@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/tp.ui-5K3AAXDW.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/tp.classes.js", "../src/tp.gene.geneexpression.js", "../src/tp.gene.js", "../src/tp.pathway.js", "../src/hcmap.js", "../src/tp.e2pca.js", "../src/tp.ui.js"],
-  "sourcesContent": ["import * as common from '#shared/common.js'\n\n/*\nlist mutation classes\n*/\n\nexport default function (cohort, button, folder) {\n\tlet nothing = true\n\tfor (const k in cohort.dsset) {\n\t\tnothing = false\n\t}\n\tif (nothing) {\n\t\tbutton.remove()\n\t\tfolder.remove()\n\t\treturn null\n\t}\n\n\tconst cbreakdown = new Map()\n\t/*\n\tmclass breakdown per ds\n\tk: dskey\n\tv: map\n\t   k: mclass key\n\t   v: case count\n\t*/\n\n\tlet totalcount = 0\n\t// sum of variants from all ds, to show on button\n\n\tfor (const dskey in cohort.dsset) {\n\t\tconst data = cohort.dsset[dskey].bulkdata\n\t\tif (!data) continue\n\n\t\tconst class2count = new Map()\n\t\t// class 2 count in this ds\n\t\t// k: class, v: count\n\n\t\t// need to count sv/fusion separately to avoid duplicating\n\t\tconst svstr = new Set()\n\t\tconst fusionstr = new Set()\n\n\t\tfor (const n in data) {\n\t\t\tfor (const m of data[n]) {\n\t\t\t\tconst c = m.class\n\t\t\t\tif (c == common.mclasssv) {\n\t\t\t\t\tsvstr.add((m.sample ? m.sample : '') + '.' + (m.sampletype ? m.sampletype : '') + JSON.stringify(m.pairlst))\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tif (c == common.mclassfusionrna) {\n\t\t\t\t\tfusionstr.add(\n\t\t\t\t\t\t(m.sample ? m.sample : '') + '.' + (m.sampletype ? m.sampletype : '') + JSON.stringify(m.pairlst)\n\t\t\t\t\t)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\t// not sv/fusion, add to total\n\t\t\t\ttotalcount++\n\n\t\t\t\tif (!class2count.has(c)) {\n\t\t\t\t\tclass2count.set(c, 0)\n\t\t\t\t}\n\t\t\t\tclass2count.set(c, class2count.get(c) + 1)\n\t\t\t}\n\t\t}\n\n\t\tif (svstr.size) {\n\t\t\tclass2count.set(common.mclasssv, svstr.size)\n\t\t\ttotalcount += svstr.size\n\t\t}\n\t\tif (fusionstr.size) {\n\t\t\tclass2count.set(common.mclassfusionrna, fusionstr.size)\n\t\t\ttotalcount += fusionstr.size\n\t\t}\n\t\tcbreakdown.set(dskey, class2count)\n\t}\n\n\tbutton\n\t\t.html(totalcount + ' <span style=\"font-size:.8em\">VARIANTS</span>')\n\t\t.attr('aria-label', 'A summary of variant hits from all genes, in descending order.')\n\tconst table = folder.append('table').style('margin-right', '20px')\n\tconst trup = table.append('tr')\n\tconst trdown = table.append('tr')\n\tconst showclst = (lst, holder, number) => {\n\t\tholder.selectAll('*').remove()\n\t\tfor (const i of lst) {\n\t\t\tconst d = holder.append('div').style('margin', '10px')\n\t\t\td.append('span')\n\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t.style('background-color', i.color)\n\t\t\t\t.style('padding', '2px 5px')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.html(number ? i.count : '&nbsp;&nbsp;')\n\t\t\td.append('span').style('color', i.color).text(i.label)\n\t\t}\n\t}\n\n\tconst ds2clst = {}\n\tfor (const [dskey, class2count] of cbreakdown) {\n\t\tconst lst = []\n\t\tfor (const [k, count] of class2count) {\n\t\t\tconst mc = common.mclass[k]\n\t\t\tif (\n\t\t\t\tmc.dt == common.dtsnvindel ||\n\t\t\t\tmc.dt == common.dtitd ||\n\t\t\t\tmc.dt == common.dtdel ||\n\t\t\t\tmc.dt == common.dtnloss ||\n\t\t\t\tmc.dt == common.dtcloss\n\t\t\t) {\n\t\t\t\tlst.push({\n\t\t\t\t\tkey: k,\n\t\t\t\t\tlabel: mc.label,\n\t\t\t\t\tcolor: mc.color,\n\t\t\t\t\tcount: count\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tlst.sort((a, b) => b.count - a.count)\n\n\t\t// hardcoded order for the following classes\n\t\tfor (const thisclass of [common.mclasscnvloss, common.mclasscnvgain, common.mclasssv, common.mclassfusionrna]) {\n\t\t\tif (class2count.has(thisclass)) {\n\t\t\t\tconst c = common.mclass[thisclass]\n\t\t\t\tlst.push({\n\t\t\t\t\tkey: thisclass,\n\t\t\t\t\tlabel: c.label,\n\t\t\t\t\tcolor: c.color,\n\t\t\t\t\tcount: class2count.get(thisclass)\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tds2clst[dskey] = lst\n\n\t\tconst cholder = trdown.append('td').attr('valign', 'top').attr('shownumber', 0)\n\t\tshowclst(lst, cholder, true)\n\t\tconst td = trup\n\t\t\t.append('td')\n\t\t\t.style('border-bottom', 'solid 1px #ccc')\n\t\t\t.style('padding', '5px 10px')\n\t\t\t.style('color', '#858585')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text(cohort.dsset[dskey].label)\n\t\ttd.append('button')\n\t\t\t.style('margin', '5px')\n\t\t\t.text('Hide number')\n\t\t\t.on('click', event => {\n\t\t\t\tconst number = cholder.attr('shownumber') == '1'\n\t\t\t\tshowclst(lst, cholder, number)\n\t\t\t\tcholder.attr('shownumber', number ? '0' : '1')\n\t\t\t\tevent.target.innerHTML = number ? 'Hide number' : 'Show number'\n\t\t\t})\n\t}\n\treturn totalcount ? ds2clst : null\n}\n", "import * as client from './client'\n\n\n/*\nthis is only a quick fix\n\nplaces from tp that call blockinit()\n- tp.gene\n- tp.hm2.handlers\n\nin the context of pecan, when showing a study view for a disease cohort, blockinit() will show variants of a gene\nin this case, also need to show expression from Pediatric for this gene\n\nhowever: study view is not connected to the *Pediatric* official dataset, and the mutations from that cohort are stored on client\nthus need to explicitly indicate in the study config, that when launching blockinit() for a gene, need to query official ds to get gene data\n*/\n\n\n\n\nexport default function tp_getgeneexpression(arg) {\n\n/*\narg\n\t.x\n\t.y\n\t\tposition for pane\n\t.gene\n\t\tgene name\n\t.genome str\n\t.loadgeneexpressionfromofficialds\n\t.hostURL\n*/\n\n\nPromise.resolve()\n.then(()=>{\n\n\tif(!arg.gene) throw({message:'gene name missing'})\n\tif(!arg.genome) throw({message:'genome name missing'})\n\tif(arg.hostURL==undefined) throw({message:'no hostURL'})\n\tif(!arg.loadgeneexpressionfromofficialds) throw({message:'loadgeneexpressionfromofficialds missing'})\n\tif(!arg.loadgeneexpressionfromofficialds.dataset) throw({message:'dataset missing from loadgeneexpressionfromofficialds'})\n\tconst par={\n\t\tgenome:arg.genome,\n\t\tdsname:arg.loadgeneexpressionfromofficialds.dataset,\n\t\texpressiononly:1,\n\t\tgenename:arg.gene,\n\t\tjwt:arg.jwt\n\t}\n\treturn fetch( new Request(arg.hostURL+'/dsdata',{\n\t\tmethod:'POST',\n\t\tbody:JSON.stringify(par)\n\t}))\n\t.then(data=>{return data.json()})\n\t.then(data=>{\n\t\tif(data.error) throw({message:data.error})\n\t\tif(!data.data) throw({message:'cannot get data'})\n\t\treturn data.data\n\t})\n\n})\n\n.then(data=>{\n\n\tfor(let i=0; i<data.length; i++) {\n\t\tconst par={\n\t\t\tdata:data[i].lst,\n\t\t\texpp:data[i].config,\n\t\t\tgenename:arg.gene,\n\t\t\tpresize:{\n\t\t\t\tx:(arg.x+40*i),\n\t\t\t\ty:(arg.y+40*i),\n\t\t\t\twidth:350,\n\t\t\t\theight:650\n\t\t\t}\n\t\t}\n\t\timport('./ep').then(p=>{\n\t\t\tnew p.default(par)\n\t\t})\n\t}\n})\n\n.catch(err=>{\n\tconst pane = client.newpane({x:(arg.x || 600), y:(arg.y || 80)})\n\tpane.body.append('p').text('Error getting gene expression: '+err)\n})\n}\n", "import { select as d3select, selectAll as d3selectAll } from 'd3-selection'\nimport { json as d3json } from 'd3-fetch'\nimport * as client from './client'\nimport * as common from '#shared/common.js'\nimport blockinit from './block.init'\nimport tp_getgeneexpression from './tp.gene.geneexpression'\nimport { Menu } from '../dom/menu'\n\nconst tip = new Menu()\n\nexport default function (cohort, ds2clst, butt, folder, defaulthide, host) {\n\tif (!ds2clst) return null\n\tconst hostURL = host || ''\n\n\tconst union = {}\n\t// always contain all genes\n\t// k: gene name, v: { mcount:0, isoform:{} }\n\tlet genelst = []\n\t// mutable, build table according to its order\n\t// gene name only!\n\tfor (const k in cohort.dsset) {\n\t\tfor (const gn in cohort.dsset[k].bulkdata) {\n\t\t\tif (!(gn in union)) {\n\t\t\t\tunion[gn] = { mcount: 0, isoform: {} }\n\t\t\t\tgenelst.push(gn)\n\t\t\t}\n\t\t\tunion[gn].mcount += cohort.dsset[k].bulkdata[gn].length\n\t\t\tfor (const m of cohort.dsset[k].bulkdata[gn]) {\n\t\t\t\tconst i = m.isoform\n\t\t\t\tif (!i) continue\n\t\t\t\tunion[gn].isoform[i] = 1\n\t\t\t}\n\t\t}\n\t}\n\tlet genelimit = Math.min(100, genelst.length)\n\t// FIXME hardcoded\n\tconst noncodingclass = new Set(['Intron', 'P', 'S', 'E', common.mclassutr3, common.mclassutr5])\n\tconst gene2import = {}\n\tconst ds2import = {}\n\tlet usenoncoding = true,\n\t\t// k: isoform, v: {}\n\t\t// k: dsname, v: {stat}\n\t\t// k: dsname\n\t\timportsilent = false\n\n\tbutt\n\t\t.html(genelst.length + ' <span style=\"font-size:.8em\">GENES</span>')\n\t\t.attr('aria-label', 'A summary table of gene by variant type, order by number of hits in descending order.')\n\tconst errdiv = folder.append('div')\n\tconst sayerror = m => {\n\t\tclient.sayerror(errdiv, m)\n\t}\n\n\t// top row\n\tconst toprow = folder.append('div').style('margin-bottom', '8px')\n\ttoprow\n\t\t.append('button')\n\t\t.style('margin-right', '10px')\n\t\t.text('Configure')\n\t\t.on('click', () => {\n\t\t\tif (optiondiv.style('display') == 'block') {\n\t\t\t\tclient.disappear(optiondiv)\n\t\t\t} else {\n\t\t\t\tclient.appear(optiondiv)\n\t\t\t}\n\t\t})\n\n\ttoprow\n\t\t.append('button')\n\t\t.style('margin-right', '10px')\n\t\t.text('Download')\n\t\t.on('click', () => {\n\t\t\tconst txt = dotable()\n\t\t\tclient.export_data('Gene summary', [{ text: txt }])\n\t\t})\n\n\ttoprow\n\t\t.append('input')\n\t\t.attr('type', 'search')\n\t\t.attr('size', 10)\n\t\t.attr('placeholder', 'Find gene')\n\t\t.style('margin', '0px 20px 0px 5px')\n\t\t.on('keyup', event => {\n\t\t\tlet n = event.target.value\n\t\t\tif (n == '') {\n\t\t\t\ttip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (cohort.geneToUpper) {\n\t\t\t\tn = n.toUpperCase()\n\t\t\t}\n\t\t\tif (event.code == 'Enter') {\n\t\t\t\ttip.hide()\n\t\t\t\tevent.target.value = ''\n\t\t\t\tif (n in union) {\n\t\t\t\t\tpaintgene(n)\n\t\t\t\t}\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst hit = []\n\t\t\tfor (const gn in union) {\n\t\t\t\tif (gn.indexOf(n) == 0) {\n\t\t\t\t\thit.push({ name: gn, count: union[gn].mcount })\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (hit.length == 0) {\n\t\t\t\ttip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\thit.sort((a, b) => b.count - a.count)\n\t\t\ttip.clear().showunder(event.target)\n\t\t\tfor (let i = 0; i < Math.min(30, hit.length); i++) {\n\t\t\t\tconst n = hit[i].name\n\t\t\t\tconst row = tip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption_y')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tpaintgene(n)\n\t\t\t\t\t})\n\t\t\t\trow.append('span').text(n)\n\t\t\t\trow.append('span').style('font-size', '.7em').text(hit[i].count)\n\t\t\t}\n\t\t})\n\ttoprow\n\t\t.append('a')\n\t\t.attr('href', 'https://docs.google.com/document/d/1NrH1H-FUWJtEKLk69V-k8uaYHOr9YO2obM9ZLZslEQ0/edit?usp=sharing')\n\t\t.attr('target', '_blank')\n\t\t.text('Help')\n\tconst secondrow = folder.append('div').style('border', 'solid 1px #ccc').style('margin', '10px 0px')\n\tconst optiondiv = secondrow.append('div').style('display', 'none').style('background-color', '#f1f1f1')\n\tconst scrolltoppad = 140\n\tconst scrollholder = secondrow\n\t\t.append('div')\n\t\t.style('padding-top', scrolltoppad + 'px')\n\t\t.style('position', 'relative')\n\tconst scrolldiv = scrollholder\n\t\t.append('div')\n\t\t.style('overflow-y', 'scroll')\n\t\t.style('height', '400px')\n\t\t.style('resize', 'vertical')\n\tconst table = scrolldiv.append('table').style('border-spacing', '1px').style('border-collapse', 'separate')\n\n\t// options\n\tconst oprow1 = optiondiv.append('div').style('padding', '10px').style('border-bottom', 'dashed 1px #ccc')\n\tconst oprow2 = optiondiv.append('div').style('padding', '10px').style('border-bottom', 'dashed 1px #ccc')\n\tconst oprow3 = optiondiv.append('div').style('padding', '10px').style('border-bottom', 'dashed 1px #ccc')\n\t// option row1\n\tconst gcsays = oprow1\n\t\t.append('span')\n\t\t.style('padding-right', '10px')\n\t\t.text('Showing ' + (genelimit < genelst.length ? 