@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-MNRYCG2S.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/regression.results.js"],
+  "sourcesContent": ["import { scaleLinear, scaleLog } from 'd3-scale'\nimport { axisBottom } from 'd3-axis'\nimport { first_genetrack_tolist } from '../common/1stGenetk'\nimport { interpolateRgb } from 'd3-interpolate'\nimport { sayerror, axisstyle, drawBoxplot, makeSsmLink, ColorScale, Menu } from '#dom'\nimport { roundValue } from '#shared/roundValue.js'\n\n/*************\ncan dynamically add following attributes\n\n- this.snplocusBlock:\n\tfor snplocus term\n\tdisplay in this.dom.snplocusBlockDiv\n- this.hasUnsubmittedEdits_nullify_singleuse:\n\tto negate hasUnsubmittedEdits and keep running analysis\n\n**************** R result object\nresult.data: {}\n\twarnings\n\tsampleSize: int\n\theaderRow: { k:str, v:str }\n\tresiduals: { header[], rows[], label:str }\n\tcoefficients: { header[], intercept[], terms{}, interactions[], label }\n\ttype3: {header[], intercept[], terms{}, interactions[], label }\n\ttotalSnpEffect: {header[], intercept[], snp, interactions[], lst, label }\n\tother: {header[], rows[], label}\n\n\n*************** function cascade\nmain\n\tdisplayResult\n\t\tcreateGenomebrowser\n\t\t\tgetMtooltipValues\n\t\t\tmayCheckLD\n\t\t\t\tshowLDlegend\n\t\tupdateMds3Tk\n\t\t\tmake_mds3_variants\n\t\tshow_genomebrowser_snplocus\n\t\tdisplayResult_oneset\n\t\t\tmayshow_warn\n\t\t\tmayshow_splinePlots\n\t\t\tmayshow_residuals\n\t\t\tmayshow_coefficients\n\t\t\tmayshow_totalSnpEffect\n\t\t\tmayshow_type3\n\t\t\tmayshow_other\n\t\t\tmayshow_fisher\n\t\t\tmayshow_wilcoxon\n\t\t\tmayshow_cuminc\n*/\n\nconst refGrp_NA = 'NA' // refGrp value is not applicable, hardcoded for R\nconst forestcolor = '#126e08' // forest plot color\nconst boxplotcolor = forestcolor\n\nexport class RegressionResults {\n\tconstructor(opts) {\n\t\tthis.opts = opts\n\t\tthis.app = opts.app\n\t\t// reference to the parent component's mutable instance (not its API)\n\t\tthis.parent = opts.parent\n\t\tthis.type = 'regression'\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\n\t\tconst holder = this.opts.holder\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('padding-top', '20px')\n\t\t\t.style('font-size', '1.2em')\n\t\t\t.style('opacity', 0.3)\n\t\t\t.html('Results')\n\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\terr_div: holder.append('div'),\n\t\t\tsnplocusBlockDiv: holder.append('div'),\n\t\t\t// is where newDiv() and displayResult_oneset() writes to\n\t\t\toneSetResultDiv: holder.append('div').style('margin', '10px'),\n\t\t\ttip: new Menu({ padding: '9px' })\n\t\t}\n\t}\n\n\tasync main() {\n\t\ttry {\n\t\t\tthis.parent.inputs.dom.submitBtn.text('Running...')\n\t\t\t// share the writable config copy\n\t\t\tthis.config = this.parent.config\n\t\t\tthis.state = this.parent.state\n\t\t\tif (\n\t\t\t\t!this.state.formIsComplete ||\n\t\t\t\tthis.parent.inputs.hasError ||\n\t\t\t\t(this.config.hasUnsubmittedEdits && !this.hasUnsubmittedEdits_nullify_singleuse)\n\t\t\t) {\n\t\t\t\t// no result to show\n\t\t\t\t// remove block instance when input variables are edited\n\t\t\t\tdelete this.snplocusBlock\n\t\t\t\tthis.dom.snplocusBlockDiv.selectAll('*').remove()\n\t\t\t\tthis.dom.holder.style('display', 'none')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tdelete this.hasUnsubmittedEdits_nullify_singleuse // single-use, delete\n\n\t\t\tif (this.snplocusBlock) {\n\t\t\t\t// if a block instance is already made, cloak it\n\t\t\t\tthis.snplocusBlock.cloakOn()\n\t\t\t}\n\n\t\t\t// submit server request to run analysis\n\t\t\tconst data = await this.app.vocabApi.getRegressionData(this.getDataRequestOpts())\n\t\t\tif (data.error) throw data.error\n\t\t\tthis.dom.err_div.style('display', 'none')\n\t\t\tthis.dom.oneSetResultDiv.selectAll('*').remove()\n\t\t\tthis.dom.holder.style('display', 'block')\n\t\t\tawait this.displayResult(data)\n\n\t\t\t// scroll to results\n\t\t\tconst results_y = this.dom.holder.node().getBoundingClientRect().top + window.scrollY\n\t\t\tconst nav_height = document.querySelector('.sjpp-nav').getBoundingClientRect().height\n\t\t\twindow.scroll({ behavior: 'smooth', top: results_y - nav_height })\n\t\t} catch (e) {\n\t\t\tthis.hasError = true\n\t\t\tthis.dom.holder.style('display', 'block')\n\t\t\tthis.dom.err_div.style('display', 'block')\n\t\t\tsayerror(this.dom.err_div, 'Error: ' + (e.error || e))\n\t\t\tthis.parent.inputs.dom.submitBtn.property('disabled', true)\n\t\t\tconsole.error(e)\n\t\t}\n\t}\n\n\t// creates an opts object for the vocabApi.getRegressionData()\n\tgetDataRequestOpts() {\n\t\tconst c = this.config\n\t\tconst opts = {\n\t\t\tregressionType: c.regressionType,\n\t\t\toutcome: c.outcome,\n\t\t\tindependent: c.independent,\n\t\t\tincludeUnivariate: c.includeUnivariate\n\t\t}\n\t\topts.filter = this.parent.filter\n\t\treturn opts\n\t}\n\n\tgetIndependentInput(tid) {\n\t\t/* arg is independent tw $id or snpid\n\t\treturn input instance\n\t\tfor accessing input.orderedLabels and input.term{refGrp, term{}, q{}} which is term-wrapper\n\n\t\tin order to reliably access refGrp,\n\t\tmust use termwrapper from Input instance but not this.state.config\n\t\tdue to a specific condition when refGrp is set in self.config, but is missing from state\n\t\tthis happens when launching from a parameterized url that's missing refgrp for the term\n\t\tand the refGrp is dynamically filled by input.updateTerm() but not propagated to state\n\t\t*/\n\t\tfor (const i of this.parent.inputs.independent.inputLst) {\n\t\t\tif (!i.term) continue\n\t\t\tif (i.term.term && i.term.term.snps) {\n\t\t\t\t// is a snplst or snplocus term with .snps[]\n\t\t\t\tfor (const snp of i.term.term.snps) {\n\t\t\t\t\tif (snp.snpid == tid) {\n\t\t\t\t\t\t// tid matches with a snpid\n\t\t\t\t\t\t// make up an object looking like an Input instance for this snp/variant\n\t\t\t\t\t\tconst tw = {\n\t\t\t\t\t\t\tid: tid,\n\t\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\t\tgeneticModel: i.term.q.geneticModel\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\tid: tid,\n\t\t\t\t\t\t\t\tname: tid\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tinteractions: i.term.interactions,\n\t\t\t\t\t\t\teffectAllele: i.term.q.snp2effAle[tid],\n\t\t\t\t\t\t\tgt2count: snp.gt2count\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (i.term.q.snp2refGrp) {\n\t\t\t\t\t\t\ttw.refGrp = i.term.q.snp2refGrp[tid]\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (snp.mlst) {\n\t\t\t\t\t\t\t// try to update tw.term.name\n\t\t\t\t\t\t\tconst m = snp.mlst.find(j => j.alt == i.term.q.snp2effAle[tid])\n\t\t\t\t\t\t\tif (m) {\n\t\t\t\t\t\t\t\ttw.term.name = m.mname\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\ttw.term.name = snp.mlst[0].mname\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn { term: tw }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (i.term.