.refs.byTermId[t]||{},s[t])}this.data={samples:t,lst:r,refs:e.refs}}setHierColorScale(e){const t=this.settings.hierCluster;const r=s(i[t.colorScale].domain,i[t.colorScale].range).clamp(true);const a=[];for(const t of e.matrix){a.push(...p(t))}const o=Math.min(t.zScoreCap,Math.max(...p(a).map(Math.abs)));const[l,n]=[-o,o];this.hierClusterValues={scale:r,min:l,max:n}}getValueColor(e){const t=this.settings.hierCluster.zScoreCap;return this.hierClusterValues.scale((e- -t)/(t*2))}getClusterRowTermsAsParameter(){const e=[...this.hcTermGroup.lst.map((e=>e.term))];e.sort(((e,t)=>e.name<t.name?-1:1));return e}}for(const e of[o,c]){for(const t in e)f.prototype[t]=e[t]}const u=a(f);const g=u;export{f as HierCluster,g as componentInit,u as hierClusterInit};

package/dist/hierCluster.config-98e82dff.js

@@ -0,0 +1 @@
+import{P as e}from"./app-b369b169.js";import{getPlotConfig as t}from"./matrix.config-6ce74dfe.js";import{T as r,f as s}from"./termsetting-33ea66f1.js";import"./matrix.sort-014d798d.js";import"./tslib.es6-c3c2d88f.js";import"path";async function i(i={},a){i.chartType="hierCluster";const o=await t(i,a);delete o.genes;o.settings.hierCluster={dataType:o.dataType,clusterSamples:true,clusterMethod:"average",distanceMethod:"euclidean",zScoreCap:5,xDendrogramHeight:100,yDendrogramHeight:200,colorScale:"blueWhiteRed"};const n=a.vocabApi.termdbConfig.hierCluster||{};e(o.settings.hierCluster,n.settings,i.settings?.hierCluster||{});{const e=o.settings.hierCluster.colorScale;if(!e)throw"colorScale missing"}o.settings.matrix.collabelpos="top";const p=o.settings.hierCluster.termGroupName;const m=o.termgroups.find((e=>e.type=="hierCluster"||e.name==p))||{name:p};m.type="hierCluster";if(!m.lst?.length){if(!Array.isArray(i.terms))throw"opts.terms[] not array (may show geneset edit ui)";const e=[];for(const t of i.terms){const i=t.term?t:{term:t};if(!i.term.type){if(o.dataType==r.GENE_EXPRESSION||o.dataType==r.METABOLITE_INTENSITY){i.term.type=o.dataType}else{throw`term type missing and cannot be assigned by dataType`}}else if(!["geneExpression","metaboliteIntensity","float"].includes(i.term.type)){throw"term type not supported in hierCluster"}else if(o.dataType&&i.term.type!==o.dataType){throw`cannot have term type ${i.term.type} in ${o.dataType} term group`}e.push(s(i,a.vocabApi))}m.lst=await Promise.all(e);if(o.termgroups.indexOf(m)==-1)o.termgroups.unshift(m)}o.settings.matrix.maxSample=1e5;return o}export{i as getPlotConfig};

package/dist/{hierCluster.interactivity-9b433033.js → hierCluster.interactivity-e56f6542.js}

@@ -1 +1 @@
-import{r as e}from"./table-79e3e776.js";const t=[{label:"Average",value:"average",title:`Cluster by average value`},{label:`Complete`,value:"complete",title:`Use the complete clustering method`},{label:`Single`,value:"single",title:`Use the single clustering method`},{label:`Ward.D`,value:"ward.D",title:`Use the ward.D clustering method`},{label:`Ward.D2`,value:"ward.D2",title:`Use the ward.D2 clustering method`},{label:`Mcquitty`,value:"mcquitty",title:`Use the Mcquity clustering method`}];const l=[{label:"Euclidean",value:"euclidean",title:`Calculate distance using euclidean method`},{label:"Maximum",value:"maximum",title:`Maximum distance between two components of x and y`},{label:"Manhattan",value:"manhattan",title:`Calculate distance using the absolute distance between the two vectors`},{label:"Canberra",value:"canberra",title:`Calculate distance using Canberra method`}];function s(e,t){const l=t?this.hierClusterData.clustering.row.mergedClusters:this.hierClusterData.clustering.col.mergedClusters;const s=l.get(e).childrenClusters||[];let a=[...s];for(const e of s){a=a.concat(this.getAllChildrenClusterIds(e,t))}return a}function a(e,t){const l=this.settings.matrix.controlLabels;const s=this.opts.allow2selectSamples;const a=[{label:"Zoom in",callback:()=>{this.triggerZoomBranch(this,e)}},{label:`List ${e.length} ${l.samples}`,callback:()=>this.showTable4selectedSamples(e)}];if(s){a.push({label:s.buttonText||`Select ${l.samples}`,callback:async()=>{s.callback({samples:e.map((e=>({"cases.case_id":e}))),source:s.defaultSelectionLabel||`Selected ${l.samples} from gene expression`})}})}else{if(this.state.nav&&this.state.nav.header_mode!=="hidden"){const t=e.map((e=>this.sampleOrder.find((t=>t.row.sample==e)).row));for(const e of t){if(!e.sampleId)e.sampleId=e.sample}a.push({label:"Add to a group",callback:async()=>{const e={name:"Group",items:t};this.addGroup(e)}})}}this.mouseout();this.dom.tip.hide();this.dom.dendroClickMenu.d.selectAll("*").remove();this.dom.dendroClickMenu.d.selectAll("div").data(a).enter().append("div").attr("class","sja_menuoption").style("border-radius","0px").html((e=>e.label)).attr("data-testid",(e=>`hierCluster_dendro_menu_${e.label.split(" ")[0]}`)).on("click",(e=>{this.dom.dendroClickMenu.d.selectAll("*").remove();e.target.__data__.callback()}));this.dom.dendroClickMenu.show(t.clientX,t.clientY)}function i(e,t){const l=this.config.dataType=="geneExpression"?"genes":this.config.dataType=="metaboliteIntensity"?"metabolites":"items";const s=[{label:`List ${e.length} ${l}`,callback:()=>this.showTable4selectedRows(e,l)}];if(this.app.opts.genome.termdbs){s.push({label:`Gene set overrepresentation analysis`,disabled:e.length<15||e.length>500,callback:()=>{if(e.length<15||e.length>500)return;this.dom.dendroClickMenu.d.selectAll("*").remove();const t=e;const l={sample_genes:t.toString(),genome:this.app.vocabApi.opts.state.vocab.genome};const s={chartType:"geneORA",geneORAparams:l};this.app.dispatch({type:"plot_create",config:s})}})}this.mouseout();this.dom.tip.hide();this.dom.dendroClickMenu.d.selectAll("*").remove();this.dom.dendroClickMenu.d.selectAll("div").data(s).enter().append("div").attr("class",(e=>e.disabled?"sja_menuoption_not_interactive":"sja_menuoption")).style("opacity",(e=>e.disabled?.5:1)).style("border-radius","0px").html((e=>e.disabled?`${e.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>`:e.label)).attr("data-testid",(e=>`hierCluster_dendro_menu_${e.label.split(" ")[0]}`)).on("click",(e=>{if(e.target.__data__?.callback)e.target.__data__.callback()}));this.dom.dendroClickMenu.show(t.clientX,t.clientY)}function n(e,t){if(e.zoomArea){e.zoomArea.remove();delete e.zoomArea}const l={startCell:e.serieses[0].cells.find((e=>e.sample==t[0])),endCell:e.serieses[0].cells.find((e=>e.sample==t[t.length-1]))};const s=e.settings.matrix;const a=e.dimensions;const i=l.startCell.totalIndex<l.endCell.totalIndex?l.startCell:l.endCell;const n=Math.floor(i.totalIndex+Math.abs(l.endCell.totalIndex-l.startCell.totalIndex)/2);const o=e.sampleOrder[n];const r=e.computedSettings.colw||e.settings.matrix.colw;const c=s.colwMax/r;const d=s.colwMin/r;const h=Math.max(1,s.zoomLevel*a.mainw/Math.max(l.endCell.x-l.startCell.x,2*a.colw)*.7);const m=Math.max(d,Math.min(h,c));e.app.dispatch({type:"plot_edit",id:e.id,config:{settings:{matrix:{zoomLevel:m,zoomCenterPct:.5,zoomIndex:n,zoomGrpIndex:o.grpIndex}}}});e.resetInteractions()}function o(t){const l=this.state.termdbConfig.urlTemplates;const s=l?.sample?t.map((e=>[{value:this.hierClusterData.bySampleId[e].label,url:`${l.sample.base}${e}`}])):t.map((e=>[{value:this.hierClusterData.bySampleId[e].label}]));const a=[{label:this.settings.matrix.controlLabels.Sample}];e({rows:s,columns:a,div:this.dom.dendroClickMenu.clear().d.append("div").style("margin","10px"),showLines:true,maxHeight:"35vh",resize:true})}function r(t,l){const s=this.state.termdbConfig.urlTemplates;const a=s?.gene&&this.config.dataType=="geneExpression"&&this.hierClusterData.byTermId?t.map((e=>this.hierClusterData.byTermId[e]?.gencodeId?[{value:e,url:`${s.gene.base}${this.hierClusterData.byTermId[e].gencodeId}`}]:[{value:e}])):t.map((e=>[{value:e}]));const i=[{label:l}];e({rows:a,columns:i,div:this.dom.dendroClickMenu.clear().d.append("div").style("margin","10px"),showLines:true,maxHeight:"35vh",resize:true})}async function c(e){e.plotId=this.id;await this.app.vocabApi.addGroup(e);this.dom.tip.hide()}function d(e){if(e.target.tagName=="image")this.imgBox=e.target.getBoundingClientRect();else return;const t=e.clientY-this.imgBox.y-e.target.clientTop;const l=this.dimensions.xMin;const s=e.clientX-this.imgBox.x-e.target.clientLeft+l;for(const[e,l]of this.hierClusterData.clustering.col.mergedClusters){const{x1:a,y1:i,x2:n,y2:o,clusterY:r}=l.clusterPosition;if(a<=s&&s<=n&&r-5<t&&t<r+5||r<=t&&t<=i&&a-5<s&&s<a+5||r<=t&&t<=o&&n-5<s&&s<n+5){return e}}}function h(e){if(e.target.tagName=="image")this.imgBox=e.target.getBoundingClientRect();else return;const t=e.clientY-this.imgBox.y-e.target.clientTop;const l=this.dimensions.xMin;const s=e.clientX-this.imgBox.x-e.target.clientLeft+l;for(const[e,l]of this.hierClusterData.clustering.row.mergedClusters){const{x1:a,y1:i,x2:n,y2:o,clusterX:r}=l.clusterPosition;if(i<=t&&t<=o&&r-5<s&&s<r+5||r<=s&&s<=a&&i-5<t&&t<i+5||r<=s&&s<=n&&o-5<t&&t<o+5){return e}}}function m(e,s){const a=this.config.settings.matrix.controlLabels;const i=`Cluster ${a.Samples}`;e.append("button").datum({label:`Clustering`,rows:[{label:i,title:`Option to enable ${a.samples} clustering, instead of enable ${a.samples} sorting.`,type:"checkbox",chartType:"hierCluster",settingsKey:"clusterSamples",boxLabel:`Cluster ${a.samples} (Disable ${a.samples} sorting)`,callback:e=>{if(!e){this.config.settings.hierCluster.yDendrogramHeight=0;this.config.settings.hierCluster.clusterSamples=false}else{this.config.divideBy=null;this.config.settings.hierCluster.yDendrogramHeight=200;this.config.settings.hierCluster.clusterSamples=true}this.app.dispatch({type:"plot_edit",id:this.id,config:this.config})}},{label:`Clustering Method`,title:`Sets which clustering method to use`,type:"radio",chartType:"hierCluster",settingsKey:"clusterMethod",options:t},{label:`Distance Method`,title:`Sets which distance method to use for clustering`,type:"radio",chartType:"hierCluster",settingsKey:"distanceMethod",options:l},{label:`Column Dendrogram Height`,title:`The maximum height to render the column dendrogram`,type:"number",chartType:"hierCluster",settingsKey:"yDendrogramHeight",getDisplayStyle(e){return e.settings.hierCluster.clusterSamples?"table-row":"none"}},{label:`Row Dendrogram Width`,title:`The maximum width to render the row dendrogram`,type:"number",chartType:"hierCluster",settingsKey:"xDendrogramHeight"},{label:`z-score Cap`,title:`Cap the z-score scale to not exceed this absolute value`,type:"number",chartType:"hierCluster",settingsKey:"zScoreCap"},{label:`Color Scheme`,title:`Sets which color scheme to use`,type:"radio",chartType:"hierCluster",settingsKey:"colorScale",options:[{label:"Blue-White-Red",value:"blueWhiteRed",title:`color scheme Blue-White-Red`},{label:"Green-Black-Red",value:"greenBlackRed",title:`color scheme Green-Black-Red`},{label:"Blue-Yellow-Red",value:"blueYellowRed",title:`color scheme Blue-Yellow-Red`},{label:"Green-White-Red",value:"greenWhiteRed",title:`color scheme Green-White-Red`},{label:"Blue-Black-Yellow",value:"blueBlackYellow",title:`color scheme Blue-Black-Yellow`}]}]}).html((e=>e.label)).style("margin","2px 0").on("click",s)}var u=Object.freeze({__proto__:null,getAllChildrenClusterIds:s,addSelectedSamplesOptions:a,addSelectedRowsOptions:i,triggerZoomBranch:n,showTable4selectedSamples:o,showTable4selectedRows:r,addGroup:c,getClusterFromTopDendrogram:d,getClusterFromLeftDendrogram:h,setClusteringBtn:m});export{t as c,l as d,u as i};
+import{r as e}from"./table-29d5a973.js";const t=[{label:"Average",value:"average",title:`Cluster by average value`},{label:`Complete`,value:"complete",title:`Use the complete clustering method`},{label:`Single`,value:"single",title:`Use the single clustering method`},{label:`Ward.D`,value:"ward.D",title:`Use the ward.D clustering method`},{label:`Ward.D2`,value:"ward.D2",title:`Use the ward.D2 clustering method`},{label:`Mcquitty`,value:"mcquitty",title:`Use the Mcquity clustering method`}];const l=[{label:"Euclidean",value:"euclidean",title:`Calculate distance using euclidean method`},{label:"Maximum",value:"maximum",title:`Maximum distance between two components of x and y`},{label:"Manhattan",value:"manhattan",title:`Calculate distance using the absolute distance between the two vectors`},{label:"Canberra",value:"canberra",title:`Calculate distance using Canberra method`}];function s(e,t){const l=t?this.hierClusterData.clustering.row.mergedClusters:this.hierClusterData.clustering.col.mergedClusters;const s=l.get(e).childrenClusters||[];let a=[...s];for(const e of s){a=a.concat(this.getAllChildrenClusterIds(e,t))}return a}function a(e,t){const l=this.settings.matrix.controlLabels;const s=this.opts.allow2selectSamples;const a=[{label:"Zoom in",callback:()=>{this.triggerZoomBranch(this,e)}},{label:`List ${e.length} ${l.samples}`,callback:()=>this.showTable4selectedSamples(e)}];if(s){a.push({label:s.buttonText||`Select ${l.samples}`,callback:async()=>{s.callback({samples:e.map((e=>({"cases.case_id":e}))),source:s.defaultSelectionLabel||`Selected ${l.samples} from gene expression`})}})}else{if(this.state.nav&&this.state.nav.header_mode!=="hidden"){const t=e.map((e=>this.sampleOrder.find((t=>t.row.sample==e)).row));for(const e of t){if(!e.sampleId)e.sampleId=e.sample}a.push({label:"Add to a group",callback:async()=>{const e={name:"Group",items:t};this.addGroup(e)}})}}this.mouseout();this.dom.tip.hide();this.dom.dendroClickMenu.d.selectAll("*").remove();this.dom.dendroClickMenu.d.selectAll("div").data(a).enter().append("div").attr("class","sja_menuoption").style("border-radius","0px").html((e=>e.label)).attr("data-testid",(e=>`hierCluster_dendro_menu_${e.label.split(" ")[0]}`)).on("click",(e=>{this.dom.dendroClickMenu.d.selectAll("*").remove();e.target.__data__.callback()}));this.dom.dendroClickMenu.show(t.clientX,t.clientY)}function i(e,t){const l=this.config.dataType=="geneExpression"?"genes":this.config.dataType=="metaboliteIntensity"?"metabolites":"items";const s=[{label:`List ${e.length} ${l}`,callback:()=>this.showTable4selectedRows(e,l)}];if(this.app.opts.genome.termdbs){s.push({label:`Gene set overrepresentation analysis`,disabled:e.length<15||e.length>500,callback:()=>{if(e.length<15||e.length>500)return;this.dom.dendroClickMenu.d.selectAll("*").remove();const t=e;const l={sample_genes:t.toString(),genome:this.app.vocabApi.opts.state.vocab.genome};const s={chartType:"geneORA",geneORAparams:l};this.app.dispatch({type:"plot_create",config:s})}})}this.mouseout();this.dom.tip.hide();this.dom.dendroClickMenu.d.selectAll("*").remove();this.dom.dendroClickMenu.d.selectAll("div").data(s).enter().append("div").attr("class",(e=>e.disabled?"sja_menuoption_not_interactive":"sja_menuoption")).style("opacity",(e=>e.disabled?.5:1)).style("border-radius","0px").html((e=>e.disabled?`${e.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>`:e.label)).attr("data-testid",(e=>`hierCluster_dendro_menu_${e.label.split(" ")[0]}`)).on("click",(e=>{if(e.target.__data__?.callback)e.target.__data__.callback()}));this.dom.dendroClickMenu.show(t.clientX,t.clientY)}function n(e,t){if(e.zoomArea){e.zoomArea.remove();delete e.zoomArea}const l={startCell:e.serieses[0].cells.find((e=>e.sample==t[0])),endCell:e.serieses[0].cells.find((e=>e.sample==t[t.length-1]))};const s=e.settings.matrix;const a=e.dimensions;const i=l.startCell.totalIndex<l.endCell.totalIndex?l.startCell:l.endCell;const n=Math.floor(i.totalIndex+Math.abs(l.endCell.totalIndex-l.startCell.totalIndex)/2);const o=e.sampleOrder[n];const r=e.computedSettings.colw||e.settings.matrix.colw;const c=s.colwMax/r;const d=s.colwMin/r;const h=Math.max(1,s.zoomLevel*a.mainw/Math.max(l.endCell.x-l.startCell.x,2*a.colw)*.7);const m=Math.max(d,Math.min(h,c));e.app.dispatch({type:"plot_edit",id:e.id,config:{settings:{matrix:{zoomLevel:m,zoomCenterPct:.5,zoomIndex:n,zoomGrpIndex:o.grpIndex}}}});e.resetInteractions()}function o(t){const l=this.state.termdbConfig.urlTemplates;const s=l?.sample?t.map((e=>[{value:this.hierClusterData.bySampleId[e].label,url:`${l.sample.base}${e}`}])):t.map((e=>[{value:this.hierClusterData.bySampleId[e].label}]));const a=[{label:this.settings.matrix.controlLabels.Sample}];e({rows:s,columns:a,div:this.dom.dendroClickMenu.clear().d.append("div").style("margin","10px"),showLines:true,maxHeight:"35vh",resize:true})}function r(t,l){const s=this.state.termdbConfig.urlTemplates;const a=s?.gene&&this.config.dataType=="geneExpression"&&this.hierClusterData.byTermId?t.map((e=>this.hierClusterData.byTermId[e]?.gencodeId?[{value:e,url:`${s.gene.base}${this.hierClusterData.byTermId[e].gencodeId}`}]:[{value:e}])):t.map((e=>[{value:e}]));const i=[{label:l}];e({rows:a,columns:i,div:this.dom.dendroClickMenu.clear().d.append("div").style("margin","10px"),showLines:true,maxHeight:"35vh",resize:true})}async function c(e){e.plotId=this.id;await this.app.vocabApi.addGroup(e);this.dom.tip.hide()}function d(e){if(e.target.tagName=="image")this.imgBox=e.target.getBoundingClientRect();else return;const t=e.clientY-this.imgBox.y-e.target.clientTop;const l=this.dimensions.xMin;const s=e.clientX-this.imgBox.x-e.target.clientLeft+l;for(const[e,l]of this.hierClusterData.clustering.col.mergedClusters){const{x1:a,y1:i,x2:n,y2:o,clusterY:r}=l.clusterPosition;if(a<=s&&s<=n&&r-5<t&&t<r+5||r<=t&&t<=i&&a-5<s&&s<a+5||r<=t&&t<=o&&n-5<s&&s<n+5){return e}}}function h(e){if(e.target.tagName=="image")this.imgBox=e.target.getBoundingClientRect();else return;const t=e.clientY-this.imgBox.y-e.target.clientTop;const l=this.dimensions.xMin;const s=e.clientX-this.imgBox.x-e.target.clientLeft+l;for(const[e,l]of this.hierClusterData.clustering.row.mergedClusters){const{x1:a,y1:i,x2:n,y2:o,clusterX:r}=l.clusterPosition;if(i<=t&&t<=o&&r-5<s&&s<r+5||r<=s&&s<=a&&i-5<t&&t<i+5||r<=s&&s<=n&&o-5<t&&t<o+5){return e}}}function m(e,s){const a=this.config.settings.matrix.controlLabels;const i=`Cluster ${a.Samples}`;e.append("button").datum({label:`Clustering`,rows:[{label:i,title:`Option to enable ${a.samples} clustering, instead of enable ${a.samples} sorting.`,type:"checkbox",chartType:"hierCluster",settingsKey:"clusterSamples",boxLabel:`Cluster ${a.samples} (Disable ${a.samples} sorting)`,callback:e=>{if(!e){this.config.settings.hierCluster.yDendrogramHeight=0;this.config.settings.hierCluster.clusterSamples=false}else{this.config.divideBy=null;this.config.settings.hierCluster.yDendrogramHeight=200;this.config.settings.hierCluster.clusterSamples=true}this.app.dispatch({type:"plot_edit",id:this.id,config:this.config})}},{label:`Clustering Method`,title:`Sets which clustering method to use`,type:"radio",chartType:"hierCluster",settingsKey:"clusterMethod",options:t},{label:`Distance Method`,title:`Sets which distance method to use for clustering`,type:"radio",chartType:"hierCluster",settingsKey:"distanceMethod",options:l},{label:`Column Dendrogram Height`,title:`The maximum height to render the column dendrogram`,type:"number",chartType:"hierCluster",settingsKey:"yDendrogramHeight",getDisplayStyle(e){return e.settings.hierCluster.clusterSamples?"table-row":"none"}},{label:`Row Dendrogram Width`,title:`The maximum width to render the row dendrogram`,type:"number",chartType:"hierCluster",settingsKey:"xDendrogramHeight"},{label:`z-score Cap`,title:`Cap the z-score scale to not exceed this absolute value`,type:"number",chartType:"hierCluster",settingsKey:"zScoreCap"},{label:`Color Scheme`,title:`Sets which color scheme to use`,type:"radio",chartType:"hierCluster",settingsKey:"colorScale",options:[{label:"Blue-White-Red",value:"blueWhiteRed",title:`color scheme Blue-White-Red`},{label:"Green-Black-Red",value:"greenBlackRed",title:`color scheme Green-Black-Red`},{label:"Blue-Yellow-Red",value:"blueYellowRed",title:`color scheme Blue-Yellow-Red`},{label:"Green-White-Red",value:"greenWhiteRed",title:`color scheme Green-White-Red`},{label:"Blue-Black-Yellow",value:"blueBlackYellow",title:`color scheme Blue-Black-Yellow`}]}]}).html((e=>e.label)).style("margin","2px 0").on("click",s)}var u=Object.freeze({__proto__:null,getAllChildrenClusterIds:s,addSelectedSamplesOptions:a,addSelectedRowsOptions:i,triggerZoomBranch:n,showTable4selectedSamples:o,showTable4selectedRows:r,addGroup:c,getClusterFromTopDendrogram:d,getClusterFromLeftDendrogram:h,setClusteringBtn:m});export{t as c,l as d,u as i};