'top ' + genelimit + ' genes' : 'all genes'))\n\toprow1\n\t\t.append('button')\n\t\t.text('more')\n\t\t.on('click', () => {\n\t\t\tgenelimit = Math.min(genelst.length, genelimit + 10)\n\t\t\tgcsays.text('Showing ' + (genelimit < genelst.length ? 'top ' + genelimit : 'all genes'))\n\t\t\tdotable()\n\t\t})\n\toprow1\n\t\t.append('button')\n\t\t.text('less')\n\t\t.on('click', () => {\n\t\t\tgenelimit = Math.max(1, genelimit - 10)\n\t\t\tgcsays.text('Showing ' + (genelimit < genelst.length ? 'top ' + genelimit : 'all genes'))\n\t\t\tdotable()\n\t\t})\n\t// option row2\n\toprow2.append('span').text('Show subset').style('padding-right', '10px')\n\tconst genesetta = oprow2\n\t\t.append('textarea')\n\t\t.attr('rows', 1)\n\t\t.attr('cols', 20)\n\t\t.attr('placeholder', 'enter gene names')\n\t\t.style('margin-right', '10px')\n\toprow2\n\t\t.append('button')\n\t\t.text('Submit')\n\t\t.on('click', () => {\n\t\t\tconst v = genesetta.property('value').trim()\n\t\t\tif (v == '') return\n\t\t\tconst lst = v.split(/[\\s\\t\\n]+/),\n\t\t\t\tgood = [],\n\t\t\t\tnomatch = []\n\t\t\tfor (const s of lst) {\n\t\t\t\tif (s == '') continue\n\t\t\t\tconst n = cohort.geneToUpper ? s.trim().toUpperCase() : s.trim()\n\t\t\t\tif (n in union) {\n\t\t\t\t\tgood.push(n)\n\t\t\t\t} else {\n\t\t\t\t\tnomatch.push(s)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (nomatch.length) {\n\t\t\t\tsayerror('No match found for ' + nomatch.join(', '))\n\t\t\t}\n\t\t\tif (good.length == 0) return\n\t\t\tgenelst = good\n\t\t\tgenelimit = good.length\n\t\t\tdotable()\n\t\t})\n\toprow2\n\t\t.append('button')\n\t\t.text('Use default')\n\t\t.on('click', () => {\n\t\t\t// to default gene list\n\t\t\tgenelst = []\n\t\t\tfor (const n in union) {\n\t\t\t\tgenelst.push(n)\n\t\t\t}\n\t\t\tgenelimit = Math.min(100, genelst.length)\n\t\t\tdotable()\n\t\t})\n\t// option row3\n\toprow3.append('span').html('Noncoding mutation visibility:&nbsp;')\n\tconst oprow3select = oprow3.append('select').on('change', () => {\n\t\tusenoncoding = !usenoncoding\n\t\tfor (const dat of attrlst) {\n\t\t\tif (!dat.atlst) {\n\t\t\t\t// mutation class only in dataset\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tfor (const at of dat.atlst) {\n\t\t\t\tif (!at.ismclass) continue\n\t\t\t\tif (usenoncoding) {\n\t\t\t\t\tat.hide = false\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tat.hide = noncodingclass.has(at.key)\n\t\t\t}\n\t\t}\n\t\tdotable()\n\t})\n\toprow3select.append('option').text('show').attr('value', 'y')\n\toprow3select.append('option').text('hide').attr('value', 'n')\n\toprow3\n\t\t.append('p')\n\t\t.style('font-size', '.8em')\n\t\t.style('color', '#858585')\n\t\t.text('Including: silent, splice_region, exon, UTR, and intron.')\n\n\tconst hassamplelst = []\n\tfor (const k in cohort.dsset) {\n\t\tconst d = cohort.dsset[k]\n\t\tif (d.hassample) {\n\t\t\thassamplelst.push(d)\n\t\t}\n\t}\n\t// option row5\n\tif (hassamplelst.length) {\n\t\tconst oprow5 = optiondiv.append('div').style('padding', '10px').style('border-bottom', 'dashed 1px #ccc')\n\t\toprow5.append('span').html('Gene recurrence (# of samples for each gene):&nbsp;')\n\t\tfor (const ds of hassamplelst) {\n\t\t\toprow5\n\t\t\t\t.append('button')\n\t\t\t\t.text(hassamplelst.length == 1 ? 'show' : ds.label)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tconst bars = []\n\t\t\t\t\tfor (const gene of genelst) {\n\t\t\t\t\t\tconst hash = {}\n\t\t\t\t\t\tlet samplecount = 0\n\t\t\t\t\t\tif (gene in ds.bulkdata) {\n\t\t\t\t\t\t\tfor (const m of ds.bulkdata[gene]) {\n\t\t\t\t\t\t\t\tif (!usenoncoding && noncodingclass.has(m.class)) return\n\t\t\t\t\t\t\t\tif (!(m.sample in hash)) {\n\t\t\t\t\t\t\t\t\thash[m.sample] = 1\n\t\t\t\t\t\t\t\t\tsamplecount++\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbars.push({\n\t\t\t\t\t\t\tname: gene,\n\t\t\t\t\t\t\tsize: samplecount\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tconst pos = event.target.getBoundingClientRect()\n\t\t\t\t\tbarplot(bars, '#76B38C', 'Number of samples' + (usenoncoding ? '' : ', excluding noncoding mutations'), pos)\n\t\t\t\t})\n\t\t}\n\t\t// option row6\n\t\tconst oprow6 = optiondiv.append('div').style('padding', '10px').style('border-bottom', 'dashed 1px #ccc')\n\t\toprow6.append('span').html('Mutation burden (# mutations for each sample):&nbsp;')\n\t\tfor (const ds of hassamplelst) {\n\t\t\toprow6\n\t\t\t\t.append('button')\n\t\t\t\t.text(hassamplelst.length == 1 ? 'show' : ds.label)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tconst samplehash = {}\n\t\t\t\t\tfor (const g in ds.bulkdata) {\n\t\t\t\t\t\tfor (const m of ds.bulkdata[g]) {\n\t\t\t\t\t\t\tconst n = m.sample\n\t\t\t\t\t\t\tif (n) {\n\t\t\t\t\t\t\t\tif (!usenoncoding && noncodingclass.has(m.class)) continue\n\t\t\t\t\t\t\t\tif (!(n in samplehash)) {\n\t\t\t\t\t\t\t\t\tsamplehash[n] = 0\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tsamplehash[n]++\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tconst bars = []\n\t\t\t\t\tfor (const n in samplehash) {\n\t\t\t\t\t\tbars.push({\n\t\t\t\t\t\t\tname: n,\n\t\t\t\t\t\t\tsize: samplehash[n]\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tconst pos = event.target.getBoundingClientRect()\n\t\t\t\t\tbarplot(bars, '#76B38C', 'Mutation burden' + (usenoncoding ? '' : ', excluding noncoding mutations'), pos)\n\t\t\t\t})\n\t\t}\n\t}\n\t// option row7\n\tconst oprow7 = optiondiv\n\t\t.append('div')\n\t\t.style('padding', '10px')\n\t\t.style('border-bottom', 'dashed 1px #ccc')\n\t\t.text('Click on a column header to rank genes.')\n\t// table columns\n\tconst attrlst = [\n\t\t{\n\t\t\tlabel: 'Name',\n\t\t\tisgenename: true\n\t\t}\n\t]\n\tlet firstsort = true\n\tlet dscount = 0\n\tfor (const dsname in cohort.dsset) {\n\t\tdscount++\n\t\tconst thisds = {\n\t\t\tname: cohort.dsset[dsname].label,\n\t\t\tatlst: [\n\t\t\t\t{\n\t\t\t\t\tlabel: '# mutation',\n\t\t\t\t\tget: gn => {\n\t\t\t\t\t\tif (!(gn in cohort.dsset[dsname].bulkdata)) return 0\n\t\t\t\t\t\tif (usenoncoding) {\n\t\t\t\t\t\t\treturn cohort.dsset[dsname].bulkdata[gn].length\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet c = 0\n\t\t\t\t\t\tfor (const i of cohort.dsset[dsname].bulkdata[gn]) {\n\t\t\t\t\t\t\tif (!noncodingclass.has(i.class)) c++\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn c\n\t\t\t\t\t},\n\t\t\t\t\trotate: true,\n\t\t\t\t\tdescend: true,\n\t\t\t\t\tsort: firstsort\n\t\t\t\t\t//secondsort:true, // secondary, so to keep order persistant when sorting on classes with many genes having same number in sorted class\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\tfirstsort = false\n\t\tif (cohort.dsset[dsname].hassample) {\n\t\t\tthisds.atlst.push({\n\t\t\t\tlabel: '# sample',\n\t\t\t\tget: gn => {\n\t\t\t\t\tif (!(gn in cohort.dsset[dsname].bulkdata)) return 0\n\t\t\t\t\tconst set = new Set()\n\t\t\t\t\tfor (const m of cohort.dsset[dsname].bulkdata[gn]) {\n\t\t\t\t\t\tif (!usenoncoding && noncodingclass.has(m.class)) continue\n\t\t\t\t\t\tif (!m.sample) continue\n\t\t\t\t\t\tset.add(m.sample)\n\t\t\t\t\t}\n\t\t\t\t\treturn set.size\n\t\t\t\t},\n\t\t\t\trotate: true,\n\t\t\t\tdescend: true\n\t\t\t})\n\t\t}\n\t\tfor (const c of ds2clst[dsname]) {\n\t\t\tc.ismclass = true\n\t\t\tc.get = gn => {\n\t\t\t\tif (!(gn in cohort.dsset[dsname].bulkdata)) return 0\n\t\t\t\tlet total = 0\n\t\t\t\tfor (const m of cohort.dsset[dsname].bulkdata[gn]) {\n\t\t\t\t\tif (m.class == c.key) total++\n\t\t\t\t}\n\t\t\t\treturn total\n\t\t\t}\n\t\t\tc.rotate = true\n\t\t\tc.descend = true\n\t\t\tthisds.atlst.push(c)\n\t\t}\n\t\tattrlst.push(thisds)\n\t}\n\n\tconst dotable = () => {\n\t\t// imported data won't be reflected in attrlst\n\t\tlet sortkey = null,\n\t\t\tsortkey2 = null\n\t\tfor (const a of attrlst) {\n\t\t\tif (a.hide) continue\n\t\t\tif (a.atlst) {\n\t\t\t\tfor (const b of a.atlst) {\n\t\t\t\t\tif (b.hide) continue\n\t\t\t\t\tif (b.sort) {\n\t\t\t\t\t\tsortkey = b\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tif (b.secondsort) {\n\t\t\t\t\t\tsortkey2 = b\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (a.sort) {\n\t\t\t\tsortkey = a\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (a.secondsort) {\n\t\t\t\tsortkey2 = a\n\t\t\t}\n\t\t}\n\t\tif (sortkey) {\n\t\t\tgenelst.sort((a, b) => {\n\t\t\t\t// a/b is gene name\n\t\t\t\tif (sortkey.isgenename) {\n\t\t\t\t\t// no getter, directly sort on gene name\n\t\t\t\t\tif (a < b) {\n\t\t\t\t\t\treturn sortkey.descend ? 1 : -1\n\t\t\t\t\t}\n\t\t\t\t\treturn sortkey.descend ? -1 : 1\n\t\t\t\t}\n\t\t\t\tconst i = sortkey.get(a),\n\t\t\t\t\tj = sortkey.get(b)\n\t\t\t\tif (typeof i == 'string') {\n\t\t\t\t\tif (i < j) {\n\t\t\t\t\t\treturn sortkey.descend ? 1 : -1\n\t\t\t\t\t}\n\t\t\t\t\treturn sortkey.descend ? -1 : 1\n\t\t\t\t}\n\t\t\t\t// numeric\n\t\t\t\tif (i == j) {\n\t\t\t\t\tif (sortkey2) {\n\t\t\t\t\t\t// second sort is currently numerical only\n\t\t\t\t\t\tconst i2 = sortkey2.get(a),\n\t\t\t\t\t\t\tj2 = sortkey2.get(b)\n\t\t\t\t\t\tif (i2 == j2) {\n\t\t\t\t\t\t\t// get isoform for a and b so to look into import\n\t\t\t\t\t\t\tif (a in gene2import) {\n\t\t\t\t\t\t\t\tif (!(b in gene2import)) return -1\n\t\t\t\t\t\t\t} else if (b in gene2import) {\n\t\t\t\t\t\t\t\treturn 1\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\treturn j2 - i2\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// get isoform for a and b so to look into import\n\t\t\t\t\t\tif (a in gene2import) {\n\t\t\t\t\t\t\tif (!(b in gene2import)) return -1\n\t\t\t\t\t\t} else if (b in gene2import) {\n\t\t\t\t\t\t\treturn 1\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\t// last resort, alphabetic order\n\t\t\t\t\treturn a < b ? -1 : 1\n\t\t\t\t}\n\t\t\t\treturn sortkey.descend ? j - i : i - j\n\t\t\t})\n\t\t}\n\t\t// count how many classes at total in each imported\n\t\tconst importclass = {}\n\t\tlet hasimport = false\n\t\tfor (const dsname in ds2import) {\n\t\t\thasimport = true\n\t\t\tconst classcount = {}\n\t\t\tfor (let i = 0; i < genelimit; i++) {\n\t\t\t\tconst gene = genelst[i]\n\t\t\t\tif (gene in gene2import && dsname in gene2import[gene]) {\n\t\t\t\t\tfor (const c in gene2import[gene][dsname].class) {\n\t\t\t\t\t\tif (!(c in classcount)) {\n\t\t\t\t\t\t\tclasscount[c] = 0\n\t\t\t\t\t\t}\n\t\t\t\t\t\tclasscount[c] += gene2import[gene][dsname].class[c]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst clst = []\n\t\t\tfor (const c in classcount) {\n\t\t\t\tclst.push({\n\t\t\t\t\tclass: c,\n\t\t\t\t\tn: classcount[c]\n\t\t\t\t})\n\t\t\t}\n\t\t\tclst.sort((a, b) => b.n - a.n)\n\t\t\timportclass[dsname] = clst\n\t\t}\n\t\tconst impspace = 'solid 10px white'\n\t\ttable.selectAll('*').remove()\n\t\t// tr 1, overspanning header\n\t\tconst tr1 = table.append('tr')\n\t\ttr1\n\t\t\t.append('td') // numeritor\n\t\t\t.style('height', '0px')\n\t\t\t.style('padding', '0px')\n\t\ttr1\n\t\t\t.append('td') // gene name\n\t\t\t.style('height', '0px')\n\t\t\t.style('padding', '0px')\n\t\tfor (const ds of attrlst) {\n\t\t\tif (!ds.atlst) continue\n\t\t\tlet spannum = 0\n\t\t\tfor (const a of ds.atlst) {\n\t\t\t\tif (!a.hide) spannum++\n\t\t\t}\n\t\t\ttr1\n\t\t\t\t.append('td')\n\t\t\t\t.attr('colspan', spannum)\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('border-right', impspace)\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('top', '1px')\n\t\t\t\t.style('border-bottom', dscount > 1 ? 