$id == tid) return i\n\t\t}\n\t\t// given tid does not match with an Input\n\t\t// can be an ancestry PC which is automatically added by serverside and not recorded on client\n\t\t// quick fix: return dummy tw so it won't break\n\t\treturn {\n\t\t\tterm: {\n\t\t\t\tid: tid,\n\t\t\t\tq: { mode: 'continuous' },\n\t\t\t\tterm: { name: tid }\n\t\t\t}\n\t\t}\n\t\t//throw 'cannot find Input for a tid: ' + tid\n\t}\n}\n\nfunction setInteractivity(self) {}\n\nfunction setRenderers(self) {\n\tself.displayResult = async result => {\n\t\t/*\n\t\tresult {\n\t\t\tresultLst [\n\t\t\t\t{ data: { err, splinePlots, residuals, ... }, id:'snp1' },\n\t\t\t\t{ data: { err, splinePlots, residuals, ... }, id:'snp2' },\n\t\t\t\t...\n\t\t\t]\n\t\t}\n\t\t*/\n\n\t\t// if there is a snplocus Input\n\t\tconst snplocusInput = self.parent.inputs.independent.inputLst.find(i => i.term && i.term.term.type == 'snplocus')\n\t\tif (snplocusInput) {\n\t\t\t/* has a snploucs term\n\t\t\tin result[], there's one set of result for each variant, identified by id\n\t\t\tshow a genome browser and a mds3 tk to show dots for the variants from snplocus term\n\t\t\tclicking on a dot in browser tk will call displayResult_oneset() to display its results\n\t\t\t*/\n\t\t\tif (!self.snplocusBlock) {\n\t\t\t\tself.dom.snplocusBlockDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('margin-top', '30px')\n\t\t\t\t\t.style('opacity', 0.3)\n\t\t\t\t\t.text('Click on a variant within the browser to view its regression results')\n\t\t\t\tself.snplocusBlock = await createGenomebrowser(self, snplocusInput, result.resultLst)\n\t\t\t} else {\n\t\t\t\tawait updateMds3Tk(self, snplocusInput, result.resultLst)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\t// no snplocus, clear things if had it before\n\t\tdelete self.snplocusBlock\n\t\tself.dom.snplocusBlockDiv.selectAll('*').remove()\n\t\t// resultLst[] has only one set of result, from analyzing one model\n\t\tif (!result.resultLst[0] || !result.resultLst[0].data) throw 'result is not [ {data:{}} ]'\n\n\t\tself.displayResult_oneset(result.resultLst[0].data)\n\t}\n\n\tself.displayResult_oneset = result => {\n\t\tself.dom.oneSetResultDiv.selectAll('*').remove()\n\n\t\t// may be used when clicking snplocus dot\n\t\tself.dom.LDresultDiv = self.dom.oneSetResultDiv.append('div')\n\n\t\tself.mayshow_warn(result)\n\t\tif (result.sampleSize) self.newDiv('Sample size:', result.sampleSize)\n\t\tif (result.eventCnt) self.newDiv('Number of events:', result.eventCnt)\n\t\tself.mayshow_headerRow(result)\n\t\tself.mayshow_splinePlots(result)\n\t\tself.mayshow_residuals(result)\n\t\tself.mayshow_coefficients(result)\n\t\tself.mayshow_coxDisclaimer()\n\t\tself.mayshow_totalSnpEffect(result)\n\t\tself.mayshow_type3(result)\n\t\tself.mayshow_tests(result)\n\t\tself.mayshow_other(result)\n\t\tself.mayshow_fisher(result)\n\t\tself.mayshow_wilcoxon(result)\n\t\tself.mayshow_cuminc(result)\n\t}\n\n\tself.newDiv = (label, label2, getrow) => {\n\t\t// create div to show a section of the result\n\t\t// label is required, label2 is optional\n\t\t// specify getrow=true to return row instead of div\n\t\tconst div = self.dom.oneSetResultDiv.append('div').style('margin', '20px 0px 10px 0px').attr('name', label) //For integration testing\n\t\tconst row = div.append('div')\n\t\trow.append('span').style('text-decoration', 'underline').text(label)\n\t\tif (label2) {\n\t\t\trow.append('span').html(label2).style('margin-left', '5px')\n\t\t}\n\t\treturn getrow ? row : div.append('div').style('margin-left', '20px')\n\t}\n\n\tself.mayshow_warn = result => {\n\t\tif (!result.warnings) return\n\t\tconst div = self.newDiv('Warnings')\n\t\tconst warnings = new Set(result.warnings)\n\t\tfor (const line of warnings) {\n\t\t\tdiv.append('p').style('margin', '5px').text(line)\n\t\t}\n\t}\n\n\tself.mayshow_headerRow = result => {\n\t\tif (!result.headerRow) return\n\t\tconst k = result.headerRow.k\n\t\tconst v = result.headerRow.v\n\t\tconst snplocusInput = self.parent.inputs.independent.inputLst.find(i => i.term && i.term.term.type == 'snplocus')\n\t\tif (snplocusInput) {\n\t\t\t// header row is for snplocus results\n\t\t\t// variant label\n\t\t\tconst snp = snplocusInput.term.term.snps.find(snp => snp.snpid == v.snpid)\n\t\t\tconst m = snp.mlst[0]\n\t\t\tm.chr = snp.chr\n\t\t\tconst row = self.newDiv(k, null, true)\n\t\t\tconst snpLabelDom = row\n\t\t\t\t.append('span')\n\t\t\t\t.text(`${m.chr}:${m.pos + 1} ${m.ref && m.alt ? m.ref + '>' + m.alt : ''}`)\n\t\t\t\t.style('margin-left', '5px')\n\t\t\tconst urlConfig =\n\t\t\t\tself.app.vocabApi.termdbConfig.urlTemplates?.ssm || self.app.vocabApi.termdbConfig.queries?.snvindel?.ssmUrl\n\t\t\tif (urlConfig) {\n\t\t\t\t// add urls to snp label\n\t\t\t\tconst separateUrls = makeSsmLink(urlConfig, m, snpLabelDom, self.parent.genomeObj.name)\n\t\t\t\tif (separateUrls?.length) {\n\t\t\t\t\trow.append('span').style('margin-left', '10px').html(separateUrls.join(' '))\n\t\t\t\t}\n\t\t\t}\n\t\t\t// gt label\n\t\t\tlet labels\n\t\t\tconst gt_label = `Genotypes: ${v.gtcounts.join(', ')}`\n\t\t\tif (v.monomorphic) {\n\t\t\t\tlabels = [gt_label]\n\t\t\t} else {\n\t\t\t\t// effect allele label\n\t\t\t\tconst effale_label = `Effect allele: ${v.effAle}`\n\t\t\t\t// allel frequency label\n\t\t\t\tconst af_label = `Allele frequency: ${v.af}`\n\t\t\t\tlabels = [effale_label, af_label, gt_label]\n\t\t\t}\n\t\t\trow.append('span').html(`&nbsp;&#65372;&nbsp;${labels.join('&nbsp;&#65372;&nbsp;')}`)\n\t\t} else {\n\t\t\t// header row is not for snplocus results\n\t\t\tself.newDiv(k, v)\n\t\t}\n\t}\n\n\tself.mayshow_splinePlots = result => {\n\t\tif (!result.splinePlots) return\n\t\tconst div = self.newDiv('Cubic spline plots')\n\t\tdiv.style('display', 'flex').style('align-items', 'center')\n\t\tresult.splinePlots.sort((a, b) => {\n\t\t\t// univariate plots should appear before multivariate plots\n\t\t\tif (a.type == 'univariate' && b.type == 'multivariate') return -1\n\t\t\tif (a.type == 'multivariate' && b.type == 'univariate') return 1\n\t\t\treturn 0\n\t\t})\n\t\tfor (const plot of result.splinePlots) {\n\t\t\tconst plotDiv = div.append('div').style('margin', '0px 50px 5px 0px')\n\t\t\tplotDiv.append('img').attr('src', plot.src).attr('width', 670) // quick fix to hardcode width as half of what's used in R/src/regression.utils.R, for crisp img on high-res screen\n\t\t}\n\t}\n\n\tself.mayshow_residuals = result => {\n\t\tif (!result.residuals) return\n\t\tconst div = self.newDiv(result.residuals.label)\n\t\tconst table = div.append('table').style('border-spacing', '8px').attr('name', 'sjpp-residuals-table') //For integration tests\n\t\tconst tr1 = table.append('tr').style('opacity', 0.4)\n\t\tconst tr2 = table.append('tr')\n\t\tfor (let i = 0; i < result.residuals.header.length; i++) {\n\t\t\ttr1.append('td').text(result.residuals.header[i])\n\t\t\ttr2.append('td').text(result.residuals.rows[i])\n\t\t}\n\t}\n\n\tself.mayshow_cuminc = async result => {\n\t\tif (!result.cuminc) return\n\t\tconst holder = self.newDiv('Cumulative incidence test:' /*, 'p-value = ' + result.cuminc.pvalue*/)\n\t\tconst _ = await import('./cuminc')\n\t\tconst plotter = new _.Cuminc({\n\t\t\tholder,\n\t\t\tconfig: {\n\t\t\t\tterm: self.config.outcome,\n\t\t\t\tterm2: {\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tname: 'Variant',\n\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t1: { key: 1, label: 'Has minor allele' },\n\t\t\t\t\t\t\t2: { key: 2, label: 'No minor allele' }\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\n\t\tif (result.cuminc.ci_data) {\n\t\t\tplotter.main(result.cuminc.ci_data)\n\t\t} else {\n\t\t\tholder.append('div').style('margin', '20px').text(result.cuminc.msg)\n\t\t}\n\t}\n\n\tself.mayshow_wilcoxon = result => {\n\t\tif (!result.wilcoxon) return\n\t\tconst div = self.newDiv('Wilcoxon rank sum test:', 'p-value = ' + result.wilcoxon.pvalue)\n\t\tif (result.wilcoxon.boxplots) {\n\t\t\tconst bs = result.wilcoxon.boxplots\n\t\t\t// {hasEff{}, noEff{}, minv, maxv}\n\n\t\t\tconst boxplotHeight = 20,\n\t\t\t\tboxplotWidth = 400,\n\t\t\t\tleftLabelWidth = 160, // hardcoded number, must fit the boxplot labels\n\t\t\t\taxisheight = 40,\n\t\t\t\tlabpad = 20,\n\t\t\t\tvpad = 10\n\n\t\t\tconst scale = scaleLinear().domain([bs.minv, bs.maxv]).range([0, boxplotWidth])\n\n\t\t\tconst svg = div\n\t\t\t\t.append('svg')\n\t\t\t\t.style('margin-top', '10px')\n\t\t\t\t.attr('width', leftLabelWidth + labpad + boxplotWidth + 10)\n\t\t\t\t.attr('height', vpad * 3 + boxplotHeight * 2 + axisheight)\n\t\t\t// anchor\n\t\t\tconst g = svg.append('g').attr('transform', `translate(${leftLabelWidth + labpad},${vpad})`)\n\t\t\tdrawBoxplot({\n\t\t\t\tg: g.append('g'),\n\t\t\t\tbp: bs.hasEff,\n\t\t\t\tscale,\n\t\t\t\trowheight: boxplotHeight,\n\t\t\t\tcolor: boxplotcolor,\n\t\t\t\tlabpad\n\t\t\t})\n\t\t\tdrawBoxplot({\n\t\t\t\tg: g.append('g').attr('transform', `translate(0,${boxplotHeight + vpad})`),\n\t\t\t\tbp: bs.noEff,\n\t\t\t\tscale,\n\t\t\t\trowheight: boxplotHeight,\n\t\t\t\tcolor: boxplotcolor,\n\t\t\t\tlabpad\n\t\t\t})\n\t\t\t// axis\n\t\t\t{\n\t\t\t\tconst axisg = g.append('g').attr('transform', `translate(0,${boxplotHeight * 2 + vpad * 2})`)\n\t\t\t\tconst axis = axisBottom().scale(scale)\n\t\t\t\taxisstyle({\n\t\t\t\t\taxis: axisg.call(axis),\n\t\t\t\t\tcolor: boxplotcolor,\n\t\t\t\t\tshowline: true\n\t\t\t\t})\n\t\t\t\taxisg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(self.config.outcome.term.name)\n\t\t\t\t\t.attr('font-size', 15)\n\t\t\t\t\t.attr('x', boxplotWidth / 2)\n\t\t\t\t\t.attr('y', axisheight - 5)\n\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t.attr('fill', boxplotcolor)\n\t\t\t}\n\t\t}\n\t}\n\n\tself.mayshow_fisher = result => {\n\t\tif (!result.fisher) return\n\t\tconst div = self.newDiv(\n\t\t\tresult.fisher.isChi ? 'Chi-square test:' : \"Fisher's exact test:\",\n\t\t\t'p-value = ' + result.fisher.pvalue\n\t\t)\n\t\tconst table = div\n\t\t\t.append('table')\n\t\t\t.style('margin', '20px')\n\t\t\t.style('border-spacing', '5px')\n\t\t\t.style('border-collapse', 'separate')\n\t\tfor (const r of result.fisher.rows) {\n\t\t\tconst tr = table.append('tr')\n\t\t\tfor (const c of r) {\n\t\t\t\ttr.append('td').text(c)\n\t\t\t}\n\t\t}\n\t}\n\n\tself.mayshow_coefficients = result => {\n\t\tif (!result.coefficients) {\n\t\t\tif (result.coefficients_uni && result.coefficients_multi) {\n\t\t\t\t// coefficients from univariate and multivariate analyses\n\t\t\t\tself.mayshow_coefficients_uniMulti(result)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\tconst div = self.newDiv(result.coefficients.label)\n\t\tconst table = div\n\t\t\t.append('table')\n\t\t\t.style('border-spacing', '0px')\n\t\t\t.attr('data-testid', 'sjpp_regression_resultCoefficientTable')\n\n\t\t// padding is set on every <td>. need a better solution\n\n\t\t// header row\n\t\tlet header\n\t\t{\n\t\t\tconst tr = table.append('tr').style('opacity', 0.4)\n\t\t\theader = result.coefficients.header\n\t\t\t// header for variable column\n\t\t\ttr.append('td').text(header.shift()).style('padding', '8px')\n\t\t\t// header for category column\n\t\t\ttr.append('td').text(header.shift()).style('padding', '8px')\n\t\t\t// skip headers for sample and event count columns\n\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\theader.shift()\n\t\t\t\theader.shift()\n\t\t\t}\n\t\t\t// combine headers for 95% CI columns\n\t\t\theader.splice(1, 2, '95% CI')\n\t\t\t// display remaining headers\n\t\t\tself.fillDataHeaders(header, tr)\n\t\t}\n\n\t\t// get tws of all independent variables\n\t\t// will be used for tooltip message of estimate value\n\t\tself.independentTws = Object.keys(result.coefficients.terms).map(tid => self.getIndependentInput(tid).term)\n\n\t\tlet varcount = 0\n\t\t// intercept row\n\t\tconst intercept = result.coefficients.intercept\n\t\tif (intercept) {\n\t\t\tconst tr = table.append('tr').style('background', ++varcount % 2 ? '#eee' : 'none')\n\t\t\t// variable column\n\t\t\ttr.append('td').text(intercept.shift()).style('padding', '8px')\n\t\t\t// category column\n\t\t\ttr.append('td').text(intercept.shift()).style('padding', '8px')\n\t\t\t// forest plot column\n\t\t\ttr.append('td')\n\t\t\t// data columns\n\t\t\tself.fillCoefDataCols({ tr, cols: intercept, isIntercept: true })\n\t\t}\n\n\t\t/* term rows:\n\t\tfor each independent terms, show 1 or multiple rows\n\t\tthese rows do not cover interactions, which are rendered afterwards\n\n\t\t* forest plot *\n\t\tshown for both interacting and non-interacting rows\n\t\ta plot is added to 3rd column of each row\n\t\tplotter can be a blank function if there's no valid value for plotting\n\t\t*/\n\t\tconst forestPlotter = self.getForestPlotter(result.coefficients.terms, result.coefficients.interactions)\n\t\tlet rowcolor\n\t\tfor (const tid in result.coefficients.terms) {\n\t\t\tconst termdata = result.coefficients.terms[tid]\n\t\t\tconst tw = self.getIndependentInput(tid).term\n\t\t\trowcolor = ++varcount % 2 ? '#eee' : 'none' // all rows of a variable will have same color\n\t\t\tlet tr = table.append('tr').style('background', rowcolor)\n\n\t\t\t// col 1: term name\n\t\t\tconst termNameTd = tr.append('td').style('padding', '8px')\n\t\t\tfillCoefficientTermname(tw, termNameTd)\n\n\t\t\tif (termdata.fields) {\n\t\t\t\t// create only 1 row for this term in coefficients table, as it doesn't have categories\n\n\t\t\t\tconst cols = termdata.fields\n\n\t\t\t\t// col 2: category column\n\t\t\t\t{\n\t\t\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\t\t\tfillColumn2coefficientsTable(td, tw)\n\t\t\t\t}\n\n\t\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\t\t// sample size and event count columns are present\n\t\t\t\t\t// but do not need to report for continuous variable\n\t\t\t\t\tcols.shift()\n\t\t\t\t\tcols.shift()\n\t\t\t\t}\n\n\t\t\t\t// display forest plot\n\t\t\t\tforestPlotter(tr.append('td'), cols)\n\n\t\t\t\t// display data columns\n\t\t\t\tself.fillCoefDataCols({ tr, cols, tw })\n\t\t\t} else if (termdata.categories) {\n\t\t\t\t// term has categories, create one sub-row for each category in coefficient tables\n\n\t\t\t\tconst orderedCategories = []\n\t\t\t\tconst input = self.getIndependentInput(tid)\n\t\t\t\tif (input.orderedLabels) {\n\t\t\t\t\t// reorder rows by predefined order\n\t\t\t\t\tfor (const k of input.orderedLabels) {\n\t\t\t\t\t\tif (termdata.categories[k]) orderedCategories.push(k)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tfor (const k in termdata.categories) {\n\t\t\t\t\tif (!orderedCategories.includes(k)) orderedCategories.push(k)\n\t\t\t\t}\n\n\t\t\t\t// multiple categories\n\t\t\t\t// show first category as full row, with first cell spanning rest of categories\n\t\t\t\ttermNameTd.attr('rowspan', orderedCategories.length).style('vertical-align', 'top')\n\n\t\t\t\tlet