package/dist/hierCluster.renderers-74a64cf5.js

@@ -0,0 +1 @@
+import{T as e}from"./termsetting-33ea66f1.js";function t(){if(!this.dom.header)return;switch(this.config.dataType){case e.GENE_EXPRESSION:this.dom.header.text("Gene Expression Clustering");break;case e.METABOLITE_INTENSITY:this.dom.header.text("Metabolite Intensity Clustering");break;default:throw`dataType '${this.config.dataType}' not recognized`}}function n(e){const t=this.dimensions;const n=this.config.settings.matrix;t.seriesXoffset;const s=window.devicePixelRatio<=1?1:window.devicePixelRatio;const r=this.hierClusterData.clustering;const a=r.row;const c=r.col;const h=this.settings.matrix.clusterRowh,{xDendrogramHeight:l,yDendrogramHeight:d}=this.settings.hierCluster,g=this.dimensions.dx;if(e!=="left"){if(!this.settings.hierCluster.clusterSamples){this.dom.topDendrogram.selectAll("*").remove()}else{const e=o(c.height,d);const t=d+1e-7;const r=g*c.inputOrder.length;const a=new OffscreenCanvas(r*s,t*s);const h=a.getContext("2d");h.scale(s,s);h.imageSmoothingEnabled=false;h.imageSmoothingQuality="high";h.strokeStyle="black";const u=new Map;for(const[t,n]of c.merge.entries()){const s=t+1;const o=[];const r=[];let a,l,m,p;if(n.n1<0){const[e,t]=i(n.n1,c.inputOrder,c.order);a=g*(t+.5);m=d;o.push({name:e})}else{if(!u.has(n.n1))throw"pair.n1 is positive but not seen before";const e=u.get(n.n1);a=e.x;m=e.y;o.push(...e.children);r.push(n.n1)}if(n.n2<0){const[e,t]=i(n.n2,c.inputOrder,c.order);l=g*(t+.5);p=d;o.push({name:e})}else{if(!u.has(n.n2))throw"pair.n1 is positive but not seen before";const e=u.get(n.n2);l=e.x;p=e.y;o.push(...e.children);r.push(n.n2)}const f=d-c.height[t].height*e;const x=this.clickedClusterIds?.includes(s);h.strokeStyle=x?"red":"black";h.beginPath();h.moveTo(a,m);h.lineTo(a,f);h.lineTo(l,f);h.lineTo(l,p);h.stroke();h.closePath();u.set(s,{x:(a+l)/2,y:f,children:o,childrenClusters:r,clusterPosition:{x1:a,x2:l,y1:m,y2:p,clusterY:f}})}this.renderImage(this.dom.topDendrogram,a,r,t,l+.5*g,n.margin.top+n.scrollHeight);c.mergedClusters=u}}if(e!=="top"){const e=o(a.height,l);const t=l+1e-7;const r=h*a.inputOrder.length;const c=new OffscreenCanvas(t*s,r*s);const g=c.getContext("2d");g.scale(s,s);g.imageSmoothingEnabled=false;g.imageSmoothingQuality="high";g.strokeStyle="black";const u=new Map;for(const[t,n]of a.merge.entries()){const s=t+1;const o=[];const r=[];let c,d,m,p;if(n.n1<0){const[e,t]=i(n.n1,a.inputOrder,a.order);m=h*(t+.5);c=l;o.push({name:e})}else{if(!u.has(n.n1))throw"pair.n1 is positive but not seen before";const e=u.get(n.n1);c=e.x;m=e.y;o.push(...e.children);r.push(n.n1)}if(n.n2<0){const[e,t]=i(n.n2,a.inputOrder,a.order);p=h*(t+.5);d=l;o.push({name:e})}else{if(!u.has(n.n2))throw"pair.n1 is positive but not seen before";const e=u.get(n.n2);d=e.x;p=e.y;o.push(...e.children);r.push(n.n2)}const f=l-a.height[t].height*e;const x=this.clickedLeftClusterIds?.includes(s);g.strokeStyle=x?"red":"black";g.beginPath();g.moveTo(c,m);g.lineTo(f,m);g.lineTo(f,p);g.lineTo(d,p);g.stroke();g.closePath();u.set(s,{x:f,y:(m+p)/2,children:o,childrenClusters:r,clusterPosition:{x1:c,x2:d,y1:m,y2:p,clusterX:f}})}const m=this.termOrder.find((e=>e.grp.type=="hierCluster"||e.grp.name==this.hcTermGroup.name));const p=m.grpIndex*n.rowgspace+m.prevGrpTotalIndex*n.rowh+m.totalHtAdjustments+n.margin.top+n.scrollHeight+d;this.renderImage(this.dom.leftDendrogram,c,t,r,0,p);a.mergedClusters=u}}async function s(e,t,n,s,o,i){const r=new FileReader;r.addEventListener("load",(()=>{e.selectAll("*").remove();e.append("image").attr("x",o+.033).attr("y",i+.033).attr("xlink:href",r.result).attr("width",n).attr("height",s)}),false);const a=await t.convertToBlob({quality:1});r.readAsDataURL(a)}function o(e,t){let n=e[0].height;for(const t of e)n=Math.max(n,t.height);return t/n}function i(e,t,n){const s=t[-e-1];if(!s)throw"minus not in inputOrder";const o=n.findIndex((e=>e.name==s));if(o==-1)throw"name not found in hc$order";return[s,o]}var r=Object.freeze({__proto__:null,maySetSandboxHeader:t,plotDendrogramHclust:n,renderImage:s});export{r};