'solid 1px black' : '')\n\t\t\t\t.text(dscount > 1 ? ds.name : '')\n\t\t}\n\t\tfor (const dsname in ds2import) {\n\t\t\t// 2 stands for #m, and #sample\n\t\t\tconst td = tr1\n\t\t\t\t.append('td')\n\t\t\t\t.attr('colspan', 2 + importclass[dsname].length)\n\t\t\t\t.style('border-right', impspace)\n\t\t\t\t.append('div')\n\t\t\t\t.style('top', '2px')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('color', cohort.genome.datasets[dsname].color)\n\t\t\t\t.style('border-bottom', 'solid 1px ' + cohort.genome.datasets[dsname].color)\n\t\t\ttd.append('span').text(\n\t\t\t\tcohort.genome.datasets[dsname].label +\n\t\t\t\t\t(ds2import[dsname].totalsample ? ', ' + ds2import[dsname].totalsample + ' total samples' : '')\n\t\t\t)\n\t\t\ttd.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('right', '0px')\n\t\t\t\t.style('top', '-5px')\n\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t.html('&#10005;')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tdelete ds2import[dsname]\n\t\t\t\t\tfor (const n in gene2import) {\n\t\t\t\t\t\tdelete gene2import[n][dsname]\n\t\t\t\t\t}\n\t\t\t\t\tdotable()\n\t\t\t\t})\n\t\t}\n\n\t\t// collect table matrix for export\n\t\tconst exportlines = []\n\n\t\tconst exportheader = []\n\n\t\t// tr 2, header\n\t\tconst tr2 = table.append('tr')\n\t\ttr2.append('td').style('height', '0px').style('padding', '0px')\n\n\t\t//exportheader.push('')\n\n\t\tfor (const a of attrlst) {\n\t\t\tif (a.hide) continue\n\t\t\tlet lst = []\n\t\t\tif (a.atlst) {\n\t\t\t\tlst = a.atlst\n\t\t\t} else {\n\t\t\t\tlst = [a]\n\t\t\t}\n\t\t\tlet td\n\t\t\tfor (const at of lst) {\n\t\t\t\tif (at.hide) continue\n\t\t\t\ttd = tr2\n\t\t\t\t\t.append('td')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t.style('height', '0px')\n\t\t\t\t\t.style('padding', '0px')\n\t\t\t\t\t.style('color', at.color ? at.color : 'black')\n\t\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(\n\t\t\t\t\t\tat.rotate\n\t\t\t\t\t\t\t? at.sort\n\t\t\t\t\t\t\t\t? (at.descend ? '&#9664;' : '&#9654;') + ' ' + at.label\n\t\t\t\t\t\t\t\t: at.label\n\t\t\t\t\t\t\t: at.label + (at.sort ? ' ' + (at.descend ? '&#9662;' : '&#9652;') : '')\n\t\t\t\t\t)\n\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t.style('top', scrolltoppad - 25 + 'px')\n\t\t\t\t\t.style('transform', at.rotate ? 'translate(-3px,0px) rotate(-90deg)' : '')\n\t\t\t\t\t.style('width', at.rotate ? '25px' : 'auto')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tconst ps = at.sort\n\t\t\t\t\t\tfor (const a of attrlst) {\n\t\t\t\t\t\t\tif (a.atlst) {\n\t\t\t\t\t\t\t\tfor (const b of a.atlst) {\n\t\t\t\t\t\t\t\t\tb.sort = false\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\ta.sort = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tat.sort = true\n\t\t\t\t\t\tif (ps) {\n\t\t\t\t\t\t\tat.descend = !at.descend\n\t\t\t\t\t\t}\n\t\t\t\t\t\tdotable()\n\t\t\t\t\t})\n\n\t\t\t\texportheader.push(at.label + (a.name ? '.' + a.name : ''))\n\t\t\t}\n\t\t\ttd.style('border-right', impspace)\n\t\t}\n\t\t// imported ds header items\n\t\tfor (const dsname in ds2import) {\n\t\t\t// # m count\n\t\t\ttr2\n\t\t\t\t.append('td')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('height', '0px')\n\t\t\t\t.style('padding', '0px')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.append('div')\n\t\t\t\t.html('# mutation')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('top', scrolltoppad - 25 + 'px')\n\t\t\t\t.style('transform', 'translate(-3px,0px) rotate(-90deg)')\n\t\t\t\t.style('width', '25px')\n\n\t\t\texportheader.push(dsname + '.#mutation')\n\n\t\t\t// # sample\n\t\t\ttr2\n\t\t\t\t.append('td')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('height', '0px')\n\t\t\t\t.style('padding', '0px')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.append('div')\n\t\t\t\t.html('# sample')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('top', scrolltoppad - 25 + 'px')\n\t\t\t\t.style('transform', 'translate(-3px,0px) rotate(-90deg)')\n\t\t\t\t.style('width', '25px')\n\n\t\t\texportheader.push(dsname + '.#sample')\n\n\t\t\tlet td\n\t\t\tfor (const cls of importclass[dsname]) {\n\t\t\t\ttd = tr2\n\t\t\t\t\t.append('td')\n\t\t\t\t\t.style('font-size', '80%')\n\t\t\t\t\t.style('overflow-y', 'hidden')\n\t\t\t\t\t.style('height', '0px')\n\t\t\t\t\t.style('padding', '0px')\n\t\t\t\t\t.style('color', common.mclass[cls.class].color)\n\t\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(common.mclass[cls.class].label)\n\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t.style('top', scrolltoppad - 25 + 'px')\n\t\t\t\t\t.style('transform', 'translate(-3px,0px) rotate(-90deg)')\n\t\t\t\t\t.style('width', '25px')\n\n\t\t\t\texportheader.push(dsname + '.' + common.mclass[cls.class].label)\n\t\t\t}\n\t\t\tif (td) {\n\t\t\t\ttd.style('border-right', impspace)\n\t\t\t}\n\t\t}\n\n\t\texportlines.push(exportheader.join('\\t'))\n\n\t\tfor (let i = 0; i < genelimit; i++) {\n\t\t\tconst gene = genelst[i]\n\n\t\t\tconst exportline = [gene]\n\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td')\n\t\t\t\t.text(i + 1)\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('text-align', 'right')\n\t\t\tfor (const at of attrlst) {\n\t\t\t\tif (at.hide) continue\n\t\t\t\tif (at.isgenename) {\n\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t.text(genelst[i])\n\t\t\t\t\t\t.attr('class', 'sja_menuoption_y')\n\t\t\t\t\t\t.style('color', 'black')\n\t\t\t\t\t\t.style('display', 'table-cell')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tpaintgene(genelst[i])\n\t\t\t\t\t\t})\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\t// no testing?\n\t\t\t\tlet td\n\t\t\t\tfor (const bt of at.atlst) {\n\t\t\t\t\tif (bt.hide) continue\n\t\t\t\t\ttd = tr.append('td').style('color', 'black').style('background-color', '#f1f1f1')\n\t\t\t\t\tconst m = bt.get(gene)\n\t\t\t\t\tif (typeof m == 'number') {\n\t\t\t\t\t\tif (bt.color) {\n\t\t\t\t\t\t\tif (m > 0) {\n\t\t\t\t\t\t\t\ttd.style('text-align', 'center')\n\t\t\t\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t\t\t\t\t\t.style('background-color', bt.color)\n\t\t\t\t\t\t\t\t\t.html(m > 1 ? m : '&nbsp;')\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\ttd.append('span').attr('class', 'sja_mcdot').style('margin', '0px 4px').html('&nbsp;')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\ttd.text(m)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttd.text(m)\n\t\t\t\t\t}\n\n\t\t\t\t\texportline.push(m)\n\t\t\t\t}\n\t\t\t\ttd.style('border-right', impspace)\n\t\t\t}\n\t\t\tfor (const dsname in ds2import) {\n\t\t\t\tlet sample = 0,\n\t\t\t\t\ttotal = 0,\n\t\t\t\t\tclasssum = {},\n\t\t\t\t\tnotexist = true,\n\t\t\t\t\tpending = false\n\t\t\t\tif (gene in gene2import) {\n\t\t\t\t\tconst ipd = gene2import[gene][dsname]\n\t\t\t\t\tif (!ipd) continue\n\t\t\t\t\tnotexist = false\n\t\t\t\t\tif (ipd.pending) {\n\t\t\t\t\t\tpending = true\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tsample += ipd.sample\n\t\t\t\t\ttotal += ipd.total\n\t\t\t\t\tfor (const c in ipd.class) {\n\t\t\t\t\t\tif (!(c in classsum)) {\n\t\t\t\t\t\t\tclasssum[c] = 0\n\t\t\t\t\t\t}\n\t\t\t\t\t\tclasssum[c] += ipd.class[c]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (notexist) {\n\t\t\t\t\ttr.append('td').attr('colspan', 2 + importclass[dsname].length)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tif (pending) {\n\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t.attr('colspan', 2 + importclass[dsname].length)\n\t\t\t\t\t\t.text('loading ...')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\ttr.append('td').text(total).style('background-color', '#f1f1f1')\n\n\t\t\t\texportline.push(total)\n\n\t\t\t\ttr.append('td').text(sample).style('background-color', '#f1f1f1')\n\n\t\t\t\texportline.push(sample)\n\n\t\t\t\tlet td\n\t\t\t\tfor (const cls of importclass[dsname]) {\n\t\t\t\t\ttd = tr.append('td').style('text-align', 'center').style('background-color', '#f1f1f1')\n\t\t\t\t\tconst _count = classsum[cls.class]\n\t\t\t\t\tif (_count) {\n\t\t\t\t\t\ttd.append('span')\n\t\t\t\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t\t\t\t.style('background-color', common.mclass[cls.class].color)\n\t\t\t\t\t\t\t.html(_count > 1 ? _count : '&nbsp;')\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttd.append('span').attr('class', 'sja_mcdot').style('margin', '0px 4px').html('&nbsp;')\n\t\t\t\t\t}\n\n\t\t\t\t\texportline.push(_count)\n\t\t\t\t}\n\t\t\t\ttd.style('border-right', impspace)\n\t\t\t}\n\n\t\t\texportlines.push(exportline.join('\\t'))\n\t\t}\n\t\treturn exportlines.join('\\n')\n\t}\n\n\tdotable()\n\tfunction paintgene(gene) {\n\t\tif (!(gene in union)) return\n\t\ttip.hide()\n\t\tconst dslst = []\n\t\tfor (const k in cohort.dsset) {\n\t\t\tdslst.push(k)\n\t\t}\n\t\tlet pane\n\t\tfor (const isoform in union[gene].isoform) {\n\t\t\tif (!pane) {\n\t\t\t\tpane = client.newpane({ x: 100, y: 100 })\n\t\t\t}\n\t\t\tblockinit({\n\t\t\t\thostURL: hostURL,\n\t\t\t\tjwt: cohort.jwt,\n\t\t\t\tholder: pane.body,\n\t\t\t\tgenome: cohort.genome,\n\t\t\t\tquery: isoform,\n\t\t\t\tnopopup: true,\n\t\t\t\tdataset: dslst\n\t\t\t})\n\t\t}\n\n\t\tif (cohort.loadgeneexpressionfromofficialds) {\n\t\t\ttp_getgeneexpression({\n\t\t\t\tgene: gene,\n\t\t\t\tgenome: cohort.genome.name,\n\t\t\t\tloadgeneexpressionfromofficialds: cohort.loadgeneexpressionfromofficialds,\n\t\t\t\thostURL: cohort.hostURL,\n\t\t\t\tjwt: cohort.jwt,\n\t\t\t\tx: 1000,\n\t\t\t\ty: 80\n\t\t\t})\n\t\t}\n\t}\n}\n\nasync function barplot(bars, color, label, pos) {\n\tconst barplot = await import('./old/plot.barplot')\n\treturn barplot.default(bars, color, label, pos)\n}\n", "import { select as d3select, selectAll as d3selectAll, pointer } from 'd3-selection'\nimport { pie as d3pie, arc as d3arc } from 'd3-shape'\nimport { scaleLinear, scaleOrdinal } from 'd3-scale'\nimport { pack as d3pack, hierarchy as d3hierarchy } from 'd3-hierarchy'\nimport * as d3drag from 'd3-drag'\nimport * as d3force from 'd3-force'\nimport * as common from '#shared/common.js'\nimport * as client from './client'\nimport { Menu } from '../dom/menu'\n\nconst tip = new Menu()\n\nexport default function (cohort, folder) {\n\tconst dslst = []\n\tfor (const n in cohort.dsset) {\n\t\tconst ds = cohort.genome.datasets[n]\n\t\tif (!ds) {\n\t\t\tfolder.text('error: dataset not found by name ' + n)\n\t\t\treturn\n\t\t}\n\t\tdslst.push(ds)\n\t}\n\tconst config = {\n\t\tgeneToUpper: cohort.geneToUpper\n\t}\n\tif (cohort.diseasecolor) {\n\t\tconfig.diseasecolor = cohort.diseasecolor\n\t}\n\n\tif (cohort.genenetwork && cohort.genenetwork.list) {\n\t\t// pre-configured network\n\t\t// use only first dataset FIXME\n\t\tconst ds = dslst[0]\n\t\tfor (const network of cohort.genenetwork.list) {\n\t\t\tconst holder = folder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('border', 'solid 1px #ccc')\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.style('background-color', '#f1f1f1')\n\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t.text(network.name || 'network.name is undefined')\n\t\t\tconst div = holder.append('div').style('margin', '10px')\n\t\t\tprepdata(ds, network, div, cohort)\n\t\t}\n\t\treturn\n\t}\n\tfor (const ds of dslst) {\n\t\tconst holder = folder.append('div').style('margin', '10px')\n\t\tif (dslst.length > 1) {\n\t\t\tholder.style('border', 'solid 1px #ccc')\n\t\t\tholder.append('div').style('padding', '5px').style('background-color', '#ededed').text(ds.label)\n\t\t}\n\t\tconst table = holder.append('table')\n\t\tconst tr = table.append('tr')\n\t\tconst td1 = tr.append('td').style('vertical-align', 'top')\n\t\tconst td2 = tr.append('td').style('vertical-align', 'top')\n\t\tconst row1 = td1.append('div').style('margin-bottom', '5px')\n\t\trow1\n\t\t\t.append('button')\n\t\t\t.text('Submit')\n\t\t\t.style('margin-right', '3px')\n\t\t\t.on('click', () => {\n\t\t\t\tprepdata_input(ds, input, td2, config)\n\t\t\t})\n\t\trow1\n\t\t\t.append('button')\n\t\t\t.text('Clear')\n\t\t\t.style('margin-right', '10px')\n\t\t\t.on('click', () => {\n\t\t\t\tinput.node().value = ''\n\t\t\t})\n\t\trow1\n\t\t\t.append('a')\n\t\t\t.text('Help')\n\t\t\t.attr('href', 'https://docs.google.com/document/d/1PAlu-bJMBuHRVpGhB_eVaOmlhhbWneC_94_7RRItuA8/edit?usp=sharing')\n\t\t\t.attr('target', '_blank')\n\t\tconst input = td1.append('textarea').attr('rows', 10).attr('cols', 20).attr('placeholder', 'enter pathway schema')\n\t}\n}\n\nfunction prepdata_input(ds, input, holder, config) {\n\tconst text = input.node().value\n\tif (text == '') return\n\tlet json\n\ttry {\n\t\tjson = JSON.parse(text)\n\t} catch (e) {\n\t\tholder.text('Invalid JSON')\n\t\tconsole.log(e)\n\t\treturn\n\t}\n\tprepdata(ds, json, holder, config)\n}\n\nfunction prepdata(ds, json, holder, config) {\n\tconst err = m => holder.html('<span style=\"color:red\">' + m + '</span>')\n\tif (!json.nodes) return err('.nodes missing')\n\tif (!Array.isArray(json.nodes)) return err('.nodes should be an array')\n\tif (json.nodes.length == 0) return err('no nodes')\n\tconst nodeid = new Map()\n\tfor (const node of json.nodes) {\n\t\tif (!node.id) return err('.id missing for node ' + JSON.stringify(node))\n\t\tif (nodeid.has(node.id)) return err('duplicating node id: ' + node.id)\n\t\tnodeid.set(node.id, 1)\n\t\tconst root = {\n\t\t\tname: node.name || 'nameless',\n\t\t\tchildren: [],\n\t\t\tnode: node // refer to force-laying node\n\t\t}\n\t\tif (node.gene) {\n\t\t\troot.children.push({\n\t\t\t\tgene: node.gene\n\t\t\t})\n\t\t} else if (node.geneset) {\n\t\t\t// recursive structure\n\t\t\troot.children = node.geneset\n\t\t}\n\t\tconst root2 = d3hierarchy(root)\n\t\tlet genecount = 0\n\t\tfor (const gene of root2.leaves()) {\n\t\t\tif (!gene.data.gene) return err('a gene has no gene name in node ' + JSON.stringify(node))\n\t\t\tgenecount++\n\t\t}\n\t\tif (genecount == 0) return err('no gene in node ' + JSON.stringify(node))\n\t\tdelete node.gene\n\t\tdelete node.geneset\n\t\tnode.root = root2\n\t}\n\tif (!json.links) return err('.links missing')\n\tif (!Array.isArray(json.links)) return err('.links should be an array')\n\tfor (const link of json.links) {\n\t\tif (!link.source) return err('.source missing from a link ' + JSON.stringify(link))\n\t\tif (!nodeid.has(link.source)) return err('invalid \"source\" node in link ' + JSON.stringify(link))\n\t\tif (!link.target) return err('.target missing from a link ' + JSON.stringify(link))\n\t\tif (!nodeid.has(link.target)) return err('invalid \"target\" node in link ' + JSON.stringify(link))\n\t}\n\tholder.text('')\n\tmakegraph(ds, json, holder, config)\n}\n\nfunction makegraph(ds, json, holder, config) {\n\tlet diseasecolor\n\tif (config.diseasecolor) {\n\t\tconst lst1 = [],\n\t\t\tlst2 = []\n\t\tfor (const n in config.diseasecolor) {\n\t\t\tlst1.push(n)\n\t\t\tlst2.push(config.diseasecolor[n])\n\t\t}\n\t\tdiseasecolor = scaleOrdinal().domain(lst1).range(lst2)\n\t} else {\n\t\tconsole.log('using hardcoded target color') //////////////////\n\t\t////////////////////\n\t\t/* hard coded diseases for pan-target study\n\n\t\t\t\"AML\":\"#dc5ce2\",\n\t\t\t\"NBL\":\"#ff1111\",\n\t\t\t\"TALL\":\"#ffa500\",\n\t\t\t\"BALL\":\"#1f78b4\",\n\t\t\t\"WT\":\"#3e8320\",\n\t\t\t\"OS\":\"#6a3d9a\"\n\t\t*/ diseasecolor = scaleOrdinal()\n\t\t\t.domain(['AML', 'NBL', 'TALL', 'BALL', 'WT', 'OS'])\n\t\t\t.range(['#dc5ce2', '#ff1111', '#ffa500', '#1f78b4', '#3e8320', '#6a3d9a'])\n\t}\n\t// getting data, mlst\n\tfor (const node of json.nodes) {\n\t\tfor (const gene of node.root.leaves()) {\n\t\t\tgene.datasize = 0\n\t\t\tconst genename = config.geneToUpper ? gene.data.gene.toUpperCase() : gene.data.gene\n\t\t\tconst mlst = ds.bulkdata[genename]\n\t\t\tif (mlst) {\n\t\t\t\tif (ds.hasdisease && ds.hassample) {\n\t\t\t\t\t// disease as pie\n\t\t\t\t\t// sample # as pie size\n\t\t\t\t\tconst sampleset = new Set()\n\t\t\t\t\tconst disease2sset = new Map()\n\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\tif (!m.disease) continue\n\t\t\t\t\t\tif (!m.sample) continue\n\t\t\t\t\t\tsampleset.add(m.sample)\n\t\t\t\t\t\tif (!disease2sset.has(m.disease)) {\n\t\t\t\t\t\t\tdisease2sset.set(m.disease, new Set())\n\t\t\t\t\t\t}\n\t\t\t\t\t\tdisease2sset.get(m.disease).add(m.sample)\n\t\t\t\t\t}\n\t\t\t\t\tconst piedata = []\n\t\t\t\t\tfor (const [diseasename, sset] of disease2sset) {\n\t\t\t\t\t\tpiedata.push({\n\t\t\t\t\t\t\tname: diseasename,\n\t\t\t\t\t\t\tcolor: diseasecolor(diseasename),\n\t\t\t\t\t\t\tsize: sset.size\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tgene.pie = d3pie().value(d => d.size)(piedata)\n\t\t\t\t\t// !!!! somehow the value must be set to gene.data\n\t\t\t\t\t// won't work if set to gene.value\n\t\t\t\t\tgene.datasize = sampleset.size\n\t\t\t\t} else if (ds.hassample) {\n\t\t\t\t\t// mclass as pie\n\t\t\t\t\t// sample # as pie size\n\t\t\t\t\tconst sampleset = new Map()\n\t\t\t\t\tconst mclass2sset = new Map()\n\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\tif (!m.sample) continue\n\t\t\t\t\t\tif (!m.class) continue\n\t\t\t\t\t\tsampleset.set(m.sample, 1)\n\t\t\t\t\t\tif (!mclass2sset.has(m.class)) {\n\t\t\t\t\t\t\tmclass2sset.set(m.class, new Map())\n\t\t\t\t\t\t}\n\t\t\t\t\t\tmclass2sset.get(m.class).set(m.sample, 1)\n\t\t\t\t\t}\n\t\t\t\t\tconst piedata = []\n\t\t\t\t\tfor (const [cls, sset] of mclass2sset.entries()) {\n\t\t\t\t\t\tpiedata.push({\n\t\t\t\t\t\t\tname: common.mclass[cls].label,\n\t\t\t\t\t\t\tcolor: common.mclass[cls].color,\n\t\t\t\t\t\t\tsize: sset.size\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tgene.pie = d3pie().value(d => d.size)(piedata)\n\t\t\t\t\t// !!!! somehow the value must be set to gene.data\n\t\t\t\t\t// won't work if set to gene.value\n\t\t\t\t\tgene.datasize = sampleset.size\n\t\t\t\t} else {\n\t\t\t\t\t// mclass as pie\n\t\t\t\t\tconst mclass2count = new Map()\n\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\tif (!m.class) continue\n\t\t\t\t\t\tif (!mclas2count.has(m.class)) {\n\t\t\t\t\t\t\tmclass2count.set(m.class, 0)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tmclass2count.set(m.class, mclass2count.get(m.class) + 1)\n\t\t\t\t\t}\n\t\t\t\t\tconst piedata = []\n\t\t\t\t\tfor (const [cls, size] of mclass2count.entries()) {\n\t\t\t\t\t\tpiedata.push({\n\t\t\t\t\t\t\tname: common.mclass[cls].label,\n\t\t\t\t\t\t\tcolor: common.mclass[cls].color,\n\t\t\t\t\t\t\tsize: size\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tgene.pie = d3pie().value(d => d.size)(piedata)\n\t\t\t\t\tgene.datasize = mlst.length\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\t// gene value for deciding pie radius\n\tlet minvalue = 9999,\n\t\tmaxvalue = 0\n\tfor (const node of json.nodes) {\n\t\tfor (const d of node.root.leaves()) {\n\t\t\tif (d.datasize) {\n\t\t\t\tminvalue = Math.min(minvalue, d.datasize)\n\t\t\t\tmaxvalue = Math.max(maxvalue, d.datasize)\n\t\t\t}\n\t\t}\n\t}\n\tconst value2pieradius = scaleLinear().domain([minvalue, maxvalue])\n\n\tholder\n\t\t.append('div')\n\t\t.append('button')\n\t\t.text('Snapshot')\n\t\t.on('click', () => {\n\t\t\tclient.to_svg(svg.node(), 'pathway')\n\t\t})\n\tconst svg = holder.append('svg')\n\t/*\n\tconst resize=svg.append('text')\n\t\t.text('drag to resize')\n\t\t.attr('class','sja_clbtext')\n\t\t.attr('text-anchor','end')\n\t\t.attr('font-size',12)\n\t\t.attr('font-family',client.font)\n\t\t.attr('fill','black')\n\t\t.on('mousedown',(event)=>{\n\t\t\tevent.preventDefault()\n\t\t\tconst x0=event.clientX\n\t\t\tconst y0=event.clientY\n\t\t\tconst body=d3select(document.body)\n\t\t\tconst width0=width, height0=height\n\t\t\tbody.on('mousemove',()=>{\n\t\t\t\twidth=width0+event.clientX-x0\n\t\t\t\theight=height0+event.clientY-y0\n\t\t\t\trender(true)\n\t\t\t})\n\t\t\tbody.on('mouseup',()=>{\n\t\t\t\tbody.on('mousemove',null).on('mouseup',null)\n\t\t\t})\n\t\t})\n\t\t*/\n\n\tconst defs = svg.append('svg:defs')\n\tdefs\n\t\t.append('svg:marker')\n\t\t.attr('id', 'arrowactivate')\n\t\t.attr('viewBox', '0 -5 10 10')\n\t\t.attr('refX', 9)\n\t\t.attr('refY', 0)\n\t\t.attr('markerWidth', 6)\n\t\t.attr('markerHeight', 6)\n\t\t.attr('orient', 'auto')\n\t\t.append('svg:path')\n\t\t.attr('d', 'M0,-5L10,0L0,5')\n\tdefs\n\t\t.append('svg:marker')\n\t\t.attr('id', 'arrowinhibit')\n\t\t.attr('viewBox', '0 -5 10 10')\n\t\t.attr('refX', 2)\n\t\t.attr('refY', 0)\n\t\t.attr('markerWidth', 6)\n\t\t.attr('markerHeight', 6)\n\t\t.attr('orient', 'auto')\n\t\t.append('rect')\n\t\t.attr('y', -5)\n\t\t.attr('width', 2)\n\t\t.attr('height', 10)\n\t\t.attr('fill', 'red')\n\n\tconst legend = svg.append('g')\n\n\t// link lines\n\tconst linkg = svg.selectAll().data(json.links).enter().append('line')\n\tlinkg\n\t\t.attr('stroke', d => (d.inhibit ? 'red' : 'black'))\n\t\t.attr('stroke-width', '2')\n\t\t.attr('marker-end', d => (d.inhibit ? 'url(#arrowinhibit)' : 'url(#arrowactivate)'))\n\n\t// force nodes\n\tconst node1g = svg\n\t\t.selectAll()\n\t\t.data(json.nodes)\n\t\t.enter()\n\t\t.append('g')\n\t\t.each(function (d) {\n\t\t\td.nodeg = this\n\t\t})\n\n\t// pack nodes\n\tfor (const node of json.nodes) {\n\t\t// all elements are relative to node1g, position defined by render(packing())\n\t\tnode.pack = {}\n\t\tnode.pack.gs = d3select(node.nodeg).selectAll().data(node.root.descendants()).enter().append('g')\n\t\tnode.pack.circle = node.pack.gs.append('circle').attr('fill', d => {\n\t\t\tif (!d.parent) {\n\t\t\t\t// root\n\t\t\t\tif (d.children.length == 1) {\n\t\t\t\t\t// this removes gray circle background for nodes with a single gene\n\t\t\t\t\treturn 'none'\n\t\t\t\t}\n\t\t\t\treturn '#ededed'\n\t\t\t}\n\t\t\tif (!d.children) {\n\t\t\t\t// leaf\n\t\t\t\treturn 'none'\n\t\t\t}\n\t\t\treturn 'none'\n\t\t})\n\t\t/*\n\t\t\tno border\n\n\t\t\t.attr('stroke',d=>{\n\t\t\t\tif(!d.parent) {\n\t\t\t\t\treturn 'none'\n\t\t\t\t}\n\t\t\t\treturn '#ccc'\n\t\t\t})\n\t\t\t*/\n\n\t\tnode.pack.pie = node.pack.gs\n\t\t\t.filter(d => !d.children && d.pie)\n\t\t\t.selectAll()\n\t\t\t.data(d => d.pie)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('fill', d => d.data.color)\n\t}\n\tfor (const node of json.nodes) {\n\t\t// put label on top of all circles and pies\n\t\tnode.pack.gs\n\t\t\t.filter(d => !d.children)\n\t\t\t.each(d => {\n\t\t\t\td.textlabel = d3select(node.nodeg)\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.text(d.data.gene)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t//.attr('dominant-baseline','central')\n\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t.call(d3drag.drag().on('start', dragstarted).on('drag', dragged).on('end', dragended))\n\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\ttip.clear().show(event.clientX + 20, event.clientY + 20)\n\t\t\t\t\t\tconst div = tip.d\n\t\t\t\t\t\tdiv.append('div').text(d.data.gene).style('font-weight', 'bold').style('margin', '10px')\n\t\t\t\t\t\tconst p = div.append('div').style('margin', '10px')\n\t\t\t\t\t\tif (d.datasize) {\n\t\t\t\t\t\t\tp.text('In ' + d.datasize + ' sample' + (d.datasize > 1 ? 