isfirst = true\n\t\t\t\tfor (const k of orderedCategories) {\n\t\t\t\t\tif (!isfirst) {\n\t\t\t\t\t\t// create new row starting from 2nd category\n\t\t\t\t\t\ttr = table.append('tr').style('background', rowcolor)\n\t\t\t\t\t}\n\n\t\t\t\t\tconst cols = termdata.categories[k]\n\n\t\t\t\t\t// col 2: category column\n\t\t\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\t\t\tfillColumn2coefficientsTable(td, tw, k)\n\n\t\t\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\t\t\t// sample size and event count columns present\n\t\t\t\t\t\tif (tw.q.mode == 'spline') {\n\t\t\t\t\t\t\t// skip columns for cubic spline variable\n\t\t\t\t\t\t\tcols.shift()\n\t\t\t\t\t\t\tcols.shift()\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// report sample sizes and event counts of coefficients\n\t\t\t\t\t\t\t// for both ref and non-ref categories\n\t\t\t\t\t\t\tconst [samplesize_ref, samplesize_c] = cols.shift().split('/')\n\t\t\t\t\t\t\tconst [eventcnt_ref, eventcnt_c] = cols.shift().split('/')\n\t\t\t\t\t\t\tif (isfirst) {\n\t\t\t\t\t\t\t\tconst variableBottomDiv = termNameTd.select('.sjpcb-coef-variable-bottom')\n\t\t\t\t\t\t\t\tvariableBottomDiv.style('align-items', 'baseline')\n\t\t\t\t\t\t\t\tconst refGrpDiv = variableBottomDiv.selectAll('div').filter((d, i) => i === 1)\n\t\t\t\t\t\t\t\trefGrpDiv.append('div').html(`n=${samplesize_ref}<br>events=${eventcnt_ref}`)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\ttd.append('div').style('font-size', '.8em').html(`n=${samplesize_c}<br>events=${eventcnt_c}`)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\t// display forest plot\n\t\t\t\t\tforestPlotter(tr.append('td'), cols)\n\n\t\t\t\t\t// display data columns\n\t\t\t\t\tself.fillCoefDataCols({ tr, cols, tw, categoryKey: k })\n\n\t\t\t\t\tisfirst = false\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\ttr.append('td').text('ERROR: no .fields[] or .categories{}')\n\t\t\t}\n\t\t}\n\n\t\t// interactions\n\t\tfor (const i of result.coefficients.interactions) {\n\t\t\trowcolor = ++varcount % 2 ? '#eee' : 'none' // all rows of an interaction will have same color\n\t\t\tlet tr = table.append('tr').style('background', rowcolor)\n\n\t\t\tconst term1 = self.getIndependentInput(i.term1).term\n\t\t\tconst term2 = self.getIndependentInput(i.term2).term\n\n\t\t\t// col 1: variable\n\t\t\t{\n\t\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\t\tfillTdName(td.append('div'), term1 ? term1.term.name + ' : ' : row.term1 + ' : ')\n\t\t\t\tfillTdName(td.append('div'), term2 ? term2.term.name : row.term2)\n\t\t\t\ttd.attr('rowspan', i.categories.length).style('vertical-align', 'top')\n\t\t\t}\n\n\t\t\tlet isfirst = true\n\t\t\tfor (const c of i.categories) {\n\t\t\t\t// new subrow for every category\n\t\t\t\tif (!isfirst) tr = table.append('tr').style('background', rowcolor)\n\n\t\t\t\t// col 2: category\n\t\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\t\tfillColumn2coefficientsTable(td.append('div'), term1, c.category1)\n\t\t\t\tfillColumn2coefficientsTable(td.append('div'), term2, c.category2)\n\n\t\t\t\tconst cols = c.lst\n\n\t\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\t\t// sample size and event count columns are present\n\t\t\t\t\t// skip for now for interactions\n\t\t\t\t\t// TODO: how to handle sample size/event counts for interactions?\n\t\t\t\t\tcols.shift()\n\t\t\t\t\tcols.shift()\n\t\t\t\t}\n\n\t\t\t\t// display forest plot\n\t\t\t\tforestPlotter(tr.append('td'), cols)\n\n\t\t\t\t// display data columns\n\t\t\t\tself.fillCoefDataCols({ tr, cols, tw: term1, tw2: term2, categoryKey: c.category1, categoryKey2: c.category2 })\n\n\t\t\t\tisfirst = false\n\t\t\t}\n\t\t}\n\n\t\t// last row to show forest plot axis (call function without data)\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td') // col 1\n\t\ttr.append('td') // col 2\n\t\tforestPlotter(tr.append('td')) // forest plot axis\n\t\tfor (const v of header) tr.append('td')\n\t}\n\n\tself.mayshow_coefficients_uniMulti = result => {\n\t\t// generate coefficients table for\n\t\t// univariate and multivariate analyses\n\t\tif (!result.coefficients_uni || !result.coefficients_multi) return\n\n\t\tconst div = self.newDiv(result.coefficients_uni.label)\n\t\tdiv.style('margin-bottom', '200px') // to provide space for rendering result tooltips\n\t\tconst table = div\n\t\t\t.append('table')\n\t\t\t.style('border-spacing', '0px')\n\t\t\t.attr('data-testid', 'sjpp_regression_resultCoefficientTable')\n\n\t\t// padding is set on every <td>. need a better solution\n\n\t\t// header row\n\t\tlet header_uni, header_multi\n\t\t{\n\t\t\tconst tr_label = table.append('tr').style('opacity', 0.4) // labels displayed above header row\n\t\t\tconst tr = table.append('tr').style('opacity', 0.4) // header row\n\n\t\t\theader_uni = result.coefficients_uni.header\n\t\t\theader_multi = result.coefficients_multi.header\n\n\t\t\t// header for variable column\n\t\t\ttr.append('td').text(header_uni.shift()).style('padding', '8px')\n\t\t\ttr_label.append('td').style('padding', '8px')\n\t\t\theader_multi.shift() // same value as in header_uni\n\n\t\t\t// header for category column\n\t\t\ttr.append('td').text(header_uni.shift()).style('padding', '8px')\n\t\t\ttr_label.append('td').style('padding', '8px')\n\t\t\theader_multi.shift() // same value as in header_uni\n\n\t\t\t// skip headers for sample and event count columns\n\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\theader_uni.shift()\n\t\t\t\theader_uni.shift()\n\t\t\t\theader_multi.shift()\n\t\t\t\theader_multi.shift()\n\t\t\t}\n\n\t\t\t// combine headers for 95% CI columns\n\t\t\theader_uni.splice(1, 2, '95% CI')\n\t\t\theader_multi.splice(1, 2, '95% CI')\n\n\t\t\t// fill headers for data columns\n\t\t\tself.fillDataHeaders(header_uni, tr, tr_label, 'Univariate')\n\t\t\ttr.append('td').style('width', '2px') //separation between univariate/multivariate\n\t\t\ttr_label.append('td').style('width', '2px')\n\t\t\tself.fillDataHeaders(header_multi, tr, tr_label, 'Multivariable-adjusted')\n\t\t}\n\n\t\t/* term rows:\n\t\tfor each independent terms, show 1 or multiple rows\n\n\t\t* forest plot *\n\t\ta plot for univariate data and a plot for multivariate data\n\t\tare shown as separate columns in each row\n\t\t*/\n\n\t\tconst forestPlotter_uni = self.getForestPlotter(result.coefficients_uni.terms, result.coefficients_uni.interactions)\n\t\tconst forestPlotter_multi = self.getForestPlotter(\n\t\t\tresult.coefficients_multi.terms,\n\t\t\tresult.coefficients_multi.interactions\n\t\t)\n\n\t\t// get tws of all independent variables\n\t\t// will be used for tooltip message of estimate value\n\t\tself.independentTws = Object.keys(result.coefficients_uni.terms).map(tid => self.getIndependentInput(tid).term)\n\n\t\tlet varcount = 0,\n\t\t\trowcolor\n\t\tfor (const tid in result.coefficients_uni.terms) {\n\t\t\t// termdata is data from univariate analysis\n\t\t\t// will be used to fill in variable, category, and\n\t\t\t// univariate data columns\n\t\t\tconst termdata = result.coefficients_uni.terms[tid]\n\t\t\t// termdata_multi is data from multivariate analysis\n\t\t\t// will be used to fill in multivariate data columns\n\t\t\tconst termdata_multi = result.coefficients_multi.terms[tid]\n\n\t\t\tconst