package/dist/{html.legend-abb5452e.js → html.legend-a3f4ebfe.js}

@@ -1 +1 @@
-import{d as e,r as t}from"./app-a8c4854a.js";function l(l,n={settings:{},handlers:{}},i){function s(e,t={}){const s=n.settings;if(!t.div)l.selectAll("*").remove();if(e.every((e=>Array.isArray(e)))){for(let t=0;t<e.length;t++){const l=i.select(`.pp-sbar-div:nth-child(${t+1})`);o(e[t],s,l)}}else if(e.every((e=>typeof e=="object"))){o(e,s,t.div||l)}else{throw"render() only takes an array of objects or an array of arrays"}}function o(e,t,l){l.selectAll(".pp-sbar-div-oneLegend").remove();l.append("div").attr("class","pp-sbar-div-oneLegend").attr("data-testid","pp-sbar-div-oneLegend").style("width",t.mainWidth||"").style("text-align",e.legendTextAlign||t.legendTextAlign||(t.legendOrientation=="vertical"?"left":"center")).style("display",t.legendOrientation=="grid"?"grid":"").style("grid-template-rows",t.legendOrientation=="grid"?"auto auto":"").style("gap",t.legendOrientation=="grid"?"10px":"").selectAll("div").data(e).enter().append("div").each(a);if(t.legendChartSide=="right"){setTimeout((()=>{const e=n.dom.container.node().parentNode.getBoundingClientRect();const t=n.dom.container.node().getBoundingClientRect();const l=n.dom.legendDiv.node().getBoundingClientRect();const i=parseFloat(n.dom.legendDiv.style("padding-top"));const s=e.height-t.height+(t.height-l.height+i)/2;if(Math.abs(i-s)<20)return;n.dom.legendDiv.transition().duration(100).style("padding-top",s<0?0:s+"px")}),1200)}}function a(t){const l=n.settings;const i=e(this).style("display",l.legendOrientation=="vertical"||l.legendOrientation=="grid"?"block":"inline-block");if(t.name){if(l.legendChartSide=="right"){i.style("text-align","left");i.append("div").style("font-size",l.legendFontSize).style("font-weight",600).html(t.name);i.append("div").selectAll("div").data(t.items).enter().append("div").style("display",l.legendOrientation=="vertical"?"block":"inline-block").style("margin-right","5px").each(d)}else{i.style("white-space","nowrap").style("width",l.legendOrientation=="vertical"?"fit-content":null);i.append("div").style("display",l.legendOrientation=="grid"||l.legendOrientation=="vertical"?"block":"inline-block").style("width",t.rowLabelHangLeft?t.rowLabelHangLeft+"px":null).style("margin-left",l.legendOrientation=="vertical"?"15px":null).style("text-align",t.rowLabelHangLeft?"right":null).style("font-weight",600).style("vertical-align","top").html(t.name);i.append("div").style("display",l.legendOrientation=="grid"||l.legendOrientation=="vertical"?"block":"inline-block").style("max-width",1.2*t.rowLabelHangLeft+"px").style("white-space","normal").style("vertical-align","top").selectAll("div").data(t.items).enter().append("div").style("display","inline-block").style("margin-left","15px").each(d)}}else{i.selectAll("div").data(t.items).enter().append("div").style("display",l.legendOrientation=="vertical"?"block":"inline-block").style("margin-left","15px").each(d)}}function d(l){const i=n.settings;const s=e(this);const o=l.fill?l.fill:l.stroke?l.stroke:l.color;s.attr("class","legend-row").classed("sjpp-hidden-legend-item",l.isHidden?true:false).style("display",i.legendOrientation=="vertical"?"block":"inline-block").style("width",i.legendOrientation=="vertical"?"fit-content":null);if(l.svg){s.append("svg").attr("width",l.svgw).attr("height",l.svgh).style("display","inline-block").style("vertical-align","top").style("border",l.border).html((e=>e.svg))}else if(!l.noIcon){const e=l.noEditColor?o:t(o).darker();s.append("div").style("display","inline-block").style("position","relative").style("min-width","12px").style("height","12px").style("top","1px").style("border",l.border?l.border:"1px solid "+e).style("border-radius",l.shape=="circle"?"6px":"").style("background-color",l.shape=="circle"?"":o).style("cursor","isHidden"in l?"pointer":"default").style("color",l.textColor?l.textColor:"#fff").style("font-size","10px").style("vertical-align",l.inset?"top":"").style("padding",l.inset?"0 3px":"").text(l.inset).on("click",n.handlers.legend?.onColorClick)}s.append("div").classed("sjpp-htmlLegend",true).style("display","inline-block").style("margin-left",l.svg?"1px":"3px").style("cursor",l.isHidden?"pointer":"default").style("font-size",i.legendFontSize).style("line-height",i.legendFontSize).style("vertical-align",l.svg?"top":null).style("text-decoration",l.isHidden?"line-through":"none").html(l.text).on("click",n.handlers.legend?.click);if(Object.keys(n.handlers).length){s.on("mouseover",n.handlers.legend.mouseover).on("mouseout",n.handlers.legend.mouseout)}}return s}export{l as h};
+import{d as e,r as t}from"./app-b369b169.js";function l(l,n={settings:{},handlers:{}},i){function s(e,t={}){const s=n.settings;if(!t.div)l.selectAll("*").remove();if(e.every((e=>Array.isArray(e)))){for(let t=0;t<e.length;t++){const l=i.select(`.pp-sbar-div:nth-child(${t+1})`);o(e[t],s,l)}}else if(e.every((e=>typeof e=="object"))){o(e,s,t.div||l)}else{throw"render() only takes an array of objects or an array of arrays"}}function o(e,t,l){l.selectAll(".pp-sbar-div-oneLegend").remove();l.append("div").attr("class","pp-sbar-div-oneLegend").attr("data-testid","pp-sbar-div-oneLegend").style("width",t.mainWidth||"").style("text-align",e.legendTextAlign||t.legendTextAlign||(t.legendOrientation=="vertical"?"left":"center")).style("display",t.legendOrientation=="grid"?"grid":"").style("grid-template-rows",t.legendOrientation=="grid"?"auto auto":"").style("gap",t.legendOrientation=="grid"?"10px":"").selectAll("div").data(e).enter().append("div").each(a);if(t.legendChartSide=="right"){setTimeout((()=>{const e=n.dom.container.node().parentNode.getBoundingClientRect();const t=n.dom.container.node().getBoundingClientRect();const l=n.dom.legendDiv.node().getBoundingClientRect();const i=parseFloat(n.dom.legendDiv.style("padding-top"));const s=e.height-t.height+(t.height-l.height+i)/2;if(Math.abs(i-s)<20)return;n.dom.legendDiv.transition().duration(100).style("padding-top",s<0?0:s+"px")}),1200)}}function a(t){const l=n.settings;const i=e(this).style("display",l.legendOrientation=="vertical"||l.legendOrientation=="grid"?"block":"inline-block");if(t.name){if(l.legendChartSide=="right"){i.style("text-align","left");i.append("div").style("font-size",l.legendFontSize).style("font-weight",600).html(t.name);i.append("div").selectAll("div").data(t.items).enter().append("div").style("display",l.legendOrientation=="vertical"?"block":"inline-block").style("margin-right","5px").each(d)}else{i.style("white-space","nowrap").style("width",l.legendOrientation=="vertical"?"fit-content":null);i.append("div").style("display",l.legendOrientation=="grid"||l.legendOrientation=="vertical"?"block":"inline-block").style("width",t.rowLabelHangLeft?t.rowLabelHangLeft+"px":null).style("margin-left",l.legendOrientation=="vertical"?"15px":null).style("text-align",t.rowLabelHangLeft?"right":null).style("font-weight",600).style("vertical-align","top").html(t.name);i.append("div").style("display",l.legendOrientation=="grid"||l.legendOrientation=="vertical"?"block":"inline-block").style("max-width",1.2*t.rowLabelHangLeft+"px").style("white-space","normal").style("vertical-align","top").selectAll("div").data(t.items).enter().append("div").style("display","inline-block").style("margin-left","15px").each(d)}}else{i.selectAll("div").data(t.items).enter().append("div").style("display",l.legendOrientation=="vertical"?"block":"inline-block").style("margin-left","15px").each(d)}}function d(l){const i=n.settings;const s=e(this);const o=l.fill?l.fill:l.stroke?l.stroke:l.color;s.attr("class","legend-row").classed("sjpp-hidden-legend-item",l.isHidden?true:false).style("display",i.legendOrientation=="vertical"?"block":"inline-block").style("width",i.legendOrientation=="vertical"?"fit-content":null);if(l.svg){s.append("svg").attr("width",l.svgw).attr("height",l.svgh).style("display","inline-block").style("vertical-align","top").style("border",l.border).html((e=>e.svg))}else if(!l.noIcon){const e=l.noEditColor?o:t(o).darker();s.append("div").style("display","inline-block").style("position","relative").style("min-width","12px").style("height","12px").style("top","1px").style("border",l.border?l.border:"1px solid "+e).style("border-radius",l.shape=="circle"?"6px":"").style("background-color",l.shape=="circle"?"":o).style("cursor","isHidden"in l?"pointer":"default").style("color",l.textColor?l.textColor:"#fff").style("font-size","10px").style("vertical-align",l.inset?"top":"").style("padding",l.inset?"0 3px":"").text(l.inset).on("click",n.handlers.legend?.onColorClick)}s.append("div").classed("sjpp-htmlLegend",true).style("display","inline-block").style("margin-left",l.svg?"1px":"3px").style("cursor",l.isHidden?"pointer":"default").style("font-size",i.legendFontSize).style("line-height",i.legendFontSize).style("vertical-align",l.svg?"top":null).style("text-decoration",l.isHidden?"line-through":"none").html(l.text).on("click",n.handlers.legend?.click);if(Object.keys(n.handlers).length){s.on("mouseover",n.handlers.legend.mouseover).on("mouseout",n.handlers.legend.mouseout)}}return s}export{l as h};

package/dist/imagePlot-b9eae4ae.js

@@ -0,0 +1 @@
+import{P as t,h as i}from"./app-b369b169.js";import{controlsInit as s}from"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./termsetting-33ea66f1.js";import"./tslib.es6-c3c2d88f.js";import"path";class e{constructor(){this.type="imagePlot"}async init(t){const i=t.plots.find((t=>t.id===this.id));this.getState(t);const s=this.opts.holder.append("div");this.dom={holder:s,controlsHolder:s.append("div").style("display","inline-block"),imageHolder:s.append("div").style("display","inline-block")};this.setControls();const e=await this.app.vocabApi.getSampleImages(i.sample.sampleId);if(e.error)throw e.error;for(const t of e.images){this.dom.imageHolder.append("img").style("padding","10px").attr("src",t.src).attr("width",i.settings.imagePlot.width).attr("height",i.settings.imagePlot.height)}}async setControls(){this.components={controls:await s({app:this.app,id:this.id,holder:this.dom.controlsHolder,inputs:[{label:"Chart width",type:"number",chartType:this.type,settingsKey:"width"},{label:"Chart height",type:"number",chartType:this.type,settingsKey:"height"}]})}}getState(t){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)?`}return{config:i,termfilter:t.termfilter,vocab:t.vocab}}}async function o(i,s){let e=n();if(i.settings)t(e,i.settings);const o={settings:{controls:{isOpen:false},imagePlot:e}};const a=t(o,i);return a}function n(){return{width:500,height:500}}const a=i(e);const r=a;async function p(t,i,s){const e={holder:i,state:{vocab:t.vocab,plots:[{chartType:"imagePlot",sample:s}]}};const o=await import("./plot.app-30c4b8e5.js");await o.appInit(e)}export{r as componentInit,n as getDefaultImagePlotSettings,o as getPlotConfig,a as imagePlotInit,p as renderImagePlot};

package/dist/{lasso-55cf4057.js → lasso-f767f634.js}

@@ -1 +1 @@
-import{d as t}from"./drag-0b968811.js";import{p as e}from"./pointer-c7475677.js";function s(){let s=[],n,o={start:function(){},draw:function(){},end:function(){}};function l(l){const r=l.append("g").attr("class","lasso");const i=r.append("path").attr("class","drawn").style("stroke","#505050").style("stroke-width","2px").style("fill-opacity",".05");const a=r.append("circle").attr("class","origin").style("fill","#3399FF").style("fill-opacity",".5");let c,u;let f=t().on("start",d).on("drag",_).on("end",p);n.call(f);function d(t){u=[];c="";i.attr("d",null);s.nodes().forEach((function(t){t.__lasso.possible=false;t.__lasso.selected=false;t.__lasso.loopSelect=false;let e=t.getBoundingClientRect();t.__lasso.lassoPoint=[Math.round(e.left+e.width/2),Math.round(e.top+e.height/2)]}));o.start(t)}function _(t){let n,l;if(t.sourceEvent.type==="touchmove"){n=t.sourceEvent.touches[0].clientX;l=t.sourceEvent.touches[0].clientY}else{n=t.sourceEvent.clientX;l=t.sourceEvent.clientY}let[r,f]=e(t,this);if(c===""){c=c+"M "+r+" "+f;a.attr("cx",r).attr("cy",f).attr("r",7).attr("display",null)}else{c=c+" L "+r+" "+f}u.push([n,l]);i.attr("d",c);s.nodes().forEach((function(t){t.__lasso.loopSelect=h(t.__lasso.lassoPoint,u);t.__lasso.possible=t.__lasso.loopSelect}));o.draw(t)}function p(t){s.on("mouseover.lasso",null);s.nodes().forEach((function(t){t.__lasso.selected=t.__lasso.possible;t.__lasso.possible=false}));i.attr("d",null);a.attr("display","none");o.end(t)}function h(t,e){let s,n,o,l,r,i=t[0],a=t[1],c=false;for(let t=0,u=e.length-1;t<e.length;u=t++){s=e[t][0];o=e[t][1];n=e[u][0];l=e[u][1];r=o>a!=l>a&&i<(n-s)*(a-o)/(l-o)+s;if(r)c=!c}return c}}l.items=function(t){if(!arguments.length)return s;s=t;const e=s.nodes();e.forEach((function(t){t.__lasso={possible:false,selected:false}}));return l};l.possibleItems=function(){return s.filter((function(){return this.__lasso.possible}))};l.selectedItems=function(){return s.filter((function(){return this.__lasso.selected}))};l.notPossibleItems=function(){return s.filter((function(){return!this.__lasso.possible}))};l.notSelectedItems=function(){return s.filter((function(){return!this.__lasso.selected}))};l.on=function(t,e){if(!arguments.length)return o;if(arguments.length===1)return o[t];const s=["start","draw","end"];if(s.indexOf(t)>-1){o[t]=e}return l};l.targetArea=function(t){if(!arguments.length)return n;n=t;return l};return l}export{s as d};
+import{d as t}from"./drag-7b30ba17.js";import{p as e}from"./pointer-c7475677.js";function s(){let s=[],n,o={start:function(){},draw:function(){},end:function(){}};function l(l){const r=l.append("g").attr("class","lasso");const i=r.append("path").attr("class","drawn").style("stroke","#505050").style("stroke-width","2px").style("fill-opacity",".05");const a=r.append("circle").attr("class","origin").style("fill","#3399FF").style("fill-opacity",".5");let c,u;let f=t().on("start",d).on("drag",_).on("end",p);n.call(f);function d(t){u=[];c="";i.attr("d",null);s.nodes().forEach((function(t){t.__lasso.possible=false;t.__lasso.selected=false;t.__lasso.loopSelect=false;let e=t.getBoundingClientRect();t.__lasso.lassoPoint=[Math.round(e.left+e.width/2),Math.round(e.top+e.height/2)]}));o.start(t)}function _(t){let n,l;if(t.sourceEvent.type==="touchmove"){n=t.sourceEvent.touches[0].clientX;l=t.sourceEvent.touches[0].clientY}else{n=t.sourceEvent.clientX;l=t.sourceEvent.clientY}let[r,f]=e(t,this);if(c===""){c=c+"M "+r+" "+f;a.attr("cx",r).attr("cy",f).attr("r",7).attr("display",null)}else{c=c+" L "+r+" "+f}u.push([n,l]);i.attr("d",c);s.nodes().forEach((function(t){t.__lasso.loopSelect=h(t.__lasso.lassoPoint,u);t.__lasso.possible=t.__lasso.loopSelect}));o.draw(t)}function p(t){s.on("mouseover.lasso",null);s.nodes().forEach((function(t){t.__lasso.selected=t.__lasso.possible;t.__lasso.possible=false}));i.attr("d",null);a.attr("display","none");o.end(t)}function h(t,e){let s,n,o,l,r,i=t[0],a=t[1],c=false;for(let t=0,u=e.length-1;t<e.length;u=t++){s=e[t][0];o=e[t][1];n=e[u][0];l=e[u][1];r=o>a!=l>a&&i<(n-s)*(a-o)/(l-o)+s;if(r)c=!c}return c}}l.items=function(t){if(!arguments.length)return s;s=t;const e=s.nodes();e.forEach((function(t){t.__lasso={possible:false,selected:false}}));return l};l.possibleItems=function(){return s.filter((function(){return this.__lasso.possible}))};l.selectedItems=function(){return s.filter((function(){return this.__lasso.selected}))};l.notPossibleItems=function(){return s.filter((function(){return!this.__lasso.possible}))};l.notSelectedItems=function(){return s.filter((function(){return!this.__lasso.selected}))};l.on=function(t,e){if(!arguments.length)return o;if(arguments.length===1)return o[t];const s=["start","draw","end"];if(s.indexOf(t)>-1){o[t]=e}return l};l.targetArea=function(t){if(!arguments.length)return n;n=t;return l};return l}export{s as d};