's' : ''))\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tp.text('No sample')\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (d.pie) {\n\t\t\t\t\t\t\tconst p = div.append('div').style('margin', '10px')\n\t\t\t\t\t\t\td.pie.sort((a, b) => b.data.size - a.data.size)\n\t\t\t\t\t\t\tfor (const pie of d.pie) {\n\t\t\t\t\t\t\t\tp.append('div')\n\t\t\t\t\t\t\t\t\t.style('margin', '3px 0px')\n\t\t\t\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\t\t\t\t'<span style=\"background-color:' +\n\t\t\t\t\t\t\t\t\t\t\tpie.data.color +\n\t\t\t\t\t\t\t\t\t\t\t'\">&nbsp;&nbsp;&nbsp;</span> ' +\n\t\t\t\t\t\t\t\t\t\t\tpie.data.name +\n\t\t\t\t\t\t\t\t\t\t\t' ' +\n\t\t\t\t\t\t\t\t\t\t\tpie.data.size\n\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t})\n\t\t\t})\n\t}\n\n\tlet width = 800,\n\t\theight = 800\n\n\tconst simulation = d3force\n\t\t.forceSimulation(json.nodes)\n\t\t.force(\n\t\t\t'link',\n\t\t\td3force\n\t\t\t\t.forceLink()\n\t\t\t\t.id(d => d.id)\n\t\t\t\t.links(json.links)\n\t\t\t//.distance(50)\n\t\t\t//.strength(1)\n\t\t)\n\t\t.force(\n\t\t\t'charge',\n\t\t\td3force.forceManyBody().strength(() => -1000)\n\t\t\t//.distanceMax(100)\n\t\t)\n\t\t.force('x', d3force.forceX())\n\t\t.force('y', d3force.forceY())\n\t\t.alphaDecay(0.1)\n\t//.velocityDecay(.8)\n\t//.on('end',()=>simuend())\n\n\trender()\n\t//window.json=json\n\n\tfunction render(restart) {\n\t\tconst wh = Math.min(width, height)\n\t\tconst pieminr = Math.min(5, wh / 50)\n\t\tconst piemaxr = Math.min(50, wh / 20)\n\n\t\tvalue2pieradius.range([Math.pow(pieminr, 2), Math.pow(piemaxr, 2)])\n\t\tfor (const node of json.nodes) {\n\t\t\tfor (const gene of node.root.leaves()) {\n\t\t\t\tif (gene.datasize) {\n\t\t\t\t\tgene.pieradius = Math.sqrt(value2pieradius(gene.datasize))\n\t\t\t\t} else {\n\t\t\t\t\tgene.pieradius = 0\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst fontsize = Math.min(20, wh / 40)\n\t\tconst maxtextwidth = piemaxr * 1.5\n\n\t\t// leaf labels\n\t\tfor (const node of json.nodes) {\n\t\t\tnode.pack.gs\n\t\t\t\t.filter(d => !d.children)\n\t\t\t\t.each(d => {\n\t\t\t\t\td.textlabel\n\t\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t\t.each(function () {\n\t\t\t\t\t\t\tlet labelwidth = this.getBBox().width\n\t\t\t\t\t\t\tif (labelwidth > maxtextwidth) {\n\t\t\t\t\t\t\t\tlabelwidth = maxtextwidth\n\t\t\t\t\t\t\t\t//this.setAttribute('font-size',1)\n\t\t\t\t\t\t\t\tthis.setAttribute('font-size', maxtextwidth / this.getBBox().width)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tthis.setAttribute('font-size', 17) // XXX\n\t\t\t\t\t\t\td.data.value = Math.max(labelwidth / 2, d.pieradius)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.attr('dominant-baseline', () => {\n\t\t\t\t\t\t\tif (d.pieradius == 0) {\n\t\t\t\t\t\t\t\t// empty, no pie\n\t\t\t\t\t\t\t\treturn 'central'\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\treturn 'hanging'\n\t\t\t\t\t\t})\n\t\t\t\t\t// will set text y position in ticked()\n\t\t\t\t})\n\t\t}\n\n\t\tfor (const node of json.nodes) {\n\t\t\tnode.root.sum(d => d.value)\n\t\t\td3pack().radius(d => d.data.value)(node.root)\n\t\t\tnode.pack.circle\n\t\t\t\t.attr('r', d => d.r)\n\t\t\t\t.filter(d => !d.children && d.pie)\n\t\t\t\t.each(d => {\n\t\t\t\t\tfor (const pie of d.pie) pie.data.r = d.pieradius\n\t\t\t\t})\n\t\t\tnode.pack.pie.attr('d', d => {\n\t\t\t\treturn d3arc()({ innerRadius: 0, outerRadius: d.data.r, startAngle: d.startAngle, endAngle: d.endAngle })\n\t\t\t})\n\t\t}\n\t\tsimulation.force('center', d3force.forceCenter(width / 2, height / 2)).force(\n\t\t\t'collision',\n\t\t\td3force\n\t\t\t\t.forceCollide()\n\t\t\t\t.radius(d => {\n\t\t\t\t\treturn d.root.r + Math.max(20, d.root.r * 0.3)\n\t\t\t\t})\n\t\t\t\t.strength(0.9)\n\t\t)\n\t\tsimulation.on('tick', simuend)\n\t\tsvg.attr('width', width).attr('height', height)\n\t\t//resize.attr('x',width-2).attr('y',height-4)\n\t\tlegend.selectAll('*').remove()\n\t\tlet y = 0,\n\t\t\tpad = 3\n\t\tlegend\n\t\t\t.append('text')\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('y', fontsize)\n\t\t\t.text('Sample number')\n\t\ty += fontsize + pad\n\t\tlegend\n\t\t\t.append('circle')\n\t\t\t.attr('cx', pieminr)\n\t\t\t.attr('cy', y + pieminr)\n\t\t\t.attr('r', pieminr)\n\t\t\t.attr('fill', '#ccc')\n\t\tlegend\n\t\t\t.append('text')\n\t\t\t.attr('x', pieminr * 2 + pad)\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('y', y + pieminr)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.text(minvalue)\n\t\ty += Math.max(fontsize, pieminr * 2) + pad\n\t\tlegend\n\t\t\t.append('circle')\n\t\t\t.attr('cx', piemaxr)\n\t\t\t.attr('cy', y + piemaxr)\n\t\t\t.attr('r', piemaxr)\n\t\t\t.attr('fill', '#ccc')\n\t\tlegend\n\t\t\t.append('text')\n\t\t\t.attr('x', piemaxr * 2 + pad)\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('y', y + piemaxr)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.text(maxvalue)\n\t\ty += Math.max(fontsize, piemaxr * 2) + pad\n\t\tif (ds.hasdisease) {\n\t\t\tfor (const diseasename of diseasecolor.domain()) {\n\t\t\t\tlegend\n\t\t\t\t\t.append('circle')\n\t\t\t\t\t.attr('cx', fontsize)\n\t\t\t\t\t.attr('cy', y + fontsize / 2)\n\t\t\t\t\t.attr('r', fontsize / 2)\n\t\t\t\t\t.attr('fill', diseasecolor(diseasename))\n\t\t\t\tlegend\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('x', fontsize * 2 + pad)\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('y', y + fontsize / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t.text(diseasename)\n\t\t\t\ty += fontsize + pad\n\t\t\t}\n\t\t}\n\n\t\tif (restart) {\n\t\t\tsimulation.restart()\n\t\t}\n\t}\n\n\tfunction ticked() {\n\t\tlinkg\n\t\t\t.each(d => (d.linelen = Math.sqrt(Math.pow(d.source.x - d.target.x, 2) + Math.pow(d.source.y - d.target.y, 2))))\n\t\t\t.attr('x1', d => {\n\t\t\t\tconst r = d.source.root.r\n\t\t\t\treturn d.source.x + ((d.target.x - d.source.x) * r) / d.linelen\n\t\t\t})\n\t\t\t.attr('y1', d => {\n\t\t\t\tconst r = d.source.root.r\n\t\t\t\treturn d.source.y + ((d.target.y - d.source.y) * r) / d.linelen\n\t\t\t})\n\t\t\t.attr('x2', d => {\n\t\t\t\tconst r = d.target.root.r\n\t\t\t\treturn d.source.x + ((d.target.x - d.source.x) * (d.linelen - r - 5)) / d.linelen\n\t\t\t})\n\t\t\t.attr('y2', d => {\n\t\t\t\tconst r = d.target.root.r\n\t\t\t\treturn d.source.y + ((d.target.y - d.source.y) * (d.linelen - r - 5)) / d.linelen\n\t\t\t})\n\t\t//node1g.attr('transform',d=>'translate('+(d.x-d.root.r)+','+(d.y-d.root.r)+')')\n\t\tnode1g.attr('transform', d => 'translate(' + d.x + ',' + d.y + ')')\n\t\tfor (const node of json.nodes) {\n\t\t\tnode.pack.gs.attr('transform', d => 'translate(' + d.x + ',' + d.y + ')')\n\t\t\t// adjust gene label position\n\t\t\t// gene labels were attached to node.pack.gs\n\t\t\t// must be shifted by d.x d.y\n\t\t\tnode.pack.gs\n\t\t\t\t.filter(d => !d.children)\n\t\t\t\t.each(d => {\n\t\t\t\t\td.textlabel.attr('x', d.x).attr('y', d.y + d.pieradius)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tfunction dragstarted(event, d) {\n\t\t/*\n\t\tconst lst=d.ancestors()\n\t\td=lst[lst.length-1].data.node\n\t\t*/\n\t\tif (!event.active) simulation.alphaTarget(0.1).restart()\n\t\td.fx = d.x\n\t\td.fy = d.y\n\t}\n\tfunction dragged(event, d) {\n\t\t/*\n\t\tconst lst=d.ancestors()\n\t\td=lst[lst.length-1].data.node\n\t\t*/\n\t\tconst p = pointer(event, this)\n\t\td.fx = p[0]\n\t\td.fy = p[1]\n\t}\n\tfunction dragended(event, d) {\n\t\tif (!event.active) simulation.alphaTarget(0)\n\t\t/*\n\t\tconst lst=d.ancestors()\n\t\td=lst[lst.length-1].data.node\n\t\t*/\n\t\td.fx = null\n\t\td.fy = null\n\t}\n\tfunction simuend() {\n\t\tlet x1 = 0,\n\t\t\ty1 = 0,\n\t\t\tx2 = 0,\n\t\t\ty2 = 0\n\t\tfor (const node of json.nodes) {\n\t\t\tx1 = Math.min(x1, node.x - node.root.r)\n\t\t\ty1 = Math.min(y1, node.y - node.root.r)\n\t\t\tx2 = Math.max(x2, node.x + node.root.r - width)\n\t\t\ty2 = Math.max(y2, node.y + node.root.r - height)\n\t\t}\n\t\twidth = width - x1 + x2\n\t\theight = height - y1 + y2\n\t\tfor (const node of json.nodes) {\n\t\t\tnode.x -= x1\n\t\t\tnode.y -= y1\n\t\t}\n\t\tsimulation\n\t\t\t.force('center')\n\t\t\t.x(width / 2)\n\t\t\t.y(height / 2)\n\t\tsvg.attr('width', width).attr('height', height)\n\t\tticked()\n\t}\n}\n", "import * as client from './client'\n\n\n\n\nexport default function inithcmap(hm,holder)\n{\nconst err=m=>{\n\tclient.sayerror(holder,m)\n}\nif(!hm.metadata) return err('no metadata')\nconst mdh=hm.metadata\nconst legendholder=holder.append('div').style('display','inline-block').style('border','solid 1px #ccc').style('margin','20px').style('padding','20px')\nconst svg=holder.append('svg')\nif(!hm.text) return err('text missing')\nconst lines=hm.text.trim().split('\\n')\n// samples\nhm.samples=[]\nconst l=lines[0].split('\\t')\nfor(let i=2; i<l.length; i++) {\n\thm.samples.push(l[i])\n}\nif(hm.samples.length==0) return err('no column names')\nhm.items=[]\nfor(let i=1; i<lines.length; i++) {\n\tconst l=lines[i].split('\\t')\n\tconst type=l[0]\n\tconst md=mdh[type]\n\tif(!md) return err('invalid data type '+type)\n\tconst name=l[1]\n\tconst lst=[]\n\tfor(let j=2; j<l.length; j++) {\n\t\tconst vlst=l[j].split(';')\n\t\tconst colorlst=[]\n\t\tfor(const v of vlst) {\n\t\t\tif(!md[v]) {\n\t\t\t\treturn err('invalid value '+v+' at '+name+' and '+hm.samples[j-2])\n\t\t\t}\n\t\t\tcolorlst.push(md[v].color)\n\t\t}\n\t\tlst.push(colorlst)\n\t}\n\thm.items.push({\n\t\tname:name,\n\t\ttype:type,\n\t\tlst:lst\n\t})\n}\nhm.geneonrow=true\nif(!hm.rowh) {\n\thm.rowh=20\n}\nif(!hm.colw) {\n\thm.colw=20\n}\nif(!hm.rowspace) {\n\thm.rowspace=2\n}\nif(!hm.colspace) {\n\thm.colspace=2\n}\nif(!hm.rowlabtickspace) {\n\thm.rowlabtickspace=4\n}\nif(!hm.collabtickspace) {\n\thm.collabtickspace=4\n}\nif(!hm.rowtick) {\n\thm.rowtick=5\n}\nif(!hm.coltick) {\n\thm.coltick=5\n}\nrender(hm,svg,legendholder,err)\n}\n\n\n\n\n\nfunction render(hm,svg,legendholder,err)\n{\nconst mdh=hm.metadata\nfor(const key in mdh) {\n\tfor(const value in mdh[key]) {\n\t\tconst o=mdh[key][value]\n\t\tif(!o.label) return err('.label missing for metadata '+key+'['+value+']')\n\t\tif(!o.color) return err('.color missing for metadata '+key+'['+value+']')\n\t}\n}\nfor(const key in mdh) {\n\tconst d1=legendholder.append('div').style('display','inline-block').style('margin','20px').style('vertical-align','top')\n\td1.append('div').text(key).style('margin','5px 3px').style('font-weight','bold')\n\tconst d2=d1.append('div').style('margin','3px')\n\tfor(const v in mdh[key]) {\n\t\tconst o=mdh[key][v]\n\t\tconst row=d2.append('div').style('margin','3px')\n\t\trow.append('div').style('display','inline-block').style('background-color',o.color).style('width','14px').style('height','14px').style('margin-right','10px')\n\t\trow.append('span').text(o.label)\n\t}\n}\n\n\nconst rowlabfontsize=hm.rowh-3,\t\n\tcollabfontsize=hm.colw-3\n\n\n// max label width\n// label for gene and md are always shown\nlet labels=[]\nfor(const i of hm.items) {\n\tlabels.push(i.name)\n}\nlet genenamewidth=0\nfor(const n of labels) {\n\tsvg.append('text').text(n)\n\t.attr('font-size', hm.geneonrow ? rowlabfontsize : collabfontsize)\n\t.attr('font-family',client.font)\n\t.each(function(){genenamewidth=Math.max(genenamewidth,this.getBBox().width)})\n\t.remove()\n}\nlet samplenamewidth=0\nfor(const n of hm.samples) {\n\tsvg.append('text').text(n)\n\t.attr('font-size', hm.geneonrow ? collabfontsize : rowlabfontsize)\n\t.attr('font-family',client.font)\n\t.each(function(){samplenamewidth=Math.max(samplenamewidth,this.getBBox().width)})\n\t.remove()\n}\nconst rowlabw=hm.geneonrow ? genenamewidth : samplenamewidth\nconst collabh=hm.geneonrow ? samplenamewidth : genenamewidth\n\nconst mapwidth=hm.samples.length*(hm.colw+hm.colspace)-hm.colspace\nconst mapheight=hm.items.length*(hm.rowh+hm.rowspace)-hm.rowspace\nsvg.attr('width',rowlabw+hm.rowlabtickspace+hm.rowtick+mapwidth+100)\n\t.attr('height',collabh+hm.collabtickspace+hm.coltick+mapheight)\nconst originx= rowlabw+hm.rowlabtickspace+hm.rowtick \nconst originy= collabh+hm.collabtickspace+hm.coltick\n\n// row label, item\nlet y=originy\nfor(const item of hm.items) {\n\tconst g=svg.append('g').attr('transform','translate('+(originx-hm.rowlabtickspace-hm.rowtick)+','+(y+hm.rowh/2)+')')\n\tg.append('text').text(item.name)\n\t.attr('font-size',rowlabfontsize)\n\t.attr('font-family',client.font)\n\t.attr('fill', 'black')\n\t.attr('text-anchor', 'end')\n\t.attr('dominant-baseline','central')\n\t// tick\n\tg.append('line')\n\t.attr('stroke','black')\n\t.attr('shape-rendering','crispEdges')\n\t.attr('x1', hm.rowlabtickspace)\n\t.attr('x2', hm.rowlabtickspace+hm.rowtick)\n\ty+=hm.rowh+hm.rowspace\n}\n// col label, samples\nlet x= originx\nfor(const sample of hm.samples) {\n\tconst g=svg.append('g').attr('transform','translate('+(x+hm.colw/2)+','+collabh+')')\n\tg.append('text').text(sample)\n\t\t.attr('font-size',collabfontsize)\n\t\t.attr('font-family',client.font)\n\t\t.attr('fill', 'black')\n\t\t.attr('dominant-baseline','central')\n\t\t.attr('transform','rotate(-90)')\n\t// tick\n\tg.append('line')\n\t\t.attr('stroke','black')\n\t\t.attr('shape-rendering','crispEdges')\n\t\t.attr('y1', hm.collabtickspace)\n\t\t.attr('y2', hm.collabtickspace+hm.coltick)\n\tx+=hm.colw+hm.colspace\n}\n// cells\ny=originy\nfor(const item of hm.items) {\n\tlet x=originx\n\tfor(let i=0; i<hm.samples.length; i++) {\n\t\tconst sample=hm.samples[i]\n\t\tconst g=svg.append('g').attr('transform','translate('+(x+hm.colw/2)+','+(y+hm.rowh/2)+')')\n\t\tconst pieceh=hm.rowh/item.lst[i].length\n\t\tconst colorlst=item.lst[i]\n\t\tfor(let j=0; j<colorlst.length; j++) {\n\t\t\tconst v=colorlst[j]\n\t\t\tg.append('rect')\n\t\t\t\t.attr('x',-hm.colw/2)\n\t\t\t\t.attr('y',-hm.rowh/2+j*pieceh)\n\t\t\t\t.attr('width',hm.colw)\n\t\t\t\t.attr('height',pieceh)\n\t\t\t\t.attr('fill',v)\n\t\t\t\t.attr('shape-rendering','crispEdges')\n\t\t}\n\t\tx+=hm.colw+hm.colspace\n\t}\n\ty+=hm.rowh+hm.rowspace\n}\nsvg.append('rect')\n\t.attr('x',originx)\n\t.attr('y',originy)\n\t.attr('width',hm.samples.length*(hm.colw+hm.colspace)-hm.colspace)\n\t.attr('height',hm.items.length*(hm.rowh+hm.rowspace)-hm.rowspace)\n\t.attr('stroke','black')\n\t.attr('fill','none')\n\t.attr('shape-rendering','crispEdges')\n}\n", "import { json as d3json } from 'd3-fetch'\nimport * as client from './client'\n\n/*\nto call e2pca plots from study view\n\nmay apply patientannotation for sample color overlay\n\nand gene expression boxplot for categorized samples\n\n*/\n\nexport default function(cohort, folder) {\n\tfor (const obj of cohort.e2pca.list) {\n\t\tconst holder = folder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin', '20px')\n\t\t\t.style('vertical-align', 'top')\n\t\tif (cohort.e2pca.list.length > 1) {\n\t\t\tholder.style('border', 'solid 1px #ededed')\n\t\t}\n\t\tif (obj.name) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text(obj.name)\n\t\t\t\t.style('background-color', '#f1f1f1')\n\t\t\t\t.style('padding', '5px 10px')\n\t\t}\n\n\t\t/*\n\ttop row contains\n\t- svg button\n\t- gene search box\n\t- sample metadata dropdown\n\t*/\n\t\tconst toprow = holder.append('div').style('margin', '20px')\n\n\t\td3json(cohort.hostURL + '/textfile').post(JSON.stringify({ file: obj.vectorfile, jwt: cohort.jwt }), data => {\n\t\t\tif (data.error) {\n\t\t\t\tclient.sayerror(holder, 'Error getting vector file: ' + data.error)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\timport('./e2pca').then(p => {\n\t\t\t\tconst [err, numdata2plot] = p.e2pca_plot({\n\t\t\t\t\tholder: holder,\n\t\t\t\t\ttoprow: toprow,\n\t\t\t\t\ttext: data.text,\n\t\t\t\t\tmdanno: cohort.patientannotation,\n\t\t\t\t\tobj: obj\n\t\t\t\t})\n\t\t\t\tif (err) {\n\t\t\t\t\tclient.sayerror(holder, 'Error: ' + err)\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\t// pca plot made\n\n\t\t\t\tp.e2pca_genesearchui({\n\t\t\t\t\tholder: toprow,\n\t\t\t\t\tnumdata2plot: numdata2plot,\n\t\t\t\t\thostURL: cohort.hostURL,\n\t\t\t\t\tjwt: cohort.jwt,\n\t\t\t\t\tobj: obj,\n\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\tboxplot4sampleannotation(cohort, obj)\n\t\t\t\t\t}\n\t\t\t\t})\n\n\t\t\t\tif (cohort.patientannotation) {\n\t\t\t\t\t/*\n\t\t\t\thas sample metadata\n\t\t\t\t- will draw expression boxplot for samples stratified by annotation, using gene expression\n\t\t\t\t- will color samples by annotation\n\t\t\t\t*/\n\t\t\t\t\tobj.boxplotdiv = holder.append('div')\n\n\t\t\t\t\tconst div = toprow\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\tmetadataselector4pca(cohort, obj, div)\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\t}\n}\n\nfunction boxplot4sampleannotation(cohort, obj) {\n\t/*\n\tafter searching for expression data for a gene from a db\n\tmay make boxplots showing expression distribution of samples\n\tby different annotation\n\tonly do when cohort.patientannotation is available\n\n\tobj\n\t\tthe e2pca object from cohort.e2pca\n\t\t.expressiondata[]\n\t\t.usetermkey\n\t*/\n\tif (!cohort.patientannotation) {\n\t\treturn\n\t}\n\tif (!obj.expressiondata) {\n\t\t/*\n\t\texpression data is avaiable after searching for a gene in pca plot\n\t\t*/\n\t\treturn\n\t}\n\n\tif (!obj.usetermkey) {\n\t\t// use first term\n\t\tobj.usetermkey = cohort.patientannotation.metadata[0].key\n\t}\n\n\tlet term = null\n\tfor (const t of cohort.patientannotation.metadata) {\n\t\tif (t.key == obj.usetermkey) {\n\t\t\tterm = t\n\t\t\tbreak\n\t\t}\n\t}\n\tif (!term) {\n\t\tclient.sayerror(obj.boxplotdiv, 'invalid term key ' + obj.usetermkey)\n\t\treturn\n\t}\n\n\tconst samplegroups = []\n\t// by obj.usetermkey, devide samples into groups\n\tfor (const v of term.values) {\n\t\tsamplegroups.push({\n\t\t\tvaluekey: v.key,\n\t\t\tlabel: v.label,\n\t\t\tcolor: v.color,\n\t\t\tsamples: []\n\t\t})\n\t}\n\n\tlet minv = obj.expressiondata[0].value\n\tlet maxv = obj.expressiondata[0].value\n\n\tconst noattrsamples = []\n\t// collect those that are not annotated by obj.usetermkey, make last group\n\n\t// assign samples (with values) to groups\n\tfor (const s of obj.expressiondata) {\n\t\tminv = Math.min(minv, s.value)\n\t\tmaxv = Math.max(maxv, s.value)\n\n\t\tif (!cohort.patientannotation.annotation[s.sample]) {\n\t\t\t// unknown sample name\n\t\t\tnoattrsamples.push(s)\n\t\t\tcontinue\n\t\t}\n\t\tconst valuekey = cohort.patientannotation.annotation[s.sample][obj.usetermkey]\n\t\tif (valuekey == undefined) {\n\t\t\tnoattrsamples.push(s)\n\t\t\tcontinue\n\t\t}\n\t\tfor (const sg of samplegroups) {\n\t\t\tif (sg.valuekey == valuekey) {\n\t\t\t\tsg.samples.push(s)\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\n\tif (noattrsamples.length) {\n\t\tsamplegroups.push({\n\t\t\tlabel: 'unannotated',\n\t\t\tcolor: '#858585',\n\t\t\tsamples: noattrsamples\n\t\t})\n\t}\n\n\tobj.boxplotdiv.selectAll('*').remove()\n\n\timport('./old/plot.boxplot').then(p => {\n\t\tconst err = p.default({\n\t\t\tlist: samplegroups,\n\t\t\tholder: obj.boxplotdiv,\n\t\t\taxislabel: obj.searchedgene\n\t\t})\n\t\tif (err) {\n\t\t\tclient.sayerror(obj.boxplotdiv, 'Boxplot: ' + err)\n\t\t}\n\t})\n}\n\nfunction metadataselector4pca(cohort, obj, holder) {\n\t/*\n\tlist all metadata terms for selection\n\tonce selected,\n\tuse to color samples in pca\n\tand update boxplot if any\n\t*/\n\tconst tip = new client.Menu({ border: '', padding: '' })\n\tconst noannocolor = '#858585'\n\n\tholder\n\t\t.append('span')\n\t\t.text('Choose metadata')\n\t\t.attr('class', 'sja_clbtext')\n\t\t.on('click', event => {\n\t\t\t/*\n\t\tlist all terms\n\t\t*/\n\t\t\ttip.clear()\n\t\t\ttip.showunder(event.target)\n\t\t\tfor (const term of cohort.patientannotation.metadata) {\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.text(term.label)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t/*\n\t\t\t\ta term has been selected\n\t\t\t\t*/\n\t\t\t\t\t\tobj.usetermkey = term.key\n\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\tobj.circles.attr('fill', d => {\n\t\t\t\t\t\t\t/*\n\t\t\t\t\teach d is a sample\n\t\t\t\t\t.sample\n\t\t\t\t\t*/\n\t\t\t\t\t\t\tconst a = cohort.patientannotation.annotation[d.sample]\n\t\t\t\t\t\t\tif (!a) return noannocolor\n\t\t\t\t\t\t\tconst valuekey = a[term.key]\n\t\t\t\t\t\t\tif (!valuekey) return noannocolor\n\t\t\t\t\t\t\tconst b = cohort.patientannotation.mdh[term.key].values[valuekey]\n\t\t\t\t\t\t\tif (!b) {\n\t\t\t\t\t\t\t\tconsole.error('invalid value key: ' + valuekey + ' at term: ' + term.key)\n\t\t\t\t\t\t\t\treturn noannocolor\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\treturn b.color\n\t\t\t\t\t\t})\n\n\t\t\t\t\t\t// legend\n\t\t\t\t\t\tobj.legendholder.selectAll('*').remove()\n\t\t\t\t\t\tobj.legendholder\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('margin-bottom', '5px')\n\t\t\t\t\t\t\t.text(term.label)\n\t\t\t\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t\t\tfor (const v of term.values) {\n\t\t\t\t\t\t\tconst row = obj.legendholder.append('div').style('margin-bottom', '3px')\n\t\t\t\t\t\t\trow\n\t\t\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t\t\t\t\t.style('background-color', v.color)\n\t\t\t\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t\t\t\t\t.html('&nbsp;')\n\t\t\t\t\t\t\trow.append('span').text(v.label)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tif (obj.expressiondata) {\n\t\t\t\t\t\t\t/*\n\t\t\t\t\tgene expression data already loaded and boxplot must have already been shown\n\t\t\t\t\tupdate boxplot\n\t\t\t\t\t*/\n\t\t\t\t\t\t\tboxplot4sampleannotation(cohort, obj)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t}\n\t\t})\n}\n", "import * as client from './client'\nimport { init_bulk_flag } from '#shared/bulk.js'\nimport * as bulkui from './bulk.ui'\nimport * as common from '#shared/common.js'\nimport blocklazyload from './block.lazyload'\nimport blockinit from './block.init'\n\nimport tp_class from './tp.classes'\nimport tp_gene from './tp.gene'\nimport tp_sample from './tp.sample'\nimport tp_pathway from './tp.pathway'\nimport inithcmap from './hcmap'\nimport tp_e2pca from './tp.e2pca'\nimport tp_getgeneexpression from './tp.gene.geneexpression'\nimport { getsjcharts } from './getsjcharts'\n\n/*\n\nfor generating the study HTML container\nwhich has 2 pillars, left for trigger buttons (also shows stats about the dataset), right for actual apps\nand show various apps depending on the data attributes\n\n*/\n\nexport default async function tpui(cohort, holder, hostURL, app = { callbacks: { sjcharts: {} } }) {\n\tconst debugmode = app.debugmode\n\n\tif (debugmode) {\n\t\twindow.cohort = cohort\n\t}\n\n\tif (!('hostURL' in cohort)) cohort.hostURL = hostURL\n\n\t// cohort already has jwt\n\n\t// all data parsed\n\tif (cohort.headerhtml) {\n\t\tholder.append('div').html(cohort.headerhtml)\n\t}\n\tlet personcount = 0\n\tfor (const pn in cohort.p2st) {\n\t\tpersoncount++\n\t\tfor (const st in cohort.p2st[pn]) {\n\t\t\tconst s = cohort.p2st[pn][st]\n\t\t\ts.sampletype = st\n\t\t\ts.patientname = pn\n\t\t\ts.cohort = cohort\n\t\t}\n\t}\n\tconst table = holder.append('table').style('margin-top', '20px')\n\tconst tr0 = table.append('tr')\n\n\t// two pillar container, only used by makefolder\n\tcohort.