tw = self.getIndependentInput(tid).term\n\t\t\trowcolor = ++varcount % 2 ? '#eee' : 'none' // all rows of a variable will have same color\n\t\t\tlet tr = table.append('tr').style('background', rowcolor)\n\n\t\t\t// col 1: term name\n\t\t\tconst termNameTd = tr.append('td').style('padding', '8px')\n\t\t\tfillCoefficientTermname(tw, termNameTd)\n\n\t\t\tif (termdata.fields) {\n\t\t\t\t// create only 1 row for this term in coefficients table, as it doesn't have categories\n\n\t\t\t\tconst cols = termdata.fields\n\t\t\t\tconst cols_multi = termdata_multi.fields\n\n\t\t\t\t// col 2: category column\n\t\t\t\t{\n\t\t\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\t\t\tfillColumn2coefficientsTable(td, tw)\n\t\t\t\t}\n\n\t\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\t\t// cox regression\n\t\t\t\t\t// sample size and event count columns are present\n\t\t\t\t\t// but do not need to report for continuous variable\n\t\t\t\t\tcols.shift()\n\t\t\t\t\tcols.shift()\n\t\t\t\t\tcols_multi.shift()\n\t\t\t\t\tcols_multi.shift()\n\t\t\t\t}\n\n\t\t\t\t// display univariate forest plot\n\t\t\t\tforestPlotter_uni(tr.append('td'), cols)\n\n\t\t\t\t// display univariate data columns\n\t\t\t\tself.fillCoefDataCols({ tr, cols, tw, isUnivariate: true })\n\n\t\t\t\ttr.append('td').style('width', '2px') // separation between univariate/multivariate\n\n\t\t\t\t// display multivariate forest plot\n\t\t\t\tforestPlotter_multi(tr.append('td'), cols_multi)\n\n\t\t\t\t// display multivariate data columns\n\t\t\t\tself.fillCoefDataCols({ tr, cols: cols_multi, tw })\n\t\t\t} else if (termdata.categories) {\n\t\t\t\t// term has categories, create one sub-row for each category in coefficient tables\n\n\t\t\t\tconst orderedCategories = []\n\t\t\t\tconst input = self.getIndependentInput(tid)\n\t\t\t\tif (input.orderedLabels) {\n\t\t\t\t\t// reorder rows by predefined order\n\t\t\t\t\tfor (const k of input.orderedLabels) {\n\t\t\t\t\t\tif (termdata.categories[k]) orderedCategories.push(k)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tfor (const k in termdata.categories) {\n\t\t\t\t\tif (!orderedCategories.includes(k)) orderedCategories.push(k)\n\t\t\t\t}\n\n\t\t\t\t// multiple categories\n\t\t\t\t// show first category as full row, with first cell spanning rest of categories\n\t\t\t\ttermNameTd.attr('rowspan', orderedCategories.length).style('vertical-align', 'top')\n\n\t\t\t\tlet isfirst = true\n\t\t\t\tfor (const k of orderedCategories) {\n\t\t\t\t\tif (!isfirst) {\n\t\t\t\t\t\t// create new row starting from 2nd category\n\t\t\t\t\t\ttr = table.append('tr').style('background', rowcolor)\n\t\t\t\t\t}\n\n\t\t\t\t\tconst cols = termdata.categories[k]\n\t\t\t\t\tconst cols_multi = termdata_multi.categories[k]\n\n\t\t\t\t\t// col 2: category column\n\t\t\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\t\t\tfillColumn2coefficientsTable(td, tw, k)\n\n\t\t\t\t\tif (self.config.regressionType == 'cox') {\n\t\t\t\t\t\t// cox regression\n\t\t\t\t\t\t// sample size and event count columns are present\n\t\t\t\t\t\tif (tw.q.mode == 'spline') {\n\t\t\t\t\t\t\t// skip columns for cubic spline variable\n\t\t\t\t\t\t\tcols.shift()\n\t\t\t\t\t\t\tcols.shift()\n\t\t\t\t\t\t\tcols_multi.shift()\n\t\t\t\t\t\t\tcols_multi.shift()\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// report sample sizes and event counts of coefficients\n\t\t\t\t\t\t\t// for both ref and non-ref categories\n\t\t\t\t\t\t\tconst [samplesize_ref, samplesize_c] = cols.shift().split('/')\n\t\t\t\t\t\t\tconst [eventcnt_ref, eventcnt_c] = cols.shift().split('/')\n\t\t\t\t\t\t\tif (isfirst) {\n\t\t\t\t\t\t\t\tconst variableBottomDiv = termNameTd.select('.sjpcb-coef-variable-bottom')\n\t\t\t\t\t\t\t\tvariableBottomDiv.style('align-items', 'baseline')\n\t\t\t\t\t\t\t\tconst refGrpDiv = variableBottomDiv.selectAll('div').filter((d, i) => i === 1)\n\t\t\t\t\t\t\t\trefGrpDiv.append('div').html(`n=${samplesize_ref}<br>events=${eventcnt_ref}`)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\ttd.append('div').style('font-size', '.8em').html(`n=${samplesize_c}<br>events=${eventcnt_c}`)\n\t\t\t\t\t\t\tcols_multi.shift()\n\t\t\t\t\t\t\tcols_multi.shift()\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\t// display univariate forest plot\n\t\t\t\t\tforestPlotter_uni(tr.append('td'), cols)\n\n\t\t\t\t\t// display univariate data columns\n\t\t\t\t\tself.fillCoefDataCols({ tr, cols, tw, categoryKey: k, isUnivariate: true })\n\n\t\t\t\t\ttr.append('td').style('width', '2px') // separation between univariate/multivariate\n\n\t\t\t\t\t// display multivariate forest plot\n\t\t\t\t\tforestPlotter_multi(tr.append('td'), cols_multi)\n\n\t\t\t\t\t// display multivariate data columns\n\t\t\t\t\tself.fillCoefDataCols({ tr, cols: cols_multi, tw, categoryKey: k })\n\n\t\t\t\t\tisfirst = false\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\ttr.append('td').text('ERROR: no .fields[] or .categories{}')\n\t\t\t}\n\t\t}\n\n\t\t// last row to show forest plot axis (call function without data)\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td') // col 1\n\t\ttr.append('td') // col 2\n\t\tforestPlotter_uni(tr.append('td')) // forest plot axis\n\t\tfor (const v of header_uni) tr.append('td')\n\t\ttr.append('td').style('width', '2px') // separation between univariate/multivariate\n\t\tforestPlotter_multi(tr.append('td')) // forest plot axis\n\t\tfor (const v of header_multi) tr.append('td')\n\t}\n\n\t// fill headers of data columns of coefficients table\n\tself.fillDataHeaders = (header, tr, tr_label, label) => {\n\t\tconst startColN = tr.selectAll('td').size()\n\t\t// header for forest plot column\n\t\ttr.append('td')\n\t\t// headers for data columns\n\t\theader.forEach((h, i, arr) => {\n\t\t\tif (i === 0) {\n\t\t\t\t// header for estimate column\n\t\t\t\tconst est = h\n\t\t\t\tconst estTd = tr.append('td').style('padding', '8px').text(est)\n\t\t\t\tconst estInfo = estTd.append('sup').style('cursor', 'default').html('&nbsp;&#9432;')\n\t\t\t\testInfo.on('mouseover', event => {\n\t\t\t\t\tconst tip = self.dom.tip.clear()\n\t\t\t\t\ttip.d.append('div').text('Hover over each value to view explanation of the result')\n\t\t\t\t\ttip.showunder(event.target)\n\t\t\t\t})\n\t\t\t\testInfo.on('mouseout', () => self.dom.tip.hide())\n\t\t\t} else {\n\t\t\t\t// headers for all other data columns\n\t\t\t\tconst td = tr.append('td').text(h).style('padding', '8px')\n\t\t\t\tif (i === arr.length - 1) td.style('font-style', 'italic')\n\t\t\t}\n\t\t})\n\t\t// fill label row, if defined\n\t\tif (tr_label) {\n\t\t\tconst endColN = tr.selectAll('td').size()\n\t\t\ttr_label\n\t\t\t\t.append('td')\n\t\t\t\t.attr('colspan', endColN - startColN)\n\t\t\t\t.style('padding', '0px 8px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.append('div')\n\t\t\t\t.text(label)\n\t\t\t\t.style('border-bottom', '1px solid')\n\t\t\t\t.style('padding', '5px')\n\t\t}\n\t}\n\n\t// fill data columns of row of coefficients table\n\tself.fillCoefDataCols = arg => {\n\t\tconst { tr, cols, tw } = arg\n\t\t// estimate (Beta/OR/HR) column\n\t\tconst est = cols.shift()\n\t\tconst estSpan = tr.append('td').style('padding', '8px').style('cursor', 'default').append('span').text(est)\n\t\t// on mouseover, display explanation of estimate value\n\t\testSpan.on('mouseover', event => {\n\t\t\tif (tw && tw.q.mode == 'spline') return\n\t\t\tconst tip = self.dom.tip.clear()\n\t\t\tlet estimateMsg = self.getEstimateMsg(Object.assign({ est: Number(est) }, arg))\n\t\t\tif (tw) {\n\t\t\t\tconst pvalue = Number(cols[cols.length - 1])\n\t\t\t\testimateMsg += `<br><br><span style=\"font-style: italic\">This association is ${\n\t\t\t\t\tpvalue < 0.05 ? 