package/dist/launch.adhoc-abca6af3.js

@@ -0,0 +1 @@
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{appInit as e}from"./plot.app-30c4b8e5.js";import{ai as o,z as s}from"./app-b369b169.js";import"./recover-49e09de0.js";import"./termsetting-33ea66f1.js";import"path";import"./FilterRxComp-701a1480.js";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.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";function n(s,n,i){return t(this,void 0,void 0,(function*(){const[t,c]=yield r(s);if(c===null||c===void 0?void 0:c.length){return o(c,i)}const p={holder:i,vocabApi:{vocab:{terms:[]},main:()=>{},getTermdbConfig:()=>({})},state:{args:{data:t,genome:n},plots:[{chartType:"Disco",subfolder:"disco",extension:"ts"}]}};const u=yield e(p);return u}))}function r(e){return t(this,void 0,void 0,(function*(){if(Array.isArray(e.mlst)){return[e.mlst,null]}const t=[];const o=[];if(e.snvText)i(e.snvText,t,o);if(e.svText)c(e.svText,t,o);if(e.cnvText)p(e.cnvText,t,o);return[t,o]}))}function i(t,e,o){for(const s of t.trim().split("\n")){const t=s.trim().split("\t");if(t.length!=5){o.push("snv input not equal to 5 columns");continue}let n;try{n={dt:1,chr:t[0],position:Number(t[1]),gene:t[2],mname:t[3],class:u(t[4],o)}}catch(t){o.push(t);continue}e.push(n)}}function c(t,e,o){for(const s of t.trim().split("\n")){const t=s.trim().split("\t");if(t.length<4||t.length>6){o.push("sv input not equal to 4 or 6 columns");continue}let n;try{const e=t.length;if(e==4){n={dt:2,chrA:t[0],posA:Number(t[1]),chrB:t[2],posB:Number(t[3])}}else{n={dt:2,chrA:t[0],posA:Number(t[1]),geneA:t[2],chrB:t[3],posB:Number(t[4]),geneB:t[5]}}}catch(t){o.push(t);continue}e.push(n)}}function p(t,e,o){for(const s of t.trim().split("\n")){const t=s.trim().split("\t");if(t.length!=4){o.push("cnv input not equal to 4 columns");continue}let n;try{n={dt:4,chr:t[0],start:Number(t[1]),stop:Number(t[2]),value:Number(t[3])}}catch(t){o.push(t);continue}e.push(n)}}function u(t,e){const o=t.toLowerCase();const n=Object.values(s).find((t=>t.key.toLowerCase()===o||t.label.toLowerCase()===o));if(n){return n.key}else{e.push(`Invalid mutation class: ${t}`)}}export{n as launch};

package/dist/leftlabel.sample-24c2388d.js

@@ -0,0 +1 @@
+import{m as t,g as e,d as s}from"./tk-071a7550.js";import{T as a}from"./toggleButtons-dbdbad01.js";import{aN as o}from"./app-b369b169.js";import{r as l}from"./table-29d5a973.js";import{f as n}from"./FilterStateless-54c0b763.js";import{g as i}from"./FilterRxComp-701a1480.js";import"./termsetting-33ea66f1.js";import{v as r}from"./violinRenderer-f7c96a60.js";import"./block.legend-d3f61ef7.js";import"./vcf-5cc55588.js";import"./partition-db811f6b.js";import"./arc-3d6751aa.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";import"./axis-747c801e.js";import"./legacy-d3-polyfill-bdb2d792.js";import"./regression.results-69bc42d0.js";import"./axisstyle-fac7f76b.js";import"./ColorScale-21cab8d2.js";import"./log-99af3443.js";import"./block-6aedd569.js";import"./checkbox-96437f4d.js";import"./pointer-c7475677.js";import"./downloadTextfile-5723af95.js";import"./radiobutton-09bff425.js";import"./niceNumLabels-238aabce.js";import"./rehydrateFilter-12d118cb.js";import"./tslib.es6-c3c2d88f.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"path";import"./brush-aa175142.js";import"./nodrag-16ad4b03.js";import"./line-264f8f9e.js";import"./basis-3870f5ba.js";function m(e,s,a,o){if(!s.leftlabels.doms.samples){s.leftlabels.doms.samples=t(s,a,o)}if(e.sampleTotalNumber){s.leftlabels.doms.samples.attr("class","sja_clbtext2").style("opacity",1).text(`${e.sampleTotalNumber} sample${e.sampleTotalNumber>1?"s":""}`).attr("data-testid","sjpp_mds3tk_samples_label").on("click",(async t=>{s.menutip.clear().showunder(t.target);await d(s,a);const o=s.menutip.d.append("div").style("margin","10px");g(o,e,s,a)}))}else{s.leftlabels.doms.samples.text("No samples").attr("class","").style("opacity",.5).on("click",null)}}function c(s,a,o,l){if(!a.leftlabels.doms.filterObj){a.leftlabels.doms.filterObj=t(a,o,l)}a.leftlabels.doms.filterObj.text(e(a.filterObj)).on("click",(async t=>{a.menutip.clear().showunder(t.target);const e={holder:a.menutip.d.append("div").style("margin","10px"),vocabApi:a.mds.termdb.vocabApi,callback:t=>{a.filterObj=t;a.load()}};p(e,o);n(e).main(a.filterObj)}))}function p(t,e){if(e.usegm){t.getCategoriesArguments={currentGeneNames:[e.usegm.name]}}else{t.getCategoriesArguments={rglst:structuredClone(e.rglst)}}}async function d(t,e){if(!t.mds.variant2samples.twLst){return}const s=t.menutip.d.append("div").style("margin","10px");const a=s.append("div").text("Loading...");try{const{summary:o}=await t.mds.getSamples({isSummary:true});t.leftlabels.__samples_data=o;a.remove();await f(o,s.append("div").attr("class","sja_mds3samplesummarydiv"),t,e)}catch(t){a.text(`Error: ${t.message||t}`);if(t.stack)console.log(t.stack)}}async function f(t,e,s,o){const l=[];for(const{termid:e,numbycategory:a}of t){l.push({label:s.mds.variant2samples.twLst.find((t=>t.term.id==e)).term.name+(a?`<span style="opacity:.8;font-size:.8em;float:right;margin-left: 5px;">n=${a.length}</span>`:"")})}new a({holder:e,tabsPosition:"vertical",linePosition:"right",tabs:l}).main();for(const[e,a]of t.entries()){const t=l[e].contentHolder.style("padding-left","20px");if(a.numbycategory){t.append("div").text("Click a category to create new track.").style("margin-bottom","10px").style("font-size",".8em").style("opacity",.5);b(a.termid,t,a.numbycategory,s,o);continue}if(a.density_data){if(!Number.isFinite(a.density_data.minvalue)||!Number.isFinite(a.density_data.maxvalue)){t.append("div").text("No data");continue}t.append("div").text("Select a range to create new track.").style("margin-bottom","10px").style("font-size",".8em").style("opacity",.5);y(a.termid,t,a,s,o);continue}throw"unknown summary data"}}function b(t,e,s,a,n){const i=a.mds.variant2samples.twLst.find((e=>e.term.id==t));if(!i)throw"showSummary4oneTerm(): tw not found from variant2samples.twLst";const r=[];for(const[t,e,a]of s){const s=[{value:i.term.values?.[t]?.label||t},{html:a==undefined?"":o(null,{f:e/a,v1:e,v2:a})},{html:e+(a?' <span style="font-size:.8em">/ '+a+"</span>":"")}];r.push(s)}l({div:e,rows:r,columns:[{nowrap:true},{},{}],showHeader:false,singleMode:true,noRadioBtn:true,noButtonCallback:t=>{m(s[t][0])}});async function m(e){a.menutip.clear();const o=await a.mds.termdb.vocabApi.getterm(t);if(!o.values||Object.keys(o.values).length==0){o.values={};for(const t of s){o.values[t[0]]={label:t[0],samplecount:t[1]}}}const l={type:"tvs",tvs:{term:o,values:[{key:e}]}};const i={type:"mds3",dslabel:a.dslabel,filter0:a.filter0,showCloseLeftlabel:true,filterObj:u(a,l),allow2selectSamples:a.allow2selectSamples};const r=n.block_addtk_template(i);n.tk_load(r)}}function u(t,e){if(t.filterObj){return i({type:"tvslst",join:"and",in:true,lst:[t.filterObj,e]})}return{type:"tvslst",in:true,join:"",lst:[e]}}async function y(t,e,s,a,o){const l=await a.mds.termdb.vocabApi.getterm(t);const n=async t=>{a.menutip.clear();const e={type:"tvs",tvs:{term:l,ranges:[{start:t.range_start,stop:t.range_end}]}};const s={type:"mds3",dslabel:a.dslabel,filter0:a.filter0,showCloseLeftlabel:true,filterObj:u(a,e),allow2selectSamples:a.allow2selectSamples};const n=o.block_addtk_template(s);o.tk_load(n)};const i=l.valueConversion?l.valueConversion.scaleFactor:1;const m=new r(e,s.density_data,400,100,10,20,n,i);m.render()}function g(t,e,a,o){t.append("div").text(`List ${e.sampleTotalNumber} sample${e.sampleTotalNumber>1?"s":""}`).attr("class","sja_menuoption sja_mds3_slb_sampletablebtn").on("click",(async()=>{a.menutip.clear();const t=a.menutip.d.append("div").text("Loading...").style("margin","15px");try{const{samples:e}=await a.mds.getSamples();await s(e,{div:a.menutip.d,tk:a,block:o});t.remove()}catch(e){t.text(e.message||e);console.log(e)}}))}export{c as makeSampleFilterLabel,m as makeSampleLabel};

package/dist/legacyDataset-e0e201ab.js

@@ -0,0 +1 @@
+import{aM as t,aL as o,a8 as r}from"./app-b369b169.js";import{s as n}from"./legacy-d3-polyfill-bdb2d792.js";function a(a){if(a.geneexpression){if(a.geneexpression.maf){try{a.geneexpression.maf.get=new Function(...a.geneexpression.maf.get)}catch(t){return"invalid Javascript for get() of expression.maf of "+a.label}}}if(a.cohort){if(a.cohort.raw&&a.cohort.tosampleannotation){if(!a.cohort.key4annotation){return"cohort.tosampleannotation in use by .key4annotation missing of "+a.label}if(!a.cohort.annotation){a.cohort.annotation={}}let t=0;for(const o of a.cohort.raw){const r=o[a.cohort.tosampleannotation.samplekey];if(r){const t={};for(const r in o){t[r]=o[r]}a.cohort.annotation[r]=t}else{t++}}if(t)return t+" rows has no sample name from sample annotation of "+a.label;delete a.cohort.tosampleannotation}if(a.cohort.levels){if(a.cohort.raw){const r=t(a.cohort.raw,a.cohort.levels);a.cohort.root=o()(r);a.cohort.root.sum((t=>t.value))}}if(a.cohort.raw){delete a.cohort.raw}a.cohort.suncolor=r(n)}if(a.snvindel_attributes){for(const t of a.snvindel_attributes){if(t.get){try{t.get=new Function(...t.get)}catch(o){return"invalid Javascript for getter of "+JSON.stringify(t)}}else if(t.lst){for(const o of t.lst){if(o.get){try{o.get=new Function(...o.get)}catch(t){return"invalid Javascript for getter of "+JSON.stringify(o)}}}}}}if(a.stratify){if(!Array.isArray(a.stratify)){return"stratify is not an array in "+a.label}for(const t of a.stratify){if(!t.label){return"stratify method lacks label in "+a.label}if(t.bycohort){if(!a.cohort){return"stratify method "+t.label+" using cohort but no cohort in "+a.label}}else{if(!t.attr1){return"stratify method "+t.label+" not using cohort but no attr1 in "+a.label}if(!t.attr1.label){return".attr1.label missing in "+t.label+" in "+a.label}if(!t.attr1.k){return".attr1.k missing in "+t.label+" in "+a.label}}}}if(a.url4variant){for(const t of a.url4variant){t.makelabel=new Function(...t.makelabel);t.makeurl=new Function(...t.makeurl)}}}export{a as validate_oldds};

package/dist/{log-cf45fcf2.js → log-99af3443.js}

@@ -1 +1 @@
-import{a1 as t,a2 as n,a3 as e,a4 as r,a5 as i,W as o}from"./app-a8c4854a.js";function a(t,n){t=t.slice();var e=0,r=t.length-1,i=t[e],o=t[r],a;if(o<i){a=e,e=r,r=a;a=i,i=o,o=a}t[e]=n.floor(i);t[r]=n.ceil(o);return t}function l(t){return Math.log(t)}function u(t){return Math.exp(t)}function f(t){return-Math.log(-t)}function c(t){return-Math.exp(-t)}function s(t){return isFinite(t)?+("1e"+t):t<0?0:t}function h(t){return t===10?s:t===Math.E?Math.exp:n=>Math.pow(t,n)}function M(t){return t===Math.E?Math.log:t===10&&Math.log10||t===2&&Math.log2||(t=Math.log(t),n=>Math.log(n)/t)}function p(t){return(n,e)=>-t(-n,e)}function g(t){const n=t(l,u);const e=n.domain;let s=10;let g;let m;function b(){g=M(s),m=h(s);if(e()[0]<0){g=p(g),m=p(m);t(f,c)}else{t(l,u)}return n}n.base=function(t){return arguments.length?(s=+t,b()):s};n.domain=function(t){return arguments.length?(e(t),b()):e()};n.ticks=t=>{const n=e();let i=n[0];let o=n[n.length-1];const a=o<i;if(a)[i,o]=[o,i];let l=g(i);let u=g(o);let f;let c;const h=t==null?10:+t;let M=[];if(!(s%1)&&u-l<h){l=Math.floor(l),u=Math.ceil(u);if(i>0)for(;l<=u;++l){for(f=1;f<s;++f){c=l<0?f/m(-l):f*m(l);if(c<i)continue;if(c>o)break;M.push(c)}}else for(;l<=u;++l){for(f=s-1;f>=1;--f){c=l>0?f/m(-l):f*m(l);if(c<i)continue;if(c>o)break;M.push(c)}}if(M.length*2<h)M=r(i,o,h)}else{M=r(l,u,Math.min(u-l,h)).map(m)}return a?M.reverse():M};n.tickFormat=(t,e)=>{if(t==null)t=10;if(e==null)e=s===10?"s":",";if(typeof e!=="function"){if(!(s%1)&&(e=i(e)).precision==null)e.trim=true;e=o(e)}if(t===Infinity)return e;const r=Math.max(1,s*t/n.ticks().length);return t=>{let n=t/m(Math.round(g(t)));if(n*s<s-.5)n*=s;return n<=r?e(t):""}};n.nice=()=>e(a(e(),{floor:t=>m(Math.floor(g(t))),ceil:t=>m(Math.ceil(g(t)))}));return n}function m(){const r=g(t()).domain([1,10]);r.copy=()=>n(r,m()).base(r.base());e.apply(r,arguments);return r}export{m as l,a as n};
+import{a1 as t,a2 as n,a3 as e,a4 as r,a5 as i,W as o}from"./app-b369b169.js";function a(t,n){t=t.slice();var e=0,r=t.length-1,i=t[e],o=t[r],a;if(o<i){a=e,e=r,r=a;a=i,i=o,o=a}t[e]=n.floor(i);t[r]=n.ceil(o);return t}function l(t){return Math.log(t)}function u(t){return Math.exp(t)}function f(t){return-Math.log(-t)}function c(t){return-Math.exp(-t)}function s(t){return isFinite(t)?+("1e"+t):t<0?0:t}function h(t){return t===10?s:t===Math.E?Math.exp:n=>Math.pow(t,n)}function M(t){return t===Math.E?Math.log:t===10&&Math.log10||t===2&&Math.log2||(t=Math.log(t),n=>Math.log(n)/t)}function p(t){return(n,e)=>-t(-n,e)}function g(t){const n=t(l,u);const e=n.domain;let s=10;let g;let m;function b(){g=M(s),m=h(s);if(e()[0]<0){g=p(g),m=p(m);t(f,c)}else{t(l,u)}return n}n.base=function(t){return arguments.length?(s=+t,b()):s};n.domain=function(t){return arguments.length?(e(t),b()):e()};n.ticks=t=>{const n=e();let i=n[0];let o=n[n.length-1];const a=o<i;if(a)[i,o]=[o,i];let l=g(i);let u=g(o);let f;let c;const h=t==null?10:+t;let M=[];if(!(s%1)&&u-l<h){l=Math.floor(l),u=Math.ceil(u);if(i>0)for(;l<=u;++l){for(f=1;f<s;++f){c=l<0?f/m(-l):f*m(l);if(c<i)continue;if(c>o)break;M.push(c)}}else for(;l<=u;++l){for(f=s-1;f>=1;--f){c=l>0?f/m(-l):f*m(l);if(c<i)continue;if(c>o)break;M.push(c)}}if(M.length*2<h)M=r(i,o,h)}else{M=r(l,u,Math.min(u-l,h)).map(m)}return a?M.reverse():M};n.tickFormat=(t,e)=>{if(t==null)t=10;if(e==null)e=s===10?"s":",";if(typeof e!=="function"){if(!(s%1)&&(e=i(e)).precision==null)e.trim=true;e=o(e)}if(t===Infinity)return e;const r=Math.max(1,s*t/n.ticks().length);return t=>{let n=t/m(Math.round(g(t)));if(n*s<s-.5)n*=s;return n<=r?e(t):""}};n.nice=()=>e(a(e(),{floor:t=>m(Math.floor(g(t))),ceil:t=>m(Math.ceil(g(t)))}));return n}function m(){const r=g(t()).domain([1,10]);r.copy=()=>n(r,m()).base(r.base());e.apply(r,arguments);return r}export{m as l,a as n};