__tdleft = tr0.append('td').style('vertical-align', 'top').style('padding-right', '20px')\n\tcohort.__tdright = tr0.append('td').style('vertical-align', 'top')\n\n\tif (cohort.hide_navigation) {\n\t\tcohort.__tdleft.style('display', 'none')\n\t}\n\n\t/*\n// TODO from old pp, yet to be ported over\nif(cohort.render) {\n\tsja.f.tpui_render(cohort,tdleft,tdright)\n}\n*/\n\n\tif (!cohort.hide_addnewfile) {\n\t\t// add new files\n\t\t// only allow adding new files when there is just one dataset??\n\t\tconst [butt1, folder1] = makefolder(cohort)\n\t\tfolder1.style('background-color', '#f4f4f4').style('margin', '0px 20px 20px 0px').style('padding', '20px')\n\t\tbutt1.html('&#43; <span style=\"font-size:.8em\">NEW FILE</span>')\n\t\tconst saydiv = folder1.append('p')\n\t\tconst filediv = folder1.append('div')\n\t\tconst fileui = () => {\n\t\t\tfilediv.selectAll('*').remove()\n\t\t\tfilediv.append('span').html('Select data type&nbsp;')\n\t\t\tconst typeselect = client.filetypeselect(filediv).style('margin-right', '20px')\n\t\t\tconst butt = filediv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'file')\n\t\t\t\t.on('change', event => {\n\t\t\t\t\tsaydiv.text('')\n\t\t\t\t\tconst file = event.target.files[0]\n\t\t\t\t\tif (!file) {\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tif (file.size == 0) {\n\t\t\t\t\t\tsaydiv.text('Wrong file: ' + file.name)\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tconst reader = new FileReader()\n\t\t\t\t\treader.onload = event => {\n\t\t\t\t\t\tsaydiv.text(file.name + ' loaded.')\n\t\t\t\t\t\tconst flag = init_bulk_flag(cohort.genome.name)\n\t\t\t\t\t\tif (!flag) {\n\t\t\t\t\t\t\tsaydiv.text('should not happen')\n\t\t\t\t\t\t\tfileui()\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tconst error0 = bulkui.content2flag(event.target.result, typeselect.node().selectedIndex, flag)\n\n\t\t\t\t\t\tif (error0) {\n\t\t\t\t\t\t\tsaydiv.text('Error with ' + file.name + ': ' + error0)\n\t\t\t\t\t\t\tfileui()\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// new data goes to first dataset\n\t\t\t\t\t\tlet ds = null\n\t\t\t\t\t\tfor (const k in cohort.dsset) {\n\t\t\t\t\t\t\tds = cohort.dsset[k]\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (!ds) {\n\t\t\t\t\t\t\tsaydiv.text('no dataset in cohort, this should not happen')\n\t\t\t\t\t\t\tfileui()\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// flag2thisds tells the data in flag will be appended to the given ds\n\t\t\t\t\t\tconst error1 = bulkui.bulkin({\n\t\t\t\t\t\t\tflag: flag,\n\t\t\t\t\t\t\tcohort: cohort,\n\t\t\t\t\t\t\tflag2thisds: ds\n\t\t\t\t\t\t})\n\t\t\t\t\t\tif (error1) {\n\t\t\t\t\t\t\tsaydiv.text('Error with ' + file.name + ': ' + error1)\n\t\t\t\t\t\t\tfileui()\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tif (flag.good == 0) {\n\t\t\t\t\t\t\tsaydiv.text(file.name + ': no data loaded')\n\t\t\t\t\t\t\tfileui()\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsaydiv.text('')\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\t// good data ready\n\t\t\t\t\t\tholder.selectAll('*').remove()\n\t\t\t\t\t\ttpui(cohort, holder, hostURL)\n\t\t\t\t\t}\n\t\t\t\t\treader.onerror = function () {\n\t\t\t\t\t\tsaydiv.text('Error reading file ' + file.name)\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tsaydiv.text('Parsing file ' + file.name + ' ...')\n\t\t\t\t\treader.readAsText(file, 'utf8')\n\t\t\t\t})\n\t\t}\n\t\tfileui()\n\t}\n\n\tconst [butt2, folder2] = makefolder(cohort)\n\tconst ds2clst = tp_class(cohort, butt2, folder2)\n\n\tconst hassamplelst = []\n\tconst hasdiseaselst = []\n\tfor (const k in cohort.dsset) {\n\t\tconst ds = cohort.genome.datasets[k]\n\t\tif (ds.hassample) {\n\t\t\thassamplelst.push(k)\n\t\t}\n\t\tif (ds.hasdisease) {\n\t\t\thasdiseaselst.push(k)\n\t\t}\n\t}\n\n\tif (ds2clst) {\n\t\t// has mlst from text files\n\t\tconst [butt3, folder3] = makefolder(cohort, cohort.show_genetable)\n\t\ttp_gene(cohort, ds2clst, butt3, folder3, personcount > 0, hostURL)\n\t}\n\n\tlet showheatmap = false\n\n\tif (hassamplelst.length || personcount > 0) {\n\t\t/*\n\thas samples\n\tmigrate .p2st to .patientset\n\t*/\n\t\tcohort.patientset = {}\n\t\tfor (const patient in cohort.p2st) {\n\t\t\tcohort.patientset[patient] = {\n\t\t\t\ttrlst: [],\n\t\t\t\tsamples: cohort.p2st[patient]\n\t\t\t}\n\t\t}\n\n\t\t/*if (!cohort.disable_sampletable) {\n\t\t\t// show sample table\n\t\t\tconst [butt, folder] = makefolder(cohort, cohort.show_sampletable)\n\t\t\ttp_sample(cohort, ds2clst, butt, folder, hostURL)\n\t\t}*/\n\n\t\t// hm\n\t\tif (hassamplelst.length > 0 && !cohort.hardcodemap) {\n\t\t\tshowheatmap = true\n\t\t}\n\t}\n\n\tif (cohort.show_heatmap) {\n\t\tshowheatmap = true\n\t}\n\tlet hm_main\n\tif (showheatmap) {\n\t\tconst [hmbtn, hmdiv] = makefolder(cohort)\n\t\thmbtn.text('HEATMAP').style('font-size', '.8em')\n\t\tconst sjcharts = await getsjcharts()\n\t\tconst appname = (cohort.name ? cohort.name + '.' : '') + 'hm'\n\t\tsjcharts.heatmap({\n\t\t\tcohort,\n\t\t\thassamplelst,\n\t\t\tblockinit,\n\t\t\tdebugmode,\n\t\t\t// sjcharts has its own d3 instance so it has to\n\t\t\t// re-select to bind the d3 'event' properly\n\t\t\tdom: {\n\t\t\t\tbutt: hmbtn.node(),\n\t\t\t\tholder: hmdiv.node()\n\t\t\t},\n\t\t\ttp_getgeneexpression,\n\t\t\tshow_heatmap: cohort.show_heatmap,\n\t\t\t// use a subnested sjcharts object to namespace its instances\n\t\t\tinstanceTracker: app.instanceTracker && app.instanceTracker.sjcharts,\n\t\t\tcallbacks:\n\t\t\t\tapp.callbacks && app.callbacks.sjcharts && (app.callbacks.sjcharts[appname] || app.callbacks.sjcharts.hm)\n\t\t})\n\t}\n\n\t/*\nif(cohort.variantgene) {\n\tsja.f.tpui_variantgene(cohort,cohort.variantgene,d3.select(tdleft[0]),d3.select(tdright[0]))\n}\n*/\n\n\tif (cohort.hardcodemap) {\n\t\tconst [hmbut, hmdiv] = makefolder(cohort, cohort.show_hardcodemap)\n\t\thmbut.text('HEATMAP').style('font-size', '.8em')\n\t\tfor (const hcmap of cohort.hardcodemap) {\n\t\t\tconst div = hmdiv.append('div').style('display', 'inline-block').style('margin-bottom', '20px')\n\t\t\tif (hcmap.name) {\n\t\t\t\tdiv.append('h3').text(hcmap.name)\n\t\t\t}\n\t\t\tinithcmap(hcmap, div)\n\t\t}\n\t}\n\n\tif (cohort.survivalJSON) {\n\t\tconst [srvbut, srvdiv] = makefolder(cohort, cohort.show_hardcodemap)\n\t\tsrvbut.text('SURVIVAL CURVE').style('font-size', '.8em').style('border-color', 'transparent')\n\t\tconst sjcharts = await getsjcharts()\n\t\tsjcharts.survival({\n\t\t\tcohort,\n\t\t\tdom: {\n\t\t\t\tbutt: srvbut.node(),\n\t\t\t\tholder: srvdiv.node()\n\t\t\t},\n\t\t\t// use a subnested sjcharts object to namespace its instances\n\t\t\tinstanceTracker: app.instanceTracker && app.instanceTracker.sjcharts,\n\t\t\tcallbacks: app.callbacks && app.callbacks.sjcharts && app.callbacks.sjcharts.sv\n\t\t})\n\t}\n\n\t/*if (ds2clst && !cohort.disable_genenetwork) {\n\t\t// has mlst\n\t\tconst [butt, folder] = makefolder(cohort)\n\t\tbutt\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text('GENE NETWORK')\n\t\t\t.attr('aria-label', 'A force-directed graph of gene groups, shown with proportion of hits by diagnosis.')\n\t\tlet loaded = false\n\t\tbutt.on('click', () => {\n\t\t\tif (folder.style('display') == 'none') {\n\t\t\t\tbutt.style('border-color', 'black')\n\t\t\t\tclient.appear(folder)\n\t\t\t} else {\n\t\t\t\tbutt.style('border-color', 'transparent')\n\t\t\t\tclient.disappear(folder)\n\t\t\t}\n\t\t\tif (loaded) return\n\t\t\tloaded = true\n\t\t\ttp_pathway(cohort, folder)\n\t\t})\n\t}*/\n\n\t/*if (hasdiseaselst.length) {\n\t\tconst [skbtn, skdiv] = makefolder(cohort)\n\t\tskbtn\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text('RIBBON GRAPH')\n\t\t\t.attr('aria-label', 'A flow or Sankey diagram showing associated quantities by proportional ribbon widths.')\n\t\tconst sjcharts = await getsjcharts()\n\t\tsjcharts.sankey({\n\t\t\tcohort,\n\t\t\tdom: {\n\t\t\t\tbutt: skbtn.node(),\n\t\t\t\tholder: skdiv.node()\n\t\t\t},\n\t\t\t// use a subnested sjcharts object to namespace its instances\n\t\t\tinstanceTracker: app.instanceTracker && app.instanceTracker.sjcharts,\n\t\t\tcallbacks: app.callbacks && app.callbacks.sjcharts && app.callbacks.sjcharts.sk\n\t\t})\n\t}*/\n\n\t/*if (\n\t\thasdiseaselst.length ||\n\t\tcohort.piebarJSON ||\n\t\t(cohort.heatmapJSON && cohort.heatmapJSON.samplegroup && cohort.heatmapJSON.samplegroup.length)\n\t) {\n\t\tconst [piebtn, piediv] = makefolder(cohort)\n\t\tpiebtn\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text('PIE CHARTS')\n\t\t\t.attr(\n\t\t\t\t'title',\n\t\t\t\t'A sample group by gene group matrix of piecharts, with each pie wedge representing the number of hits by variant class.'\n\t\t\t)\n\t\tconst sjcharts = await getsjcharts()\n\t\tsjcharts.piebar({\n\t\t\tcohort,\n\t\t\tdom: {\n\t\t\t\tbutt: piebtn.node(),\n\t\t\t\tholder: piediv.node()\n\t\t\t},\n\t\t\t// use a subnested sjcharts object to namespace its instances\n\t\t\tinstanceTracker: app.instanceTracker && app.instanceTracker.sjcharts,\n\t\t\tcallbacks: app.callbacks && app.callbacks.sjcharts && app.callbacks.sjcharts.pb\n\t\t})\n\t}*/\n\n\tif (cohort.browserview) {\n\t\tconst [butt, folder] = makefolder(cohort)\n\t\tbutt.style('font-size', '.8em').text('BROWSER')\n\t\tlet loaded = false\n\t\tbutt.on('click', () => {\n\t\t\tif (folder.style('display') == 'none') {\n\t\t\t\tbutt.style('border-color', 'black')\n\t\t\t\tclient.appear(folder)\n\t\t\t} else {\n\t\t\t\tbutt.style('border-color', 'transparent')\n\t\t\t\tclient.disappear(folder)\n\t\t\t}\n\t\t\tif (loaded) return\n\t\t\tloaded = true\n\t\t\tconst arg = {\n\t\t\t\tholder: folder,\n\t\t\t\tgenome: cohort.genome,\n\t\t\t\tdebugmode: debugmode,\n\t\t\t\tdogtag: cohort.genome.name,\n\t\t\t\thostURL: hostURL,\n\t\t\t\tjwt: cohort.jwt,\n\t\t\t\tcohort: cohort,\n\t\t\t\tnobox: cohort.browserview.nobox,\n\t\t\t\tdatasetqueries: cohort.browserview.datasetqueries,\n\t\t\t\ttklst: []\n\t\t\t}\n\t\t\tif (cohort.browserview.position) {\n\t\t\t\t// always true\n\t\t\t\targ.chr = cohort.browserview.position.chr\n\t\t\t\targ.start = cohort.browserview.position.start\n\t\t\t\targ.stop = cohort.browserview.position.stop\n\t\t\t}\n\t\t\t// native track\n\t\t\tif (cohort.browserview.nativetracks) {\n\t\t\t\targ.nativetracks = cohort.browserview.nativetracks\n\t\t\t}\n\t\t\t// custom track\n\t\t\tif (cohort.browserview.tracks) {\n\t\t\t\tfor (const t of cohort.browserview.tracks) {\n\t\t\t\t\targ.tklst.push(t)\n\t\t\t\t}\n\t\t\t}\n\t\t\t// assay track\n\t\t\tif (cohort.browserview.assays) {\n\t\t\t\tif (!cohort.assaylst) {\n\t\t\t\t\tconsole.error('assaylst not set!')