'statistically significant (P < 0.05)' : 'not statistically significant (P \u2265 0.05)</span>'\n\t\t\t\t}.`\n\t\t\t}\n\t\t\ttip.d.append('div').style('max-width', '500px').html(estimateMsg)\n\t\t\ttip.showunder(event.target)\n\t\t})\n\t\testSpan.on('mouseout', () => self.dom.tip.hide())\n\t\t// 95% CI column\n\t\ttr.append('td').html(`${cols.shift()} &ndash; ${cols.shift()}`).style('padding', '8px')\n\t\t// rest of columns\n\t\tfor (const v of cols) tr.append('td').text(v).style('padding', '8px')\n\t}\n\n\t// get tooltip message explaining the estimate value\n\tself.getEstimateMsg = arg => {\n\t\tconst { est, tw, tw2, categoryKey, categoryKey2, isIntercept, isUnivariate } = arg\n\t\tconst independentTws = self.independentTws\n\t\tconst outcomeTw = self.config.outcome\n\t\tconst regtype = self.config.regressionType\n\t\tconst category = tw?.term?.values && tw.term.values[categoryKey] ? tw.term.values[categoryKey].label : categoryKey\n\t\tconst category2 =\n\t\t\ttw2?.term?.values && tw2.term.values[categoryKey2] ? tw2.term.values[categoryKey2].label : categoryKey2\n\t\tconst refGrp = tw?.term?.values && tw.term.values[tw.refGrp] ? tw.term.values[tw.refGrp].label : tw?.refGrp\n\t\tconst refGrp2 = tw2?.term?.values && tw2.term.values[tw2.refGrp] ? tw2.term.values[tw2.refGrp].label : tw2?.refGrp\n\n\t\t/** part 1: outcome variable **/\n\t\tlet msg\n\t\tif (regtype == 'linear') {\n\t\t\tmsg = tw2 ? getInteractionMsg() : `Mean ${styleVariable(outcomeTw)} is`\n\t\t\tmsg += ` ${Math.abs(est)} units`\n\t\t\tif (isIntercept) {\n\t\t\t\tconst baselines = getBaselines(independentTws)\n\t\t\t\treturn `${msg} when ${joinVariables(baselines)}.`\n\t\t\t}\n\t\t\tmsg += ` ${est < 0 ? 'lower' : 'higher'} `\n\t\t} else if (regtype == 'logistic') {\n\t\t\tmsg = tw2 ? getInteractionMsg() : `Odds of ${styleVariable(outcomeTw, outcomeTw.nonRefGrp)} is`\n\t\t\tif (isIntercept) {\n\t\t\t\tconst baselines = getBaselines(independentTws)\n\t\t\t\treturn `${msg} ${est} when ${joinVariables(baselines)}.`\n\t\t\t}\n\t\t\tmsg += est > 1 ? ` ${est} times higher ` : ` ${roundValue(1 / est, 3)} times lower `\n\t\t} else if (regtype == 'cox') {\n\t\t\tmsg = tw2\n\t\t\t\t? getInteractionMsg()\n\t\t\t\t: `Hazard (instantaneous rate) of ${styleVariable(outcomeTw, outcomeTw.eventLabel)} is`\n\t\t\tmsg += est > 1 ? ` ${est} times higher ` : ` ${roundValue(1 / est, 3)} times lower `\n\t\t} else {\n\t\t\tthrow 'regression type not recognized'\n\t\t}\n\n\t\t/** part 2: independent variable **/\n\t\tconst interactions = []\n\t\tconst interactionsBaselines = []\n\t\tif (tw.interactions?.length && !tw2) {\n\t\t\t// variable is part of an interaction, but the current row\n\t\t\t// is not an interaction row\n\t\t\tfor (const tid of tw.interactions) {\n\t\t\t\tconst t = self.getIndependentInput(tid).term\n\t\t\t\tif (t.term.snps) {\n\t\t\t\t\t// snplst or snplocus term\n\t\t\t\t\t// need to get term ids of individuals snps\n\t\t\t\t\tfor (const snp of t.term.snps) interactions.push(snp.snpid)\n\t\t\t\t} else {\n\t\t\t\t\tinteractions.push(tid)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!interactions.length) throw 'interactions[] is empty'\n\t\t\tconst interactingTws = independentTws.filter(t => interactions.includes(t.$id || t.id))\n\t\t\tinteractionsBaselines.push(...getBaselines(interactingTws))\n\t\t}\n\t\tif (category) {\n\t\t\t// categorical variable\n\t\t\tmsg += `in ${joinVariables([styleVariable(tw, category), ...interactionsBaselines])} compared to ${joinVariables([\n\t\t\t\tstyleVariable(tw, refGrp),\n\t\t\t\t...interactionsBaselines\n\t\t\t])}`\n\t\t} else if (tw.q.mode == 'continuous') {\n\t\t\t// continuous variable\n\t\t\tmsg += `for every one unit increase of ${styleVariable(tw)}`\n\t\t\tif (interactionsBaselines.length) msg += ` when ${joinVariables(interactionsBaselines)}`\n\t\t} else if (tw.q.geneticModel === 0) {\n\t\t\t// genetic variable, additive model\n\t\t\tmsg += `for every additional ${tw.effectAllele} allele of ${styleVariable(tw)}`\n\t\t\tif (interactionsBaselines.length) msg += ` when ${joinVariables(interactionsBaselines)}`\n\t\t} else if (tw.q.geneticModel == 1 || tw.q.geneticModel == 2) {\n\t\t\t// genetic variable, dominant or recessive model\n\t\t\tconst gts = Object.keys(tw.gt2count)\n\t\t\tconst testGts = gts.filter(gt => {\n\t\t\t\tif (tw.q.geneticModel == 1) {\n\t\t\t\t\t// dominant model\n\t\t\t\t\treturn gt.includes(tw.effectAllele)\n\t\t\t\t} else {\n\t\t\t\t\t// recessive model\n\t\t\t\t\treturn gt\n\t\t\t\t\t\t.replace(/[^a-zA-Z]/g, '')\n\t\t\t\t\t\t.split('')\n\t\t\t\t\t\t.every(c => c == tw.effectAllele)\n\t\t\t\t}\n\t\t\t})\n\t\t\tconst refGts = gts.filter(gt => !testGts.includes(gt))\n\t\t\tmsg += `in ${joinVariables([\n\t\t\t\tstyleVariable(tw, testGts.join(', ')),\n\t\t\t\t...interactionsBaselines\n\t\t\t])} compared to ${joinVariables([styleVariable(tw, refGts.join(', ')), ...interactionsBaselines])}`\n\t\t}\n\n\t\t/** part 3: adjusting for covariates **/\n\t\t// get term ids of current variable and any interacting variables\n\t\tconst tids = [tw.$id || tw.id]\n\t\tif (tw.interactions?.length) {\n\t\t\tif (tw2) tids.push(tw2.$id || tw2.id)\n\t\t\telse tids.push(...interactions)\n\t\t}\n\t\t// get covariates (i.e., all other variables)\n\t\tconst covariates = independentTws.filter(t => !tids.includes(t.$id || t.id)).map(t => styleVariable(t))\n\t\tif (regtype == 'cox') {\n\t\t\tcovariates.push(outcomeTw.q.timeScale == 'time' ? '\"Years of follow-up\"' : '\"Attained age during follow-up\"') // TODO: how to handle styling for this?\n\t\t}\n\t\t// build message for covariates\n\t\tif (!covariates.length || isUnivariate) return msg + '.'\n\t\treturn msg + `, adjusting for ${joinVariables(covariates)}.`\n\n\t\t/** helper functions **/\n\t\t// function to style a variable (and its category)\n\t\tfunction styleVariable(tw, category) {\n\t\t\tconst spans = [\n\t\t\t\t`<span class=\"term_name_btn sja_filter_tag_btn\" style=\"padding: 3px 6px; margin: 2.5px 0px; border-radius: ${\n\t\t\t\t\tcategory ? '6px 0px 0px 6px' : '6px'\n\t\t\t\t};\">${tw.term.name.length < 40 ? tw.term.name : tw.term.name.substring(0, 35) + ' ...'