package/dist/{lollipop-c5b6e615.js → lollipop-806f8fa4.js}

@@ -1 +1 @@
-import{a as e}from"./genesearch-ea59f5d4.js";import{M as o,b as s,e as t}from"./app-a8c4854a.js";import"./tslib.es6-1f85f553.js";const n="hg38";const a="GDC";const r=new o({padding:""});async function i(o,i,c){const m=c[n];if(!m)throw n+" missing";const f=i.append("div").style("margin-left","20px");f.append("div").text("To view GDC mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).");const d=i.append("div").attr("class","sja_geneSearch4GDCmds3_blockdiv");const p={genome:m,tip:r,row:f,searchOnly:"gene",callback:h,geneSymbol:o.geneSymbol};const g=e(p);let y;if(typeof o.geneSearch4GDCmds3.postRender=="function"){await o.geneSearch4GDCmds3.postRender({tip:r})}async function h(e=true){if(!g.geneSymbol){if(e)throw"geneSymbol missing"}d.selectAll("*").remove();const r=(await s(`genelookup?deep=1&input=${g.geneSymbol}&genome=${n}`)).gmlst;if(!Array.isArray(r)||r.length==0)throw"gmlst is not non-empty array";y=l(g,r);const i={query:y,genome:m,holder:d,gmmode:r.some((e=>e.coding))?"protein":"exon only",hide_dsHandles:o.hide_dsHandles,tklst:o.tracks?o.tracks:[{type:"mds3",dslabel:a,allow2selectSamples:o.allow2selectSamples}]};if(typeof o.geneSearch4GDCmds3.onloadalltk_always=="function"){i.onloadalltk_always=o.geneSearch4GDCmds3.onloadalltk_always}return await t(i)}const u={update:e=>{Object.assign(o,e);o.isoform=y;h(false)}};return u}function l(e,o){if(e.fromWhat){if(o.some((o=>o.isoform.toUpperCase()==e.fromWhat.toUpperCase()))){return e.fromWhat}if(e.fromWhat.toUpperCase().startsWith("ENSG")){for(const e of o){if(e.isdefault&&e.isoform.startsWith("ENST"))return e.isoform}}}const s=o.find((e=>e.isdefault));if(s)return s.isoform;return o[0].isoform}export{i as init};
+import{a as e}from"./genesearch-a4e19f0d.js";import{M as o,b as s,e as t}from"./app-b369b169.js";import"./tslib.es6-c3c2d88f.js";const n="hg38";const a="GDC";const r=new o({padding:""});async function i(o,i,c){const m=c[n];if(!m)throw n+" missing";const f=i.append("div").style("margin-left","20px");f.append("div").text("To view GDC mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).");const d=i.append("div").attr("class","sja_geneSearch4GDCmds3_blockdiv");const p={genome:m,tip:r,row:f,searchOnly:"gene",callback:h,geneSymbol:o.geneSymbol};const g=e(p);let y;if(typeof o.geneSearch4GDCmds3.postRender=="function"){await o.geneSearch4GDCmds3.postRender({tip:r})}async function h(e=true){if(!g.geneSymbol){if(e)throw"geneSymbol missing"}d.selectAll("*").remove();const r=(await s(`genelookup?deep=1&input=${g.geneSymbol}&genome=${n}`)).gmlst;if(!Array.isArray(r)||r.length==0)throw"gmlst is not non-empty array";y=l(g,r);const i={query:y,genome:m,holder:d,gmmode:r.some((e=>e.coding))?"protein":"exon only",hide_dsHandles:o.hide_dsHandles,tklst:o.tracks?o.tracks:[{type:"mds3",dslabel:a,allow2selectSamples:o.allow2selectSamples}]};if(typeof o.geneSearch4GDCmds3.onloadalltk_always=="function"){i.onloadalltk_always=o.geneSearch4GDCmds3.onloadalltk_always}return await t(i)}const u={update:e=>{Object.assign(o,e);o.isoform=y;h(false)}};return u}function l(e,o){if(e.fromWhat){if(o.some((o=>o.isoform.toUpperCase()==e.fromWhat.toUpperCase()))){return e.fromWhat}if(e.fromWhat.toUpperCase().startsWith("ENSG")){for(const e of o){if(e.isdefault&&e.isoform.startsWith("ENST"))return e.isoform}}}const s=o.find((e=>e.isdefault));if(s)return s.isoform;return o[0].isoform}export{i as init};

package/dist/{maf-7535f1f9.js → maf-b06579e4.js}

@@ -1 +1 @@
-import{M as e,y as t,b as l}from"./app-a8c4854a.js";import{r as c}from"./table-79e3e776.js";import{m as n}from"./radiobutton-09bff425.js";import"./tslib.es6-1f85f553.js";function o(e){if(e>1e9)return(e/1e9).toFixed(2)+" GB";if(e>1e6)return(e/1e6).toFixed(2)+" MB";if(e>1e3)return(e/1e3).toFixed(2)+" KB";return e+" Bytes"}const u=new e;const r=[{label:"Case"},{label:"Project"},{label:"Samples"},{label:"File Size"}];const s=[{column:"Hugo_Symbol",selected:true},{column:"Entrez_Gene_Id",selected:true},{column:"Center",selected:true},{column:"NCBI_Build",selected:true},{column:"Chromosome",selected:true},{column:"Start_Position",selected:true},{column:"End_Position",selected:true},{column:"Strand",selected:true},{column:"Variant_Classification",selected:true},{column:"Variant_Type",selected:true},{column:"Reference_Allele",selected:true},{column:"Tumor_Seq_Allele1",selected:true},{column:"Tumor_Seq_Allele2",selected:true},{column:"dbSNP_RS",selected:true},{column:"dbSNP_Val_Status",selected:true},{column:"Tumor_Sample_Barcode",selected:true},{column:"Matched_Norm_Sample_Barcode",selected:true},{column:"Match_Norm_Seq_Allele1",selected:true},{column:"Match_Norm_Seq_Allele2",selected:true},{column:"Tumor_Validation_Allele1",selected:true},{column:"Tumor_Validation_Allele2",selected:true},{column:"Match_Norm_Validation_Allele1",selected:true},{column:"Match_Norm_Validation_Allele2",selected:true},{column:"Verification_Status",selected:true},{column:"Validation_Status",selected:true},{column:"Mutation_Status",selected:true},{column:"Sequencing_Phase",selected:true},{column:"Sequence_Source",selected:true},{column:"Validation_Method",selected:true},{column:"Score",selected:true},{column:"BAM_File",selected:true},{column:"Sequencer",selected:true},{column:"Tumor_Sample_UUID",selected:true},{column:"Matched_Norm_Sample_UUID",selected:true},{column:"HGVSc",selected:true},{column:"HGVSp",selected:true},{column:"HGVSp_Short",selected:true},{column:"Transcript_ID",selected:true},{column:"Exon_Number",selected:true},{column:"t_depth",selected:true},{column:"t_ref_count",selected:true},{column:"t_alt_count",selected:true},{column:"n_depth",selected:true},{column:"n_ref_count",selected:true},{column:"n_alt_count",selected:true},{column:"all_effects",selected:true},{column:"Allele",selected:true},{column:"Gene",selected:true},{column:"Feature",selected:true},{column:"Feature_type",selected:true},{column:"One_Consequence",selected:true},{column:"Consequence",selected:true},{column:"cDNA_position",selected:true},{column:"CDS_position",selected:true},{column:"Protein_position",selected:true},{column:"Amino_acids",selected:true},{column:"Codons",selected:true},{column:"Existing_variation",selected:true},{column:"DISTANCE",selected:true},{column:"TRANSCRIPT_STRAND",selected:true},{column:"SYMBOL",selected:true},{column:"SYMBOL_SOURCE",selected:true},{column:"HGNC_ID",selected:true},{column:"BIOTYPE",selected:true},{column:"CANONICAL",selected:true},{column:"CCDS",selected:true},{column:"ENSP",selected:true},{column:"SWISSPROT",selected:true},{column:"TREMBL",selected:true},{column:"UNIPARC",selected:true},{column:"UNIPROT_ISOFORM",selected:true},{column:"RefSeq",selected:true},{column:"MANE",selected:true},{column:"APPRIS",selected:true},{column:"FLAGS",selected:true},{column:"SIFT",selected:true},{column:"PolyPhen",selected:true},{column:"EXON",selected:true},{column:"INTRON",selected:true},{column:"DOMAINS",selected:true},{column:"1000G_AF",selected:true},{column:"1000G_AFR_AF",selected:true},{column:"1000G_AMR_AF",selected:true},{column:"1000G_EAS_AF",selected:true},{column:"1000G_EUR_AF",selected:true},{column:"1000G_SAS_AF",selected:true},{column:"ESP_AA_AF",selected:true},{column:"ESP_EA_AF",selected:true},{column:"gnomAD_AF",selected:true},{column:"gnomAD_AFR_AF",selected:true},{column:"gnomAD_AMR_AF",selected:true},{column:"gnomAD_ASJ_AF",selected:true},{column:"gnomAD_EAS_AF",selected:true},{column:"gnomAD_FIN_AF",selected:true},{column:"gnomAD_NFE_AF",selected:true},{column:"gnomAD_OTH_AF",selected:true},{column:"gnomAD_SAS_AF",selected:true},{column:"MAX_AF",selected:true},{column:"MAX_AF_POPS",selected:true},{column:"gnomAD_non_cancer_AF",selected:true},{column:"gnomAD_non_cancer_AFR_AF",selected:true},{column:"gnomAD_non_cancer_AMI_AF",selected:true},{column:"gnomAD_non_cancer_AMR_AF",selected:true},{column:"gnomAD_non_cancer_ASJ_AF",selected:true},{column:"gnomAD_non_cancer_EAS_AF",selected:true},{column:"gnomAD_non_cancer_FIN_AF",selected:true},{column:"gnomAD_non_cancer_MID_AF",selected:true},{column:"gnomAD_non_cancer_NFE_AF",selected:true},{column:"gnomAD_non_cancer_OTH_AF",selected:true},{column:"gnomAD_non_cancer_SAS_AF",selected:true},{column:"gnomAD_non_cancer_MAX_AF_adj",selected:true},{column:"gnomAD_non_cancer_MAX_AF_POPS_adj",selected:true},{column:"CLIN_SIG",selected:true},{column:"SOMATIC",selected:true},{column:"PUBMED",selected:true},{column:"TRANSCRIPTION_FACTORS",selected:true},{column:"MOTIF_NAME",selected:true},{column:"MOTIF_POS",selected:true},{column:"HIGH_INF_POS",selected:true},{column:"MOTIF_SCORE_CHANGE",selected:true},{column:"miRNA",selected:true},{column:"IMPACT",selected:true},{column:"PICK",selected:true},{column:"VARIANT_CLASS",selected:true},{column:"TSL",selected:true},{column:"HGVS_OFFSET",selected:true},{column:"PHENO",selected:true},{column:"GENE_PHENO",selected:true},{column:"CONTEXT",selected:true},{column:"case_id",selected:true},{column:"GDC_FILTER",selected:true},{column:"COSMIC",selected:true},{column:"hotspot",selected:true},{column:"tumor_bam_uuid",selected:true},{column:"normal_bam_uuid",selected:true},{column:"RNA_Support",selected:true},{column:"RNA_depth",selected:true},{column:"RNA_ref_count",selected:true},{column:"RNA_alt_count",selected:true},{column:"callers",selected:true}];async function d({holder:e,filter0:l,callbacks:c,debugmode:n=false}){try{{const e=new Set;for(const t of s){if(!t.column)throw".column missing from an element";if(e.has(t.column))throw"duplicate column: "+t.column;e.add(t.column)}}o({filter0:l})}catch(l){console.log(l);t(e,l.message||l)}async function o({filter0:t}){e.selectAll("*").remove();const l={errDiv:e.append("div"),controlDiv:e.append("div"),tableDiv:e.append("div"),opts:{filter0:t,experimentalStrategy:"WXS"}};a(l);await m(l);if(typeof c?.postRender=="function"){c.postRender(u)}}const u={update:o};return u}function a(e){const t=e.controlDiv.append("table");{const l=t.append("tr");l.append("td").style("opacity",.5).text("Access");l.append("td").text("Open")}{const o=t.append("tr");o.append("td").style("opacity",.5).text("Workflow Type");o.append("td").text("Aliquot Ensemble Somatic Variant Merging and Masking")}{const r=t.append("tr");r.append("td").style("opacity",.5).text("Experimental Strategy");const d=r.append("td");n({holder:d,options:[{label:"WXS",value:"WXS",checked:e.opts.experimentalStrategy=="WXS"},{label:"Targeted Sequencing",value:"Targeted Sequencing",checked:e.opts.experimentalStrategy=="Targeted Sequencing"}],styles:{display:"inline"},callback:async t=>{e.opts.experimentalStrategy=t;await m(e)}})}{const a=t.append("tr");a.append("td").style("opacity",.5).text("Output Columns");const i=a.append("td");const _=i.append("span").attr("class","sja_clbtext").on("click",(e=>{const t=[],l=[];for(const[e,c]of s.entries()){t.push([{value:c.column}]);if(c.selected)l.push(e)}c({div:u.clear().showunder(e.target).d,rows:t,columns:[{label:"Column Name"}],selectedRows:l,noButtonCallback:(e,t)=>{s[e].selected=t.checked;p()}})}));p();function p(){_.text(`${s.reduce(((e,t)=>e+(t.selected?1:0)),0)} of ${s.length} columns selected, click to change`)}}}async function m(e){e.tableDiv.selectAll("*").remove();const n=e.tableDiv.append("div").text("Loading...");const u={experimentalStrategy:e.opts.experimentalStrategy};if(e.opts.filter0)u.filter0=e.opts.filter0;const d=await l("gdc/maf",{body:u});if(d.error)throw d.error;n.remove();{const t=e.tableDiv.append("div").style("margin","20px");if(d.filesTotal>d.files.length){t.append("div").text(`Showing first ${d.files.length} files out of ${d.filesTotal} total.`)}else{t.append("div").text(`Showing ${d.files.length} files.`)}}const a=[];for(const e of d.files){const t=[{html:`<a href=https://portal.gdc.cancer.gov/cases/${e.case_uuid} target=_blank>${e.case_submitter_id}</a>`},{value:e.project_id},{html:e.sample_types.map((e=>'<span class="sja_mcdot" style="padding:1px 8px;background:#ddd;color:black;white-space:nowrap">'+e+"</span>")).join(" ")},{value:o(e.file_size),url:"https://portal.gdc.cancer.gov/files/"+e.id}];a.push(t)}c({rows:a,columns:r,resize:true,div:e.tableDiv.append("div"),selectAll:true,dataTestId:"sja_mafFileTable",buttons:[{text:"Aggregate selected MAF files and download",onChange:m,callback:i}]});function m(e,t){let l=0;for(const t of e)l+=d.files[t].file_size;if(l==0){t.innerHTML="No file selected";t.disabled=true;return}t.disabled=false;t.innerHTML=l<d.maxTotalSizeCompressed?`Download ${o(l)} compressed MAF data`:`Download ${o(d.maxTotalSizeCompressed)} compressed MAF data (${o(l)} selected)`}async function i(c,n){const o=s.filter((e=>e.selected)).map((e=>e.column));if(o.length==0){window.alert("No output columns selected.");return}const u=[];for(const e of c){u.push(d.files[e].id)}if(u.length==0)return;const r=n.innerHTML;n.innerHTML="Loading... 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o){N.append("line").attr("x2",30).attr("y1",r).attr("y2",r).attr("stroke",t.color);if($e){N.append("circle").attr("cx",15).attr("cy",r).attr("r",8).attr("fill",t.color).attr("fill-opacity",.1)}N.append("text").text(t.gene).attr("dominant-baseline","central").attr("font-size",a).attr("x",30+10).attr("y",r).attr("fill",t.color).style("cursor","default").on("mouseover",(e=>{e.target.setAttribute("font-weight","bold");I.filter((e=>e.mutationname==t.mutationname)).attr("stroke-width",3)})).on("mouseout",(e=>{e.target.setAttribute("font-weight","normal");I.filter((e=>e.mutationname==t.mutationname)).attr("stroke-width",1)}));r+=a+10}};W(C,U);n.append("div").style("text-align","right").append("button").text("SVG").on("click",(()=>{y(l.node(),"maf-timeline")}))}function cn(t,e,n,r,a,o,i,u){n.selectAll("*").remove();const c=n.append("table");for(const n of t){const s=c.append("tr");const l=s.append("td");l.text(n.gene).style("color",n.color);const f=s.append("td");const p=f.append("input").attr("type","checkbox").style("zoom","150%").property("checked",n.show);n.checkbox=p;p.on("change",(a=>{n.show=a.target.checked;un(t,e,r)}));f.append("button").style("margin-left","5px").text("Only").on("click",(()=>{for(const e of t){e.show=false;e.checkbox.property("checked",false)}n.show=true;n.checkbox.property("checked",true);un(t,e,r)}));let d=Math.random();const g=s.append("td");const h=g.append("input").attr("type","checkbox").attr("id",d).on("change",(t=>T(1,t.target)));g.append("label").html("&nbsp;shared").attr("for",d);d=Math.random();const m=s.append("td");const v=m.append("input").attr("type","checkbox").attr("id",d).on("change",(t=>T(2,t.target)));m.append("label").html("&nbsp;rising").attr("for",d);d=Math.random();const y=s.append("td");const x=y.append("input").attr("type","checkbox").attr("id",d).on("change",(t=>T(3,t.target)));y.append("label").html("&nbsp;falling").attr("for",d);d=Math.random();const b=s.append("td");const M=b.append("input").attr("type","checkbox").attr("id",d).on("change",(t=>T(4,t.target)));b.append("label").html("&nbsp;R-only").attr("for",d);if(n.subidx==1)h.property("checked",true);if(n.subidx==2)v.property("checked",true);if(n.subidx==3)x.property("checked",true);if(n.subidx==4)M.property("checked",true);const T=(e,r)=>{if(!r.checked){n.subidx=-1}else{n.subidx=e;if(e==1){v.property("checked",false);x.property("checked",false);M.property("checked",false)}else if(e==2){h.property("checked",false);x.property("checked",false);M.property("checked",false)}else if(e==3){h.property("checked",false);v.property("checked",false);M.property("checked",false)}else{h.property("checked",false);v.property("checked",false);x.property("checked",false)}}on(t,a,o,i,u)}}}export{en as default};