\n\t\t\t\t\tcohort.assaylst = []\n\t\t\t\t}\n\t\t\t\tfor (const assayname in cohort.browserview.assays) {\n\t\t\t\t\tconst assayview = cohort.browserview.assays[assayname]\n\t\t\t\t\tif (!assayview.assayobj) {\n\t\t\t\t\t\t// assayobj should be defined\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tif (assayview.combined) {\n\t\t\t\t\t\tif (assayview.combinetk) {\n\t\t\t\t\t\t\targ.tklst.push(assayview.combinetk)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tfor (const pn in cohort.patientset) {\n\t\t\t\t\t\t\tfor (const st in cohort.patientset[pn].samples) {\n\t\t\t\t\t\t\t\tfor (const t of cohort.patientset[pn].samples[st].tktemplate) {\n\t\t\t\t\t\t\t\t\tif (t.id == assayview.assayobj.id) {\n\t\t\t\t\t\t\t\t\t\targ.tklst.push(t)\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (cohort.browserview.defaultassaytracks) {\n\t\t\t\tconst [err, lst] = cohort2assaytracks(cohort)\n\t\t\t\tif (err) {\n\t\t\t\t\tclient.sayerror(holder, 'error with .defaultassaytracks: ' + err)\n\t\t\t\t} else {\n\t\t\t\t\tfor (const t of lst) arg.tklst.push(t)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tfor (const t of arg.tklst) {\n\t\t\t\tt.iscustom = true // important\n\t\t\t}\n\n\t\t\tblocklazyload(arg)\n\t\t})\n\t\tif (cohort.show_browser) {\n\t\t\tbutt.node().click()\n\t\t}\n\t}\n\n\tif (cohort.e2pca) {\n\t\tconst [butt, folder] = makefolder(cohort)\n\t\tbutt.text(cohort.e2pca.label).style('font-size', '.8em')\n\n\t\tlet loaded = false\n\t\tbutt.on('click', () => {\n\t\t\tif (folder.style('display') == 'none') {\n\t\t\t\tbutt.style('border-color', 'black')\n\t\t\t\tclient.appear(folder)\n\t\t\t} else {\n\t\t\t\tbutt.style('border-color', 'transparent')\n\t\t\t\tclient.disappear(folder)\n\t\t\t}\n\t\t\tif (loaded) return\n\t\t\tloaded = true\n\t\t\ttp_e2pca(cohort, folder)\n\t\t})\n\t\tif (cohort.show_e2pca) {\n\t\t\tbutt.node().click()\n\t\t}\n\t}\n\n\t/***** end of tpui *****/\n}\n\nfunction makefolder(cohort, show) {\n\tconst butt = cohort.__tdleft\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('margin-top', '10px')\n\t\t.style('white-space', 'nowrap')\n\tconst folder = cohort.__tdright.append('div').style('padding-bottom', '20px')\n\tbutt.on('click', () => {\n\t\tif (folder.style('display') == 'block') {\n\t\t\tclient.disappear(folder)\n\t\t\tbutt.style('border', 'solid 1px transparent')\n\t\t} else {\n\t\t\tbutt.style('border', 'solid 1px #545454')\n\t\t\tclient.appear(folder)\n\t\t}\n\t})\n\tif (show) {\n\t\tbutt.style('border', 'solid 1px #545454')\n\t\tfolder.style('display', 'block')\n\t} else {\n\t\tbutt.style('border', 'solid 1px transparent')\n\t\tfolder.style('display', 'none')\n\t}\n\treturn [butt, folder]\n}\n\nfunction cohort2assaytracks(ct) {\n\t/*\n\tcohort.browserview.defaultassaytracks[]\n\n\tget the tklst from cohort.p2st\n\t*/\n\n\tif (!ct.browserview) return [null, []]\n\tif (!ct.browserview.defaultassaytracks) return [null, []]\n\n\tconst tklst = []\n\tfor (const t of ct.browserview.defaultassaytracks) {\n\t\tconst p = ct.p2st[t.level1]\n\t\tif (!p) continue\n\t\tif (t.level2) {\n\t\t\tconst p2 = p[t.level2]\n\t\t\tif (!p2) continue\n\t\t\tif (!p2.tktemplate) continue\n\t\t\tfor (const tt of p2.tktemplate) {\n\t\t\t\tif (tt.assayname == t.assay) {\n\t\t\t\t\ttklst.push(tt)\n\t\t\t\t\tif (t.justone) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t// no level2, use all tk from p\n\t\t\tfor (const st in p) {\n\t\t\t\tconst p2 = p[st]\n\t\t\t\tif (p2.tktemplate) {\n\t\t\t\t\tfor (const tt of p2.tktemplate) {\n\t\t\t\t\t\tif (tt.assayname == t.assay) {\n\t\t\t\t\t\t\ttklst.push(tt)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\treturn [null, tklst]\n}\n"],
-  "mappings": 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-  "names": ["sayerror", "n", "a", "barplot", "tip", "l", "x", "tip", "event"]
-}

package/dist/tvs.categorical-RPACB4VU.js

@@ -1,28 +0,0 @@
-import {
-  handler
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  handler
-};
-//# sourceMappingURL=tvs.categorical-RPACB4VU.js.map

package/dist/tvs.condition-O6JBUM6D.js

@@ -1,160 +0,0 @@
-import {
-  escapeHtml
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// filter/tvs.condition.js
-var handler = {
-  type: "condition",
-  term_name_gen,
-  get_pill_label,
-  getSelectRemovePos,
-  fillMenu,
-  setTvsDefaults
-};
-async function fillMenu(self, div, tvs) {
-  const bar_by_select = div.append("select").attr("class", "value_select").style("display", "block").style("margin", "5px 10px").style("padding", "3px").on("change", () => {
-    const new_tvs = JSON.parse(JSON.stringify(tvs));
-    const value = bar_by_select.node().value;
-    new_tvs.bar_by_grade = value === "grade";
-    new_tvs.bar_by_children = value === "sub";
-    if (value === "grade") {
-      new_tvs.value_by_max_grade = true;
-      delete new_tvs.value_by_most_recent;
-      delete new_tvs.value_by_computable_grade;
-    }
-    div.selectAll("*").remove();
-    fillMenu(self, div, new_tvs);
-  });
-  bar_by_select.append("option").attr("value", "grade").text("By Grade").property("selected", tvs.bar_by_grade);
-  bar_by_select.append("option").attr("value", "sub").text("By Subcondition").property("selected", tvs.bar_by_children);
-  const grade_type_select = div.append("select").attr("class", "grade_select").style("margin", "5px 10px").style("padding", "3px").style("display", tvs.bar_by_grade ? "block" : "none").on("change", () => {
-    const new_tvs = JSON.parse(JSON.stringify(tvs));
-    update_value_by(new_tvs);
-    div.selectAll("*").remove();
-    fillMenu(self, div, new_tvs);
-  });
-  grade_type_select.append("option").attr("value", "max").text("Max grade per patient").property("selected", tvs.value_by_max_grade);
-  grade_type_select.append("option").attr("value", "recent").text("Most recent grade per patient").property("selected", tvs.value_by_most_recent);
-  grade_type_select.append("option").attr("value", "computable").text("Any grade per patient").property("selected", tvs.value_by_computable_grade);
-  div.append("span").style("margin", "5px 10px").style("padding", "3px").style("display", tvs.bar_by_children ? "block" : "none").style("color", "#888").html("Using any grade per patient");
-  const body = { term1_q: {} };
-  for (const key in tvs) {
-    if (key.includes("_by_")) body.term1_q[key] = tvs[key];
-  }
-  const data = await self.opts.vocabApi.getCategories(tvs.term, self.filter, body);
-  const callback = (indexes) => {
-    const new_tvs = JSON.parse(JSON.stringify(tvs));
-    delete new_tvs.groupset_label;
-    new_tvs.values = data.lst.filter((v, i, array) => indexes.includes(i));
-    const bar_by_value = bar_by_select.node().value;
-    new_tvs.bar_by_grade = bar_by_value !== "sub";
-    new_tvs.bar_by_children = bar_by_value === "sub";
-    update_value_by(new_tvs);
-    try {
-      validateConditionTvs(new_tvs);
-    } catch (e) {
-      window.alert(e);
-      return;
-    }
-    self.dom.tip.hide();
-    self.opts.callback(new_tvs);
-  };
-  self.values_table = self.makeValueTable(div, tvs, data.lst, callback).node();
-  function update_value_by(new_tvs) {
-    const bar_by_value = bar_by_select.property("value");
-    const grade_type_value = grade_type_select.property("value");
-    if (bar_by_value === "sub") {
-      new_tvs.value_by_computable_grade = true;
-      delete new_tvs.value_by_max_grade;
-      delete new_tvs.value_by_most_recent;
-    } else {
-      new_tvs.value_by_max_grade = grade_type_value === "max";
-      new_tvs.value_by_most_recent = grade_type_value === "recent";
-      new_tvs.value_by_computable_grade = grade_type_value === "computable";
-    }
-  }
-}
-function term_name_gen(d) {
-  const name = d.term.name;
-  return name.length < 21 ? escapeHtml(name) : '<label title="' + escapeHtml(name) + '">' + escapeHtml(name.substring(0, 18)) + "...</label>";
-}
-function get_pill_label(tvs) {
-  return {
-    txt: escapeHtml(get_value_text(tvs)),
-    grade_type: tvs.bar_by_children ? "" : tvs.value_by_max_grade ? "[Max Grade]" : tvs.value_by_most_recent ? "[Most Recent Grade]" : tvs.value_by_computable_grade ? "[Any Grade]" : ""
-  };
-}
-function get_value_text(tvs) {
-  if (tvs.bar_by_grade || tvs.bar_by_children) {
-    if (tvs.values.length == 1) {
-      return tvs.values[0].label;
-    }
-    if (tvs.groupset_label) return tvs.groupset_label;
-    return tvs.values.length + (tvs.bar_by_grade ? " Grades" : "Subconditions");
-  }
-  if (tvs.grade_and_child) {
-    console.error(term);
-    return "todo";
-  }
-  throw "unknown tvs setting for a condition term";
-}
-function getSelectRemovePos(j) {
-  return j;
-}
-function setTvsDefaults(tvs) {
-  if (!tvs.values) tvs.values = [];
-  if (!tvs.bar_by_grade && !tvs.bar_by_children_) {
-    tvs.bar_by_grade = true;
-  }
-  if (!tvs.value_by_max_grade && !tvs.value_by_most_recent && !tvs.value_by_computable_grade) {
-    tvs.value_by_max_grade = true;
-  }
-}
-function validateConditionTvs(tvs) {
-  if (!tvs.term) throw "tvs.term is not defined";
-  if (!tvs.values) throw `.values[] missing for a term ${tvs.term.name}`;
-  if (!Array.isArray(tvs.values)) throw `.values[] is not an array for a term ${tvs.term.name}`;
-  if (!tvs.values.length) throw `no categories selected for ${tvs.term.name}`;
-  if (!tvs.values.every((v) => v.key !== void 0))
-    throw `every value in tvs.values[] must have 'key' defined for ${tvs.term.name}`;
-  if (tvs.term.isleaf == true) {
-    if (!tvs.bar_by_grade) throw `tvs.bar_by_grade must be true for leaf term ${tvs.term.name}`;
-    if (!tvs.value_by_max_grade && !tvs.value_by_most_recent && !tvs.value_by_computable_grade)
-      throw `unknown value_type for a bar_by_grade for condition term ${tvs.term.name}`;
-  } else {
-    if (tvs.bar_by_grade) {
-      if (!tvs.value_by_max_grade && !tvs.value_by_most_recent && !tvs.value_by_computable_grade)
-        throw `unknown value_type for a bar_by_grade for condition term ${tvs.term.name}`;
-    } else if (tvs.bar_by_children) {
-      if (!tvs.value_by_computable_grade)
-        throw `value_type must be value_by_computable_grade for bar_by_children for condition term ${tvs.term.name}`;
-    } else {
-      throw `neither bar_by_grade or bar_by_children is set for a condition term ${tvs.term.name}`;
-    }
-  }
-}
-export {
-  handler
-};
-//# sourceMappingURL=tvs.condition-O6JBUM6D.js.map

package/dist/tvs.dt-5EVBSRX3.js

@@ -1,30 +0,0 @@
-import {
-  getDtTermValues,
-  handler2 as handler
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  getDtTermValues,
-  handler
-};
-//# sourceMappingURL=tvs.dt-5EVBSRX3.js.map

package/dist/tvs.dtcnv.categorical-Y5YHBZNC.js

@@ -1,31 +0,0 @@
-import {
-  handler2 as handler
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// filter/tvs.dtcnv.categorical.js
-var handler2 = Object.assign({}, handler, { type: "dtcnv" });
-export {
-  handler2 as handler
-};
-//# sourceMappingURL=tvs.dtcnv.categorical-Y5YHBZNC.js.map

package/dist/tvs.dtcnv.continuous-WP322QUP.js

@@ -1,63 +0,0 @@
-import {
-  handler2 as handler,
-  renderCnvConfig
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// filter/tvs.dtcnv.continuous.js
-var handler2 = Object.assign({}, handler, { type: "dtcnv", fillMenu, get_pill_label });
-function fillMenu(self, div, tvs) {
-  const dscnv = self.opts.vocabApi.termdbConfig.queries?.cnv;
-  if (!dscnv) throw "cnv query is missing";
-  const cnvDefault = dscnv.cnvCutoffsByGene?.[tvs.term.parentTerm.name] || {
-    cnvMaxLength: dscnv.cnvMaxLength,
-    cnvGainCutoff: dscnv.cnvGainCutoff,
-    cnvLossCutoff: dscnv.cnvLossCutoff
-  };
-  const cnv = Object.assign({}, cnvDefault, tvs);
-  const arg = {
-    holder: div,
-    cnvGainCutoff: cnv.cnvGainCutoff,
-    cnvLossCutoff: cnv.cnvLossCutoff,
-    cnvMaxLength: cnv.cnvMaxLength,
-    cnvWT: cnv.cnvWT,
-    genotypeToggle: true,
-    fractionOverlap: cnv.fractionOverlap,
-    showOverlap: true,
-    callback: (config) => {
-      const new_tvs = structuredClone(tvs);
-      Object.assign(new_tvs, config);
-      new_tvs.continuousCnv = true;
-      self.dom.tip.hide();
-      self.opts.callback(new_tvs);
-    }
-  };
-  renderCnvConfig(arg);
-}
-function get_pill_label(tvs) {
-  return { txt: tvs.cnvWT ? "Wildtype" : "Altered" };
-}
-export {
-  handler2 as handler
-};
-//# sourceMappingURL=tvs.dtcnv.continuous-WP322QUP.js.map