}</span>`\n\t\t\t]\n\t\t\tif (category) {\n\t\t\t\tspans.push(\n\t\t\t\t\t`<span class=\"ts_summary_btn sja_filter_tag_btn\" style=\"padding: 3px 6px; margin: 2.5px 0px; border-radius: 0px 6px 6px 0px; font-style: italic;\">${category}</span>`\n\t\t\t\t)\n\t\t\t}\n\t\t\treturn `<div style=\"display: inline; white-space: nowrap; font-size: 0.9em\">${spans.join('')}</div>`\n\t\t}\n\n\t\t// function to get message for interaction term\n\t\tfunction getInteractionMsg() {\n\t\t\tlet msg =\n\t\t\t\tregtype == 'linear'\n\t\t\t\t\t? `The difference in mean ${styleVariable(outcomeTw)}`\n\t\t\t\t\t: regtype == 'logistic'\n\t\t\t\t\t? `The difference in odds of ${styleVariable(outcomeTw, outcomeTw.nonRefGrp)}`\n\t\t\t\t\t: `The difference in hazard (instantaneous rate) of ${styleVariable(outcomeTw, outcomeTw.eventLabel)}`\n\n\t\t\tif (category2) {\n\t\t\t\t// categorical variable\n\t\t\t\tmsg += ` between ${styleVariable(tw2, category2)} and ${styleVariable(tw2, refGrp2)} is`\n\t\t\t} else if (tw2.q.mode == 'continuous') {\n\t\t\t\t// continuous variable\n\t\t\t\tmsg += ` for every one unit increase of ${styleVariable(tw2)} is`\n\t\t\t} else if (tw2.q.geneticModel === 0) {\n\t\t\t\t// genetic variable, additive model\n\t\t\t\tmsg += ` for every additional ${tw2.effectAllele} allele of ${styleVariable(tw2)} is`\n\t\t\t} else if (tw2.q.geneticModel == 1 || tw2.q.geneticModel == 2) {\n\t\t\t\t// genetic variable, dominant or recessive model\n\t\t\t\tconst gts = Object.keys(tw2.gt2count)\n\t\t\t\tconst testGts = gts.filter(gt => {\n\t\t\t\t\tif (tw2.q.geneticModel == 1) {\n\t\t\t\t\t\t// dominant model\n\t\t\t\t\t\treturn gt.includes(tw2.effectAllele)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// recessive model\n\t\t\t\t\t\treturn gt\n\t\t\t\t\t\t\t.replace(/[^a-zA-Z]/g, '')\n\t\t\t\t\t\t\t.split('')\n\t\t\t\t\t\t\t.every(c => c == tw2.effectAllele)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tconst refGts = gts.filter(gt => !testGts.includes(gt))\n\t\t\t\tmsg += ` between ${styleVariable(tw2, testGts.join(', '))} and ${styleVariable(tw2, refGts.join(', '))} is`\n\t\t\t}\n\n\t\t\treturn msg\n\t\t}\n\n\t\t/* function to get the baseline level of each variable\n\t\t\t- categorical variable: refGrp\n\t\t\t- continuous variable: 0\n\t\t\t- genetic variable:\n\t\t\t\t- additive model: 0 effect alleles\n\t\t\t\t- dominant model: homozygous for non-effect allele\n\t\t\t\t- recessive model: homozygous for non-effect allele or heterozygous\n\t\t\t\t- by genotype: same as categorical variable\n\t\t*/\n\t\tfunction getBaselines(tws) {\n\t\t\tconst baselines = tws.map(tw => {\n\t\t\t\tif (tw.q.mode != 'spline' && 'refGrp' in tw && tw.refGrp != refGrp_NA) {\n\t\t\t\t\t// has refGrp, must be categorical variable\n\t\t\t\t\tconst refGrp = tw?.term?.values && tw.term.values[tw.refGrp] ? tw.term.values[tw.refGrp].label : tw?.refGrp\n\t\t\t\t\treturn styleVariable(tw, refGrp)\n\t\t\t\t} else if (tw.q.mode == 'continuous') {\n\t\t\t\t\t// continuous variable\n\t\t\t\t\treturn styleVariable(tw, '0')\n\t\t\t\t} else if (tw.q.geneticModel === 0) {\n\t\t\t\t\t// genetic variable, additive model\n\t\t\t\t\treturn styleVariable(tw, `No ${tw.effectAllele} alleles`)\n\t\t\t\t} else if (tw.q.geneticModel == 1 || tw.q.geneticModel == 2) {\n\t\t\t\t\t// genetic variable, dominant or recessive model\n\t\t\t\t\tconst gts = Object.keys(tw.gt2count)\n\t\t\t\t\tconst refGts = gts.filter(gt => {\n\t\t\t\t\t\tif (tw.q.geneticModel == 1) {\n\t\t\t\t\t\t\t// dominant model\n\t\t\t\t\t\t\treturn !gt.includes(tw.effectAllele)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// recessive model\n\t\t\t\t\t\t\treturn !gt\n\t\t\t\t\t\t\t\t.replace(/[^a-zA-Z]/g, '')\n\t\t\t\t\t\t\t\t.split('')\n\t\t\t\t\t\t\t\t.every(c => c == tw.effectAllele)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\treturn styleVariable(tw, refGts.join(', '))\n\t\t\t\t}\n\t\t\t})\n\t\t\treturn baselines\n\t\t}\n\n\t\tfunction joinVariables(variables) {\n\t\t\tif (!variables.length) return ''\n\t\t\telse if (variables.length == 1) return variables[0]\n\t\t\telse if (variables.length == 2) return variables.join(' and ')\n\t\t\telse return `${variables.slice(0, -1).join(', ')}, and ${variables.slice(-1)}`\n\t\t}\n\t}\n\n\t// show disclaimer message under the coefficient tables when\n\t// regressionType == 'cox\n\tself.mayshow_coxDisclaimer = () => {\n\t\tconst disclaimer = self.app.vocabApi.termdbConfig.regression?.settings?.coxDisclaimer\n\t\tif (disclaimer && self.config.regressionType == 'cox') {\n\t\t\tself.dom.oneSetResultDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('white-space', 'wrap') // somewhere in the parent dom there must be a nowrap setting that causes overly long text to look bad. must apply this so it will auto wrap\n\t\t\t\t.attr('data-testid', 'sjpp-regression-result-coxDisclaimer')\n\t\t\t\t.style('margin', '20px 0px 20px 10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('text-align', 'left')\n\t\t\t\t.text(disclaimer)\n\t\t}\n\t}\n\n\tself.mayshow_totalSnpEffect = result => {\n\t\tif (!result.totalSnpEffect) return\n\t\tconst div = self.newDiv(result.totalSnpEffect.label)\n\t\tconst table = div.append('table').style('border-spacing', '0px')\n\n\t\t// header row\n\t\t{\n\t\t\tconst tr = table.append('tr').style('opacity', 0.4)\n\t\t\tfor (const v of result.totalSnpEffect.header) {\n\t\t\t\ttr.append('td').text(v).style('padding', '8px')\n\t\t\t}\n\t\t}\n\n\t\t// total snp effect row\n\t\tconst tr = table.append('tr').style('background', '#eee')\n\t\tfor (const v of result.totalSnpEffect.lst) {\n\t\t\ttr.append('td').text(v).style('padding', '8px')\n\t\t}\n\t\tconst snp = self.getIndependentInput(result.totalSnpEffect.snp).term\n\t\tconst interactions = result.totalSnpEffect.interactions.map(interaction => {\n\t\t\treturn {\n\t\t\t\tt1: self.getIndependentInput(interaction.term1).term,\n\t\t\t\tt2: self.getIndependentInput(interaction.term2).term\n\t\t\t}\n\t\t})\n\t\tconst bottomInfo = `Total: total effect of removing the snp (${snp.term.name}) and its interactions (${interactions\n\t\t\t.map(interaction => interaction.t1.term.name + ' : ' + interaction.t2.term.name)\n\t\t\t.join(' ; ')}) from the model`\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('margin', '20px 0px 20px 10px')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('text-align', 'left')\n\t\t\t.style('color', '#999')\n\t\t\t.text(bottomInfo)\n\t}\n\n\tself.mayshow_type3 = result => {\n\t\tif (!result.type3 || self.app.vocabApi.termdbConfig.regression?.settings?.hideType3) return\n\t\tconst div = self.newDiv(result.type3.label)\n\t\tconst table = div.append('table').style('border-spacing', '0px')\n\n\t\t// header row\n\t\t{\n\t\t\tconst tr = table.append('tr').style('opacity', 0.4)\n\t\t\tfor (const v of result.type3.header) {\n\t\t\t\ttr.append('td').text(v).style('padding', '8px')\n\t\t\t}\n\t\t}\n\n\t\t// intercept row\n\t\tif (self.config.regressionType != 'cox') {\n\t\t\tconst tr = table.append('tr').style('background', '#eee')\n\t\t\tfor (const v of result.type3.intercept) {\n\t\t\t\ttr.append('td').text(v).style('padding', '8px')\n\t\t\t}\n\t\t}\n\n\t\t// term rows\n\t\t// independent terms (no interaction)\n\t\tlet rowcount = self.config.regressionType == 'cox' ? 