package/dist/matrix-00bb50ff.js

@@ -0,0 +1 @@
+import{V as t,P as e,F as s,h as i,z as o,B as n,O as r}from"./app-b369b169.js";import{setMatrixDom as a}from"./matrix.dom-4e10bbe9.js";import{setInteractivity as l}from"./matrix.interactivity-84169b43.js";import{setRenderers as p}from"./matrix.renderers-78010275.js";import{MatrixCluster as d}from"./matrix.cluster-783ceab0.js";import{MatrixControls as c}from"./matrix.controls-7b2a6f95.js";import{s as m}from"./svg.legend-8d490df2.js";import{m as h}from"./matrix.data-dac4f1b7.js";import{m as g}from"./matrix.layout-dd5a44fd.js";import{m as u}from"./matrix.serieses-9b4fd744.js";import{m as f}from"./matrix.legend-ac6d45e6.js";import{m as b}from"./matrix.groups-b9fca14a.js";import{setComputedConfig as y}from"./matrix.config-6ce74dfe.js";export{getPlotConfig}from"./matrix.config-6ce74dfe.js";import{l as v}from"./termsetting-33ea66f1.js";import"./table-29d5a973.js";import"./tslib.es6-c3c2d88f.js";import"./pointer-c7475677.js";import"./controls.config-28d6d6a8.js";import"path";import"./matrix.sorterUi-9bf7e6f9.js";import"./radiobutton-09bff425.js";import"./checkbox-96437f4d.js";import"./recover-49e09de0.js";import"./FilterRxComp-701a1480.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./rehydrateFilter-12d118cb.js";import"./axis-747c801e.js";import"./matrix.cells-914dd0c6.js";import"./legacy-d3-polyfill-bdb2d792.js";import"./filter-b3d3964e.js";import"./matrix.sort-014d798d.js";let x;function j(t,e){const s=structuredClone(t);if(!x)x={CatTWValues:k,CatTWPredefinedGS:k,CatTWCustomGS:k,NumTWRegularBin:k,NumTWCustomBin:k,NumTWCont:C};const i={vocabApi:e.vocabApi,addons:x};for(const t of s){const e=[];for(const s of t.lst){e.push(s.type in i.addons?v.init(s,i):s)}t.lst=e}return s}const k={setCellProps:{value:function(t,e,s,i,o,n,r,a,l,p,d){var c,m,h;const g=this.getTw();const u=e.key;const f=g.term.values||{};t.label="label"in e?e.label:((c=f[u])===null||c===void 0?void 0:c.label)?f[u].label:u;t.fill=e.color||((m=f[e.key])===null||m===void 0?void 0:m.color);t.order=o.ref.bins?o.ref.bins.findIndex((t=>t.name==u)):0;t.x=t.totalIndex*l+t.grpIndex*i.colgspace;t.y=a*d;const b=((h=g.legend)===null||h===void 0?void 0:h.group)||g.$id;return{ref:o.ref,group:b,value:u,entry:{key:u,label:t.label,fill:t.fill}}}}};const C={setCellProps:{value:function(e,s,i,o,n,r,a,l,p,d,c){var m,h,g,u,f;const b=this.getTw();const y=s.key;const v=b.term.values||{};e.label="label"in s?s.label:((m=v[y])===null||m===void 0?void 0:m.label)?v[y].label:y;e.fill=s.color||((h=v[s.key])===null||h===void 0?void 0:h.color);if(!b.settings)b.settings={};if(!b.settings.barh)b.settings.barh=o.barh;if(!("gap"in b.settings))b.settings.gap=4;const x=(g=b.term.values)===null||g===void 0?void 0:g[e.key];if(x===null||x===void 0?void 0:x.uncomputable){e.x=e.totalIndex*p+e.grpIndex*o.colgspace;e.y=l*c;e.height=b.settings.barh;e.fill="transparent";e.label=x.label;const t=((u=b.legend)===null||u===void 0?void 0:u.group)||b.$id;return{ref:n.ref,group:t,value:x.label||x.key,entry:{key:y,label:e.label,fill:e.fill}}}e.fill="#555";if(o.transpose){e.height=n.scale(e.key);e.x=b.settings.gap}else{const i=e.term.valueConversion;let r=i?e.key*i.scaleFactor:e.key;if(this.q.convert2ZScore){r=(r-n.mean)/n.std;e.fill=r>0?"#FF6666":"#6666FF";e.zscoreLabel=` (z-score: ${r.toFixed(2)})`}e.label="label"in s?s.label:((f=v[y])===null||f===void 0?void 0:f.label)?v[y].label:this.term.unit?`${e.key.toFixed(2)} ${this.term.unit}`:e.key.toFixed(2);e.height=r>=0?n.scales.pos(r):n.scales.neg(r);e.x=e.totalIndex*p+e.grpIndex*o.colgspace;e.y=r>=0?n.counts.posMaxHt+n.tw.settings.gap-e.height:n.counts.posMaxHt+n.tw.settings.gap;e.convertedValueLabel=!i?"":t(e.key,i.fromUnit,i.toUnit,i.scaleFactor)}}}};class T{constructor(t){this.type="matrix";this.holderTitle="Sample Matrix";this.optionalFeatures=JSON.parse(sessionStorage.getItem("optionalFeatures")||`{}`)?.matrix||[];l(this);p(this)}async init(t){const s=this.opts;if(s.reactsTo)this.reactsTo=s.reactsTo;this.setDom=a;this.setDom(s);this.config=t.plots.find((t=>t.id===this.id));this.settings=Object.assign({},this.config.settings.matrix);this.computed={};if(this.dom.header)this.dom.header.html(this.holderTitle);this.setControls(t);this.clusterRenderer=new d({holder:this.dom.cluster,app:this.app,parent:this});this.legendRenderer=m({holder:this.dom.legendG,rectFillFxn:t=>t.color,iconStroke:"#aaa",handlers:{legend:{click:this.legendClick}},settings:{isExcludedAttr:"isExcluded"},note:"CLICK A ROW LABEL OR ITEM TO APPLY FILTERING"});this.customTipApi=this.dom.tip.getCustomApi({d:this.dom.menubody,clear:t=>{if(t?.target)this.dom.menutop.style("display","none");this.dom.menubody.selectAll("*").remove();return this.customTipApi},show:()=>{this.dom.menubody.style("display","block")},hide:()=>{}});this.setPill(t);const i={mclass:o,dt2label:n,morigin:r};for(const s in i){const o=i[s];this[s]=e({},o,t.termdbConfig[s]||{},t.termdbConfig.matrix?.[s]||{})}}setControls(t){this.controlsRenderer=new c({app:this.app,id:this.id,parent:this,holder:this.dom.controls,getSvg:()=>this.dom.svg.node()},t)}getState(t){const e=t.plots.find((t=>t.id===this.id));const s=t.termfilter.filter0;this.prevFilter0=this.state?.filter0;return{isVisible:true,config:e,filter:t.termfilter.filter,filter0:s,hasVerifiedToken:this.app.vocabApi.hasVerifiedToken(),tokenVerificationMessage:this.app.vocabApi.tokenVerificationMessage,vocab:t.vocab,termdbConfig:t.termdbConfig,clusterMethod:e.settings.hierCluster?.clusterMethod,distanceMethod:e.settings.hierCluster?.distanceMethod,clusterSamples:e.settings.hierCluster?.clusterSamples,nav:t.nav}}async main(){try{this.config=structuredClone(this.state.config);if(this.mayRequireToken())return;this.termGroups=j(this.config.termgroups,this.app);const t=this.settings.transpose;Object.assign(this.settings,structuredClone(this.config.settings),this.controlsRenderer.getSettings());this.dom.loadingDiv.selectAll("*").remove();this.dom.loadingDiv.html("").style("display","").style("position","relative").style("left","45%");this.dom.svg.style("opacity",.1).style("pointer-events","none");delete this.clickedChildren;try{y(this.config);const t=[];if(this.setHierClusterData)t.push(this.setHierClusterData());t.push(this.setData());this.dom.loadingDiv.html("Processing data ...");await Promise.all(t);this.applyLegendValueFilter();if(this.combineData)this.combineData();this.app.save({type:"plot_edit",id:this.id,config:this.config})}catch(t){if(t=="no data"){this.showNoMatchingDataMessage();return}else if(t=="stale sequenceId"||t.name=="AbortError"){return}else{this.dom.svg.style("display","none");throw t}}this.dom.loadingDiv.html("Updating ...").style("display","");this.termOrder=this.getTermOrder(this.data);this.sampleGroups=this.getSampleGroups(this.hierClusterSamples||this.data);this.sampleOrder=this.getSampleOrder(this.data);if(!this.sampleOrder?.length&&!this.config.legendGrpFilter?.lst.length&&!this.config.legendValueFilter?.lst.length){this.showNoMatchingDataMessage();this.controlsRenderer.main();return}this.setLayout();if(this.setHierColorScale)this.setHierColorScale(this.hierClusterData.clustering);this.serieses=this.getSerieses(this.data);this.dom.loadingDiv.html("Rendering ...");if(this.plotDendrogramHclust)this.plotDendrogramHclust();this.render();this.mayDisplayCohortMessage();this.dom.svg.style("display","").style("opacity",1).style("pointer-events","");const[e,s]=!this.settings.matrix.transpose?["sampleGrps","termGrps"]:["termGrps","sampleGrps"];const i=this.dimensions;this.clusterRenderer.main({settings:this.settings.matrix,xGrps:this[e],yGrps:this[s],dimensions:i});this.legendRenderer(this.legendData,{settings:Object.assign({},this.settings.legend,{svgw:Math.max(400,i.mainw+i.xOffset-this.settings.matrix.margin.right),svgh:i.mainh+i.yOffset,dimensions:i,padleft:this.settings.legend.padleft})});await this.adjustSvgDimensions(t);this.controlsRenderer.main()}catch(t){const e=this.app.vocabApi.tokenVerificationMessage;this.mayRequireToken(e);if(!e){this.app.tip.hide();this.dom.loadingDiv.style("display","none");throw t}}this.resetInteractions()}showNoMatchingDataMessage(){this.forcedSampleCount=0;this.dom.svg.style("opacity",.001).style("display","none");if(this.termOrder&&this.dimensions)this.controlsRenderer.main({sampleCount:0});this.dom.loadingDiv.html("");const t=this.dom.loadingDiv.append("div").style("display","inline-block").style("text-align","center").style("position","relative").style("left","-150px");t.append("div").style("margin","5px 10px").html("No matching cohort sample data for the current gene list.");if(this.settings.matrix.showHints?.includes("genesetEdit")){const e=t.append("div").style("margin","5px 10px");e.append("span").html("You may change the selected cohort,");if(this.config.legendGrpFilter?.lst.length||this.config.legendValueFilter?.lst.length){e.append("br");e.append("span").html("show hidden ");e.append("span").html("CNV").style("cursor","pointer").style("text-decoration","underline").on("click",(()=>{this.controlsRenderer.btns.filter((t=>t.label=="CNV"))?.node().click()}));e.append("span").html(" or ");e.append("span").style("cursor","pointer").style("text-decoration","underline").html("Mutation").on("click",(()=>{this.controlsRenderer.btns.filter((t=>t.label=="Mutation"))?.node().click()}));e.append("span").html(" data,")}e.append("br");e.append("span").html("or edit the gene list from the ");e.append("span").style("cursor","pointer").style("text-decoration","underline").html("Gene Set Edit Group menu.").on("click",(()=>{this.controlsRenderer.btns.filter((t=>t.label=="Genes"))?.node().click();const t=setInterval((()=>{const e=this.app.tip.d.selectAll("button").filter((function(){return this.innerHTML=="Edit Group"})).node();if(e){e.click();clearInterval(t)}}),100)}))}this.dom.svg.style("display","none")}mayDisplayCohortMessage(){const t=!this.prevFilter0||s(this.state.filter0,this.prevFilter0)?"":"The gene list is persisted across cohorts.";if(t){this.dom.loadingDiv.html("");const e=this.dom.loadingDiv.append("div").style("display","inline-block").style("text-align","center").style("position","relative").style("left","-150px");e.append("div").html(t);if(this.settings.matrix.showHints?.includes("genesetEdit")){const t=e.append("div");t.append("span").html(" You may edit the gene list from the ");t.append("span").style("cursor","pointer").style("text-decoration","underline").html("Gene Set Edit Group menu.").on("click",(()=>{this.controlsRenderer.btns.filter((t=>t.label=="Genes"))?.node().click();const t=setInterval((()=>{const e=this.app.tip.d.selectAll("button").filter((function(){return this.innerHTML=="Edit Group"})).node();if(e){e.click();clearInterval(t)}}),100)}))}}this.dom.loadingDiv.style("display",t?"":"none")}sampleKey(t){return t.row.sample}sampleLabel(t){return t.label||t.row._ref_.label||""}sampleGrpKey(t){return t.grp.name}sampleGrpLabel(t){return t.grp.label||t.grp.name||""}termKey(t){return t.tw.$id}termLabel(t){return t.label}termGrpKey(t){return t.grp.name}termGrpLabel(t){return t.grp.label||t.grp.name||[{text:"⋮",dx:3,cls:"sjpp-exclude-svg-download"}]}}for(const t of[h,b,g,u,f]){for(const e in t){T.prototype[e]=t[e]}}const w=i(T);const D=w;function G(t,e){e.dom.tip.clear();const s=t.append("div");if(e.state.termdbConfig.matrixplots){for(const t of e.state.termdbConfig.matrixplots){s.append("div").attr("class","sja_menuoption sja_sharp_border").text(t.name).on("click",(async()=>{e.dom.tip.hide();const s=await e.app.vocabApi.getMatrixByName(t.name);e.app.dispatch({type:"plot_create",config:s})}))}}s.append("div").datum({label:"Term tree & search",clickTo:e.showTree_selectlst,chartType:"matrix",usecase:{target:"matrix",detail:"termgroups"},processSelection:t=>[{name:"",lst:t.map((t=>({term:t})))}]}).attr("class","sja_menuoption sja_sharp_border").text((t=>t.label)).on("click",((t,s)=>e.showTree_selectlst(s)));s.append("div").datum({label:"Text input",chartType:"matrix",clickTo:S,usecase:{target:"matrix",detail:"termgroups"},placeholder:"term\tgroup",processInput:async t=>{const s=t.split("\n").map((t=>t.split("\t")));const i=s.map((t=>t[0])).filter((t=>!!t));const o=await e.app.vocabApi.getTermTypes(i);const n={};for(const[t,e]of s){if(!(t in o))continue;if(!(e in n))n[e]={name:e,lst:[]};n[e].lst.push({term:o[t]})}return Object.values(n)}}).attr("class","sja_menuoption sja_sharp_border").text((t=>t.label)).on("click",((t,s)=>S(s,e)))}function S(t,e){e.dom.tip.clear();e.dom.submenu=e.dom.tip.d.append("div").style("text-align","center");e.dom.submenu.append("span").html(t.label);e.dom.submenu.append("button").style("margin","0 5px").html("Submit").on("click",(async()=>{const i=await t.processInput(s.property("value"));e.dom.tip.hide();const o={type:"plot_create",id:I(),config:{chartType:t.usecase.target,[t.usecase.detail]:i}};e.app.dispatch(o)}));const s=e.dom.submenu.append("div").style("text-align","left").append("textarea").attr("placeholder",t.placeholder).style("width","300px").style("height","300px").style("margin","5px").style("padding","5px").on("keydown",(t=>{const e=t.keyCode||t.which;if(e==9){t.preventDefault();const e=t.target;const s=e.selectionStart;e.value=e.value.substring(0,e.selectionStart)+"\t"+e.value.substring(e.selectionEnd);e.selectionEnd=s+1}}))}const F="_CHART_AUTOID_";let M=Date.now();function I(){return F+M++}export{T as Matrix,D as componentInit,G as makeChartBtnMenu,w as matrixInit};

package/dist/matrix.cells-914dd0c6.js

@@ -0,0 +1 @@
+import{ak as e,at as l,ap as t,R as s,as as a,bR as n,V as r}from"./app-b369b169.js";import{T as o}from"./termsetting-33ea66f1.js";import"./tslib.es6-c3c2d88f.js";import"path";function i(e,l,t,s,a,n,o,i,c,g,d,u){const f=t.key;const p=l.term.values||{};e.label="label"in t?t.label:p[f]?.label?p[f].label:f;e.fill=t.color||p[t.key]?.color;e.order=n.ref.bins?n.ref.bins.findIndex((e=>e.name==f)):0;if(l.q?.mode=="continuous"){if(!l.settings)l.settings={};if(!l.settings.barh)l.settings.barh=a.barh;if(!("gap"in l.settings))l.settings.gap=4;const s=l.term.values?.[e.key];if(s?.uncomputable){e.x=e.totalIndex*g+e.grpIndex*a.colgspace;e.y=c*u;e.height=l.settings.barh;e.fill="transparent";l.legend?.group||l.$id;return}e.fill="#555";if(a.transpose){e.height=n.scale(e.key);e.x=l.settings.gap}else{const s=e.term.valueConversion;let o=s?e.key*s.scaleFactor:e.key;if(l.q.convert2ZScore){o=(o-n.mean)/n.std;e.fill=o>0?"#FF6666":"#6666FF";e.zscoreLabel=` (z-score: ${o.toFixed(2)})`}e.label="label"in t?t.label:p[f]?.label?p[f].label:l.term.unit?`${e.key.toFixed(2)} ${l.term.unit}`:e.key.toFixed(2);e.height=o>=0?n.scales.pos(o):n.scales.neg(o);e.x=e.totalIndex*g+e.grpIndex*a.colgspace;e.y=o>=0?n.counts.posMaxHt+n.tw.settings.gap-e.height:n.counts.posMaxHt+n.tw.settings.gap;e.convertedValueLabel=!s?"":r(e.key,s.fromUnit,s.toUnit,s.scaleFactor)}}else{e.x=e.totalIndex*g+e.grpIndex*a.colgspace;e.y=c*u;const t=l.legend?.group||l.$id;return{ref:n.ref,group:t,value:f,entry:{key:f,label:e.label,fill:e.fill}}}}function c(e,l,t,s,a,n,o,i,c,g,d,u){const f=l.q?.mode=="continuous"?t.value:t.key;e.key=f;e.label=l.q?.mode=="continuous"?l.term.unit?`${f} ${l.term.unit}`:f:l.term.values?.[f].label?l.term.values?.[f].label:"Exit code: "+f;e.fill=f==1?"#a1a3a6":"#a3c88b";e.order=0;if(l.q?.mode=="continuous"){if(!l.settings)l.settings={};if(!l.settings.barh)l.settings.barh=a.barh;if(!("gap"in l.settings))l.settings.gap=4;e.exitCodeKey=l.term.values?.[t.key].label||"Exit code: "+t.key;e.fill=t.key==1?"#a1a3a6":"#a3c88b";if(a.transpose){e.height=n.scale(e.key);e.x=l.settings.gap}else{const t=e.term.valueConversion;let s=t?e.key*t.scaleFactor:e.key;if(l.q.convert2ZScore){s=(s-n.mean)/n.std;e.zscoreLabel=` (z-score: ${s.toFixed(2)})`}e.label=l.term.unit?`${e.key.toFixed(2)} ${l.term.unit}`:e.key.toFixed(2);e.height=s>=0?n.scales.pos(s):n.scales.neg(s);e.x=e.totalIndex*g+e.grpIndex*a.colgspace;e.y=s>=0?n.counts.posMaxHt+n.tw.settings.gap-e.height:n.counts.posMaxHt+n.tw.settings.gap;e.convertedValueLabel=!t?"":r(e.key,t.fromUnit,t.toUnit,t.scaleFactor)}}else{const s=e.term.valueConversion;e.timeToEventKey=s?r(t.value,s.fromUnit,s.toUnit,s.scaleFactor):t.value.toFixed(2);e.x=e.totalIndex*g+e.grpIndex*a.colgspace;e.y=c*u;const o=l.legend?.group||l.$id;return{ref:n.ref,group:o,value:f,entry:{key:f,label:e.label,fill:e.fill}}}}function g(e,l,t,s,a,n,r,o,i,c,g,d){const u=l.term.values||{};const f=t.key;e.label="label"in t?t.label:u[f]?.label?u[f].label:f;e.fill=t.color||u[f]?.color;e.x=e.totalIndex*c+e.grpIndex*a.colgspace;e.y=i*d;const p=l.legend?.group||l.$id;return{ref:n.ref,group:p,value:t.key,entry:{key:f,label:e.label,fill:e.fill}}}function d(n,r,o,i,c,g,d,u,f,p,b,x){const h=o.renderedValues||o.filteredValues||o.values||[o.value];const y=r.q?.values&&r.q?.values[i.class]?.color;if(r.q?.type=="predefined-groupset"||r.q?.type=="custom-groupset"){n.label=i;n.fill=["Mutated","Protein-changing","Truncating"].includes(i)?"#FF0000":["Wildtype","Rest"].includes(o.key)?"#0000FF":o.key=="Not tested"?"#00FF00":"#000000";n.value={value:i,dt:r.q.dt,origin:r.q.origin};n.x=n.totalIndex*p+n.grpIndex*c.colgspace;n.y=f*x;const e=r.legend?.group||r.q.origin?`${r.q.origin[0].toUpperCase()+r.q.origin.slice(1)} ${d.dt2label[r.q.dt]}`:d.dt2label[r.q.dt];return{ref:g.ref,group:e,value:o.key,order:-2,entry:{key:o.key,label:n.label,fill:n.fill,dt:r.q.dt,origin:r.q.origin}}}else{n.label=i.label||d.mclass[i.class].label;n.fill=d.getValueColor?.(i.value)||y||i.color||d.mclass[i.class]?.color;n.class=i.class;n.value=i;const o=d.dimensions.colw;if(c.cellEncoding==""){n.height=c.rowh/h.length;n.width=o;n.x=n.totalIndex*p+n.grpIndex*c.colgspace;n.y=f*x}else if(i.dt==e||i.dt==l){if(c.cellEncoding=="single"){n.height=c.rowh;n.width=o;n.x=n.totalIndex*p+n.grpIndex*c.colgspace;n.y=0}else{const e=3;n.height=c.rowh/e;n.width=o;n.x=n.totalIndex*p+n.grpIndex*c.colgspace;n.y=f*.33333}}else if(i.dt==t||i.dt==s){n.height=c.rowh;n.width=o;n.x=n.totalIndex*p+n.grpIndex*c.colgspace;n.y=0}else{throw`cannot set cell props for dt='${i.dt}'`}if(i.class=="Blank"||i.class=="WT"){n.label=`${d.dt2label[i.dt]} ${n.label}`}const u=d.state.termdbConfig.assayAvailability?.byDt;const b=i.class=="CNV_loss"?-2:i.class.startsWith("CNV_")?-1:0;if(i.dt==t){if(g.scales&&i.class.startsWith("CNV_")){g.scales.max;const{maxLoss:e,maxGain:l,minLoss:t,minGain:s}=g.scales;i.scaledValue=i.value<0?i.value/t:i.value/l;n.fill=i.value<0?g.scales.loss(i.scaledValue):g.scales.gain(i.scaledValue);return{ref:g.ref,group:"CNV",value:i.class,order:-1,entry:{key:i.class,label:n.label,scale:i.class=="CNV_loss"?g.scales.loss:g.scales.gain,domain:i.class=="CNV_loss"?[0,-t]:[0,l],minLabel:0,maxLabel:i.class=="CNV_loss"?t:l,order:b,dt:i.dt,origin:i.origin}}}else{const e="CNV";return{ref:g.ref,group:e,value:i.class,order:-1,entry:{key:i.class,label:n.label,fill:n.fill,order:b,dt:i.dt,origin:i.origin}}}}else if(i.dt==l&&u?.[l]){const e="Fusion RNA";return{ref:g.ref,group:e,value:i.class,order:-1,entry:{key:i.class,label:n.label,fill:n.fill,order:b,dt:i.dt,origin:i.origin}}}else if(i.dt==a&&u?.[a]){const e="Structural Variation";return{ref:g.ref,group:e,value:i.class,order:-1,entry:{key:i.class,label:n.label,fill:n.fill,order:b,dt:i.dt,origin:i.origin}}}else if(i.dt==s){return{ref:g.ref,group:d.config.settings.hierCluster?.termGroupName||"Gene Expression",value:i.class,order:-1,entry:{key:i.class,label:"",scale:d.geneExpValues.scale,domain:[0,.5,1],minLabel:d.geneExpValues.min,maxLabel:d.geneExpValues.max,order:b,dt:i.dt,origin:i.origin}}}else{const e=d.settings.matrix.controlLabels;const l=r.legend?.group||(i.origin?`${i.origin[0].toUpperCase()+i.origin.slice(1)} ${e.Mutations}`:e.Mutations);return{ref:g.ref,group:l,value:i.class,order:-2,entry:{key:i.class,label:n.label,fill:n.fill,order:b,dt:i.dt,origin:i.origin}}}}}function u(e,l,t,s,a,r,o,i,c,g,d,u){t.renderedValues||t.filteredValues||t.values||[t.value];e.label=s.value;e.fill=o.getValueColor?.(s.value);e.value=s;const f=o.dimensions.colw;e.height=a.clusterRowh;e.width=f;e.x=e.totalIndex*g+e.grpIndex*a.colgspace;e.y=c*u;const p=o.config.settings.hierCluster?.termGroupName?o.config.settings.hierCluster?.termGroupName:l.term.type=="geneExpression"?"Expression":l.term.type=="metaboliteIntensity"?"Intensity":"Heatmap color scale";return{ref:r.ref,group:p,order:-1,entry:{label:"",scale:o.hierClusterValues.scale,domain:n[o.settings.hierCluster.colorScale].domain,minLabel:o.hierClusterValues.min,maxLabel:o.hierClusterValues.max,order:0,dt:s.dt}}}function f(e,l,t){const s=Object.assign({},e);s.fill=l.cellbg;s.height=l.rowh;s.width=t.colw;s.x=s.totalIndex*t.dx+s.grpIndex*l.colgspace;s.y=0;return s}const p={categorical:g,condition:g,integer:i,float:i,survival:c,geneVariant:d,hierCluster:u,[o.GENE_EXPRESSION]:i,[o.METABOLITE_INTENSITY]:i};const b={geneVariant:x,integer:h,float:h,categorical:y,condition:y,survival:h,[o.GENE_EXPRESSION]:h,[o.METABOLITE_INTENSITY]:h};function x(e,l,s,a){if(e.find((e=>e.value.dt==t)))return;const n=Object.assign({},l);n.fill=s.cellbg;n.height=s.rowh;n.width=a.colw;n.x=n.totalIndex*a.dx+n.grpIndex*s.colgspace;n.y=0;return n}function h(e,l,t,s){const a=l.tw.q;if(a.mode!="continuous"){if(e.length)return;y(e,l,t,s)}else{if(a?.mode!="continuous")return;const e=l.tw.settings;const n=e?e.barh+2*e.gap:t.rowh;if(l.height>=n)return;const r=Object.assign({},l);r.fill=t.cellbg;r.height=n||t.rowh;r.width=s.colw;r.x=r.totalIndex*s.dx+r.grpIndex*t.colgspace;r.y=0;return r}}function y(e,l,t,s){if(e.length)return;const a=Object.assign({},l);a.fill=t.cellbg;a.height=t.rowh;a.width=s.colw;a.x=a.totalIndex*s.dx+a.grpIndex*t.colgspace;a.y=0;return a}export{f as getEmptyCell,b as maySetEmptyCell,p as setCellProps,d as setGeneVariantCellProps,u as setHierClusterCellProps};

package/dist/{matrix.cluster-168bc96b.js → matrix.cluster-783ceab0.js}

@@ -1 +1 @@
-import{d as t}from"./app-a8c4854a.js";class s{constructor(t){this.parent=t.parent;t.svg;this.patternId=`sjpp-matrix-grid-pattern-${this.parent.id}`;this.patternIdSuffix=0;this.dom={holder:t.holder,clusterbg:t.holder.insert("g","g").attr("class","sjpp-matrix-clusterbg").on("mouseover",this.mouseout),outlines:t.holder.append("g").attr("class","sjpp-matrix-clusteroutlines")};e(this)}main(t){this.currData=t;this.settings=t.settings;this.xGrps=t.xGrps;this.xGrpKey=!this.settings.transpose?"samplegrp":"termgrp";this.yGrps=t.yGrps;this.yGrpKey=!this.settings.transpose?"termgrp":"samplegrp";this.clusters=this.processData();this.render(this.clusters)}processData(){const t=this.settings;const s=this.currData.dimensions;const e=[];this.totalWidth=t.zoomLevel==1?-4:0;for(const r of this.xGrps){const n=s.dx;const o=r.prevGrpTotalIndex*n+t.colgspace*r.grpIndex+r.totalHtAdjustments;const a=n*(r.processedLst||r.grp.lst).length+r.grpTotals.htAdjustment-t.colspace;this.totalWidth+=a+2*Math.max(1,t.colspace);for(const n of this.yGrps){const i=n.prevGrpTotalIndex*s.dy+n.grpIndex*t.rowgspace+n.totalHtAdjustments;const c=s.dy*(n.processedLst||n.grp.lst).length+n.grpTotals.htAdjustment-t.rowspace;const p=1;const l=1;e.push({xg:r,yg:n,x:o-p,y:i-l,width:a+2*p,height:c+2*l})}}return e}}function e(s){s.render=function(t){const r=s.settings;const a=s.currData.dimensions;const i=s.dom.outlines.attr("transform")?r.duration:0;s.translateElems(0,r,a,i);if(r.prevShowGrid!=r.showGrid){s.dom.outlines.selectAll("*").remove()}if(r.showGrid!="pattern"){e(t)}else{const e=s.dom.outlines.selectAll("g").data(t,(t=>t.xg.grp.name+";;"+t.yg.grp.name));e.exit().remove();e.each(o);e.enter().append("g").each(n)}r.prevShowGrid=r.showGrid;s.parent.delayedMouseoutHandler()};s.translateElems=function(t,e,r,n=0){const o=!n?s.dom.outlines:s.dom.outlines.transition().duration(n);o.attr("transform",`translate(${r.xOffset+r.seriesXoffset+t},${r.yOffset})`)};function e(t,e,n){const o=s.dom.outlines.selectAll("rect").data(t,(t=>t.xg.grp.name+";;"+t.yg.grp.name));o.exit().remove();o.each(r);o.enter().append("rect").each(r)}function r(e){const r=s.settings;t(this).transition().duration("x"in this?r.duration:0).attr("x",e.x).attr("y",e.y).attr("width",e.width).attr("height",e.height).attr("shape-rendering","crispEdges").attr("fill",!r.showGrid?r.cellbg:r.gridStroke).attr("stroke",r.outlineStroke).attr("stroke-width",1)}function n(e){const r=t(this);const n=r.append("pattern").attr("id",`${s.patternId}-${s.patternIdSuffix++}`).attr("patternUnits","userSpaceOnUse").attr("patternUnits","userSpaceOnUse");n.append("line");n.append("line");r.append("rect");r.append("rect");o.call(this,e)}function o(e){const r=s.settings;const n=s.parent.dimensions;const o=t(this);const c=a(o,r,n);const p=o.node().querySelectorAll("rect");i.call(p[0],e,Object.assign({},r,{fill:r.cellbg}));const l=r.showGrid?`url(#${c})`:"none";i.call(p[1],e,Object.assign({},r,{fill:l,stroke:r.gridStroke}))}function a(s,e,r,n){const o=s.select("pattern").attr("x",0).attr("y",0).attr("width",r.colw+e.colspace).attr("height",e.rowh+e.rowspace);const a=.5*e.rowspace;const i=e.rowh+a;const[c,p]=o.node().querySelectorAll("line");t(c).attr("x1",0).attr("y1",i).attr("x2",r.colw+e.colspace).attr("y2",i).attr("stroke",e.gridStroke).attr("stroke-width",e.rowspace);const l=.5*e.colspace;const d=r.colw+l;t(p).attr("x1",d).attr("y1",0).attr("x2",d).attr("y2",e.rowh).attr("stroke",e.gridStroke).attr("stroke-width",e.colspace);return o.attr("id")}function i(s,e){const r=t(this);r.transition().duration(r.attr("x")?e.duration:0).attr("x",s.x).attr("y",s.y).attr("width",s.width).attr("height",s.height).attr("shape-rendering","crispEdges").attr("fill",e.fill||"none").attr("stroke",e.stroke||"none")}}export{s as MatrixCluster};
+import{d as t}from"./app-b369b169.js";class s{constructor(t){this.parent=t.parent;t.svg;this.patternId=`sjpp-matrix-grid-pattern-${this.parent.id}`;this.patternIdSuffix=0;this.dom={holder:t.holder,clusterbg:t.holder.insert("g","g").attr("class","sjpp-matrix-clusterbg").on("mouseover",this.mouseout),outlines:t.holder.append("g").attr("class","sjpp-matrix-clusteroutlines")};e(this)}main(t){this.currData=t;this.settings=t.settings;this.xGrps=t.xGrps;this.xGrpKey=!this.settings.transpose?"samplegrp":"termgrp";this.yGrps=t.yGrps;this.yGrpKey=!this.settings.transpose?"termgrp":"samplegrp";this.clusters=this.processData();this.render(this.clusters)}processData(){const t=this.settings;const s=this.currData.dimensions;const e=[];this.totalWidth=t.zoomLevel==1?-4:0;for(const r of this.xGrps){const n=s.dx;const o=r.prevGrpTotalIndex*n+t.colgspace*r.grpIndex+r.totalHtAdjustments;const a=n*(r.processedLst||r.grp.lst).length+r.grpTotals.htAdjustment-t.colspace;this.totalWidth+=a+2*Math.max(1,t.colspace);for(const n of this.yGrps){const i=n.prevGrpTotalIndex*s.dy+n.grpIndex*t.rowgspace+n.totalHtAdjustments;const c=s.dy*(n.processedLst||n.grp.lst).length+n.grpTotals.htAdjustment-t.rowspace;const p=1;const l=1;e.push({xg:r,yg:n,x:o-p,y:i-l,width:a+2*p,height:c+2*l})}}return e}}function e(s){s.render=function(t){const r=s.settings;const a=s.currData.dimensions;const i=s.dom.outlines.attr("transform")?r.duration:0;s.translateElems(0,r,a,i);if(r.prevShowGrid!=r.showGrid){s.dom.outlines.selectAll("*").remove()}if(r.showGrid!="pattern"){e(t)}else{const e=s.dom.outlines.selectAll("g").data(t,(t=>t.xg.grp.name+";;"+t.yg.grp.name));e.exit().remove();e.each(o);e.enter().append("g").each(n)}r.prevShowGrid=r.showGrid;s.parent.delayedMouseoutHandler()};s.translateElems=function(t,e,r,n=0){const o=!n?s.dom.outlines:s.dom.outlines.transition().duration(n);o.attr("transform",`translate(${r.xOffset+r.seriesXoffset+t},${r.yOffset})`)};function e(t,e,n){const o=s.dom.outlines.selectAll("rect").data(t,(t=>t.xg.grp.name+";;"+t.yg.grp.name));o.exit().remove();o.each(r);o.enter().append("rect").each(r)}function r(e){const r=s.settings;t(this).transition().duration("x"in this?r.duration:0).attr("x",e.x).attr("y",e.y).attr("width",e.width).attr("height",e.height).attr("shape-rendering","crispEdges").attr("fill",!r.showGrid?r.cellbg:r.gridStroke).attr("stroke",r.outlineStroke).attr("stroke-width",1)}function n(e){const r=t(this);const n=r.append("pattern").attr("id",`${s.patternId}-${s.patternIdSuffix++}`).attr("patternUnits","userSpaceOnUse").attr("patternUnits","userSpaceOnUse");n.append("line");n.append("line");r.append("rect");r.append("rect");o.call(this,e)}function o(e){const r=s.settings;const n=s.parent.dimensions;const o=t(this);const c=a(o,r,n);const p=o.node().querySelectorAll("rect");i.call(p[0],e,Object.assign({},r,{fill:r.cellbg}));const l=r.showGrid?`url(#${c})`:"none";i.call(p[1],e,Object.assign({},r,{fill:l,stroke:r.gridStroke}))}function a(s,e,r,n){const o=s.select("pattern").attr("x",0).attr("y",0).attr("width",r.colw+e.colspace).attr("height",e.rowh+e.rowspace);const a=.5*e.rowspace;const i=e.rowh+a;const[c,p]=o.node().querySelectorAll("line");t(c).attr("x1",0).attr("y1",i).attr("x2",r.colw+e.colspace).attr("y2",i).attr("stroke",e.gridStroke).attr("stroke-width",e.rowspace);const l=.5*e.colspace;const d=r.colw+l;t(p).attr("x1",d).attr("y1",0).attr("x2",d).attr("y2",e.rowh).attr("stroke",e.gridStroke).attr("stroke-width",e.colspace);return o.attr("id")}function i(s,e){const r=t(this);r.transition().duration(r.attr("x")?e.duration:0).attr("x",s.x).attr("y",s.y).attr("width",s.width).attr("height",s.height).attr("shape-rendering","crispEdges").attr("fill",e.fill||"none").attr("stroke",e.stroke||"none")}}export{s as MatrixCluster};

package/dist/matrix.config-6ce74dfe.js

@@ -0,0 +1 @@
+import{bM as e,bN as t,bO as s,bP as a,bQ as i,P as l,z as o,ap as r}from"./app-b369b169.js";import{getSortOptions as n}from"./matrix.sort-014d798d.js";import{b as m,f as p}from"./termsetting-33ea66f1.js";import"./tslib.es6-c3c2d88f.js";import"path";async function c(o={},r){const c={Samples:"Samples",samples:"samples",Sample:"Sample",sample:"sample",Terms:"Variables",terms:"variables",Term:"Variable",term:"Variable",Mutations:"Mutations"};const d={termgroups:[],samplegroups:[],divideBy:null,legendValueFilter:{isAtomic:true,type:"tvslst",in:true,join:"and",lst:[]},legendGrpFilter:{isAtomic:true,type:"tvslst",in:true,join:"and",lst:[]},settings:{matrix:{svgCanvasSwitch:1e3,useMinPixelWidth:true,cellEncoding:"",margin:{top:10,right:5,bottom:20,left:50},maxGenes:o.settings?.maxGenes||50,maxSample:o.settings?.maxSample||1e3,sampleNameFilter:"",sortSamplesBy:"a",sortPriority:undefined,sortSampleGrpsBy:"name",sortSamplesTieBreakers:[{$id:"sample",sortSamples:{}}],sortTermsBy:"sampleCount",samplecount4gene:o.chartType=="hierCluster"?"":"abs",geneVariantCountSamplesSkipMclass:[],cellbg:"#ececec",showGrid:"",addMutationCNVButtons:false,truncatingMutations:e,proteinChangingMutations:t,synonymousMutations:s,mutationClasses:a,CNVClasses:i,gridStroke:"#fff",outlineStroke:"#ccc",beamStroke:"#f00",colw:0,colwMin:.1/window.devicePixelRatio,colwMax:16,colspace:1,colgspace:8,colglabelpos:true,collabelpos:"bottom",collabelvisible:true,collabelgap:5,collabelpad:1,collabelmaxchars:32,rowh:18,rowhMin:1,rowhMax:20,rowspace:1,rowgspace:8,rowlabelpos:"left",rowlabelgap:5,rowlabelvisible:true,rowlabelpad:1,rowlabelmaxchars:32,legendGrpLabelMaxChars:26,grpLabelFontSize:12,minLabelFontSize:6,maxLabelFontSize:14,transpose:false,sampleLabelOffset:120,sampleGrpLabelOffset:120,sampleGrpLabelMaxChars:32,termLabelOffset:80,termGrpLabelOffset:80,termGrpLabelMaxChars:32,duration:0,zoomLevel:1,zoomCenterPct:0,zoomIndex:0,zoomGrpIndex:0,zoomMin:.5,zoomIncrement:.1,zoomStep:1,imgWMax:6e4/window.devicePixelRatio,scrollHeight:12,controlLabels:c,cnvUnit:"log2ratio",ignoreCnvValues:false,barh:32,showHints:[]}}};const f=d.settings;const u=Math.max(f.matrix.rowh+f.matrix.rowspace-3*f.matrix.rowlabelpad,12);f.legend={ontop:false,lineh:25,padx:5,padleft:0,padright:20,padbtm:30,fontsize:u,iconh:u-2,iconw:u-2,hangleft:1,linesep:false};const g=r.vocabApi.termdbConfig.matrix||{};l(d.settings.matrix,g.settings);if(g.legendGrpFilter)d.legendGrpFilter=g.legendGrpFilter;if(g.legendValueFilter)d.legendValueFilter=g.legendValueFilter;if(o.name){const e=await r.vocabApi.getMatrixByName(o.name);if(!e)throw"error from getMatrixByName()";if(e.error)throw e.error;l(d,e)}const h=o?.settings?.matrix;if(h){if((h.sortSamplesBy=="custom"||h.sortSamplesBy=="asListed")&&h.sortOptions?.custom.label=="against alteration type"){h.sortSamplesBy="a"}if(h.sortOptions){delete h.sortOptions.custom;delete h.sortOptions.asListed}}l(d,o);const b=d.settings.matrix;b.sortOptions=n(r.vocabApi.termdbConfig,c,b);b.duration=0;b.colw=0;if(b.sortSamplesBy!="asListed"&&!b.sortOptions?.[b.sortSamplesBy])b.sortSamplesBy="a";else if(["selectedTerms","class","dt","hits"].includes(b.sortSamplesBy))b.sortSamplesBy="a";if(b.samplecount4gene===true||b.samplecount4gene===1)b.samplecount4gene="abs";if(window.location.hostname=="localhost"){if(window.location.hash=="#canvas")b.svgCanvasSwitch=0}const y=[];for(const e of d.termgroups){e.lst=JSON.parse(JSON.stringify(e.lst));for(const t of e.lst){if(!t.term?.type||m(t.term.type)){if(!t.id){if(!t.term.id)throw`missing tw.id and tw.term.id`;t.id=t.term.id}delete t.term}y.push(p(t,r.vocabApi))}}if(d.divideBy)y.push(p(d.divideBy,r.vocabApi));await Promise.all(y);return d}function d(e){const t=e.settings.matrix;const s=[...t.mutationClasses,...t.CNVClasses];t.filterByClass={isAtomic:true};for(const a of e.legendGrpFilter.lst){if(!a.dt)continue;s.filter((e=>a.dt.includes(o[e].dt))).forEach((e=>{t.filterByClass[e]="value"}))}for(const s of e.legendValueFilter.lst){if(!s.legendGrpName||s.tvs?.term?.type!=="geneVariant")continue;if(s.tvs.values?.[0].mclasslst)s.tvs.values[0].mclasslst.forEach((e=>{t.filterByClass[e]=s.legendFilterType?.endsWith("_hard")?"case":"value"}));else if(s.tvs.values)s.tvs.values.forEach((e=>{t.filterByClass[key]="value"}));else throw`unhandled tvs from legendValueFilter`}t.hiddenVariants=Object.keys(t.filterByClass).filter((e=>e!=="isAtomic"));const a=new Set(t.hiddenVariants.filter((e=>o[e]?.dt===r)));t.hiddenCNVs=[...a];t.showMatrixCNV=!a.size?"all":a.size==t.CNVClasses.length?"none":"bySelection";t.allMatrixCNVHidden=a.size==t.CNVClasses.length;const i=new Set(t.hiddenVariants.filter((e=>t.mutationClasses.find((t=>t===e)))));t.hiddenMutations=[...i];const l=new Set(t.proteinChangingMutations);const n=new Set(t.truncatingMutations);t.showMatrixMutation=!i.size?"all":i.size==t.mutationClasses.length?"none":i.size===t.mutationClasses.length-l.size&&[...i].every((e=>!l.has(e)))?"onlyPC":i.size===t.mutationClasses.length-n.size&&[...i].every((e=>!n.has(e)))?"onlyTruncating":"bySelection";t.allMatrixMutationHidden=i.size==t.mutationClasses.length;const m=t.sortOptions.a?.sortPriority.find((e=>e.types.length==1&&e.types[0]=="geneVariant"))?.tiebreakers||[];t.sortByMutation=m.find((e=>e.filter?.values[0]?.dt===1))?.isOrdered?"consequence":"presence";t.sortByCNV=m.find((e=>e.filter?.values[0]?.dt===4))?.disabled!==true}export{c as getPlotConfig,d as setComputedConfig};