1 : 0\n\t\tfor (const tid in result.type3.terms) {\n\t\t\t// get term data\n\t\t\tconst termdata = result.type3.terms[tid]\n\t\t\tconst tw = self.getIndependentInput(tid).term\n\t\t\tlet tr = table.append('tr').style('background', rowcount++ % 2 ? '#eee' : 'none')\n\t\t\t// col 1: variable\n\t\t\tconst termNameTd = tr.append('td').style('padding', '8px')\n\t\t\tfillTdName(termNameTd, tw.term.name)\n\t\t\t// rest of columns\n\t\t\tfor (const v of termdata) {\n\t\t\t\ttr.append('td').text(v).style('padding', '8px')\n\t\t\t}\n\t\t}\n\t\t// interactions\n\t\tfor (const row of result.type3.interactions) {\n\t\t\tconst tr = table.append('tr').style('background', rowcount++ % 2 ? '#eee' : 'none')\n\t\t\tconst t1 = self.getIndependentInput(row.term1).term\n\t\t\tconst t2 = self.getIndependentInput(row.term2).term\n\t\t\t// col 1: variable\n\t\t\tconst td = tr.append('td').style('padding', '8px')\n\t\t\tfillTdName(td.append('div'), t1.term.name + ' : ')\n\t\t\tfillTdName(td.append('div'), t2.term.name)\n\t\t\t// rest of columns\n\t\t\tfor (const v of row.lst) {\n\t\t\t\ttr.append('td').text(v).style('padding', '8px')\n\t\t\t}\n\t\t}\n\t}\n\n\tself.mayshow_tests = result => {\n\t\tif (!result.tests || self.app.vocabApi.termdbConfig.regression?.settings?.hideTests) return\n\t\tconst div = self.newDiv(result.tests.label)\n\t\tconst table = div.append('table').style('border-spacing', '0px')\n\t\tconst header = table.append('tr').style('opacity', 0.4)\n\t\tfor (const cell of result.tests.header) {\n\t\t\theader.append('td').text(cell).style('padding', '8px')\n\t\t}\n\t\tlet rowcount = 0\n\t\tfor (const row of result.tests.rows) {\n\t\t\tconst tr = table.append('tr').style('background', rowcount++ % 2 ? 'none' : '#eee')\n\t\t\tfor (const cell of row) {\n\t\t\t\ttr.append('td').text(cell).style('padding', '8px')\n\t\t\t}\n\t\t}\n\t}\n\n\tself.mayshow_other = result => {\n\t\tif (!result.other) return\n\t\tconst div = self.newDiv(result.other.label)\n\t\tconst table = div.append('table').style('border-spacing', '8px')\n\t\tfor (let i = 0; i < result.other.header.length; i++) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').style('opacity', 0.4).text(result.other.header[i])\n\t\t\ttr.append('td').text(result.other.rows[i])\n\t\t}\n\t}\n\n\t/*\n\tthe function takes all data rows (except intercept) from coefficients table, and return a callback\n\tthe callback closures the axis range of all data\n\trun callback on each coefficient table row to plot the forest plot\n\n\tcollect all numeric data points from terms/interactons\n\tto derive forest plot axis range\n\tsort numbers in an array\n\tin logistic, if array[i]=0 then cannot use log(0) as axis min,\n\tin that case should use array[i+1] or next to find the smallest real number as axis min\n\tan arbitary cap is used to guard against extreme estimate values\n\t*/\n\tself.getForestPlotter = (terms, interactions) => {\n\t\t// array indices are the same for both non-interacting and interacting rows\n\t\tlet midIdx, // array index of the beta/odds ratio\n\t\t\tCIlow, // array(column) index of low end of confidence interval of midIdx\n\t\t\tCIhigh, // array index of high end of confidence interval\n\t\t\taxislab, // data type to show as axis label\n\t\t\tbaselineValue, // baseline value to show a vertical line\n\t\t\t// min/max value capping the axis, to guard against extreme estimates\n\t\t\t// only used for logistic odds ratio\n\t\t\t// for linear, will use actual range from estimates and confidence interval\n\t\t\tcapMin,\n\t\t\tcapMax\n\t\tif (self.config.regressionType == 'linear') {\n\t\t\tmidIdx = 0\n\t\t\tCIlow = 1\n\t\t\tCIhigh = 2\n\t\t\taxislab = 'Beta value'\n\t\t\tbaselineValue = 0\n\t\t\tcapMin = null\n\t\t\tcapMax = null\n\t\t} else if (self.config.regressionType == 'logistic') {\n\t\t\tmidIdx = 0\n\t\t\tCIlow = 1\n\t\t\tCIhigh = 2\n\t\t\taxislab = 'Odds ratio'\n\t\t\tbaselineValue = 1\n\t\t\tcapMin = 0.1\n\t\t\tcapMax = 10\n\t\t} else if (self.config.regressionType == 'cox') {\n\t\t\tmidIdx = 0\n\t\t\tCIlow = 1\n\t\t\tCIhigh = 2\n\t\t\taxislab = 'Hazard ratio'\n\t\t\tbaselineValue = 1\n\t\t\tcapMin = 0.1\n\t\t\tcapMax = 10\n\t\t} else {\n\t\t\tthrow 'unknown regressionType'\n\t\t}\n\n\t\t// collect mid/CIlow/CIhigh numeric values into a flat array\n\t\tconst values = []\n\t\tfor (const tid in terms) {\n\t\t\tconst d = terms[tid]\n\t\t\tif (d.fields) {\n\t\t\t\tnumbers2array(d.fields)\n\t\t\t} else {\n\t\t\t\tfor (const k in d.categories) {\n\t\t\t\t\tnumbers2array(d.categories[k])\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tfor (const i of interactions) {\n\t\t\tfor (const k of i.categories) {\n\t\t\t\tnumbers2array(k.lst)\n\t\t\t}\n\t\t}\n\n\t\tif (values.length == 0) {\n\t\t\t// no valid estimates\n\t\t\t// return blank function for inability to make plot\n\t\t\treturn () => {}\n\t\t}\n\n\t\t// all valid numbers are collected into values[]\n\t\tvalues.sort((a, b) => a - b) // ascending\n\n\t\tif (capMin == null) {\n\t\t\t// use actual range as cap; all values are valid numbers\n\t\t\tcapMin = values[0]\n\t\t\tcapMax = values[values.length - 1]\n\t\t}\n\n\t\t// graph dimension\n\t\tconst width = 180 // plottable dimension\n\t\tconst height = 20\n\t\tconst xleftpad = 10,\n\t\t\txrightpad = 10 // leave space for axis\n\n\t\tconst scale = get_scale(values)\n\n\t\t// todo: logistic, add center line; linear: 0 value\n\t\treturn (td, lst) => {\n\t\t\tif (!scale) {\n\t\t\t\t// scale is not built, do not plot\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// lst is data from a row from either terms or interactions\n\n\t\t\tconst svg = td\n\t\t\t\t.append('svg')\n\t\t\t\t.attr('width', width + xleftpad + xrightpad)\n\t\t\t\t.attr('height', height)\n\t\t\tconst g = svg.append('g').attr('transform', 'translate(' + xleftpad + ',0)')\n\n\t\t\tif (!lst) {\n\t\t\t\t//////////////////////////////\n\t\t\t\t// no data; render axis instead\n\n\t\t\t\t// do not apply this format for linear regression,\n\t\t\t\t// had encountered a bug that '.1r' will print \"20\" at the tick of \"15\"\n\t\t\t\tconst tickFormat = self.config.regressionType == 'logistic' ? '.1r' : undefined\n\n\t\t\t\tconst axis = axisBottom().ticks(4, tickFormat).scale(scale)\n\t\t\t\taxisstyle({\n\t\t\t\t\taxis: g.call(axis),\n\t\t\t\t\tcolor: forestcolor,\n\t\t\t\t\tshowline: true\n\t\t\t\t})\n\t\t\t\tconst fontsize = 12\n\t\t\t\tg.append('text')\n\t\t\t\t\t.attr('fill', forestcolor)\n\t\t\t\t\t.text(axislab)\n\t\t\t\t\t.attr('x', width / 2)\n\t\t\t\t\t.attr('y', height + fontsize)\n\t\t\t\tsvg.attr('height', height + fontsize)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t{\n\t\t\t\t// vertical baseline\n\t\t\t\tconst x = scale(baselineValue)\n\t\t\t\tg.append('line').attr('x1', x).attr('y1', 0).attr('x2', x).attr('y2', height).attr('stroke', '#ccc')\n\t\t\t}\n\n\t\t\tconst mid = Number(lst[midIdx]),\n\t\t\t\tcilow = Number(lst[CIlow]),\n\t\t\t\tcihigh = Number(lst[CIhigh])\n\t\t\tif (Number.isNaN(mid)) {\n\t\t\t\t// not plottable\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tg.append('circle')\n\t\t\t\t.attr('cx', scale(Math.min(Math.max(mid, capMin), capMax)))\n\t\t\t\t.attr('cy', height / 2)\n\t\t\t\t.attr('r', 3)\n\t\t\t\t.attr('fill', forestcolor)\n\n\t\t\tif (Number.isNaN(cilow) || Number.isNaN(cihigh)) {\n\t\t\t\t// cannot plot confidence interval\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// confidence interval\n\t\t\tg.append('line')\n\t\t\t\t.attr('x1', scale(Math.min(Math.max(cilow, capMin), capMax)))\n\t\t\t\t.attr('y1', height / 2)\n\t\t\t\t.attr('x2', scale(Math.min(Math.max(cihigh, capMin), capMax)))\n\t\t\t\t.attr('y2', height / 2)\n\t\t\t\t.attr('stroke', forestcolor)\n\t\t}\n\t\t///////// helpers\n\t\tfunction numbers2array(_lst) {\n\t\t\tconst lst = self.config.regressionType == 'cox' ? _lst.slice(2) : _lst // exclude sample and event count columns\n\t\t\tconst m = Number(lst[midIdx])\n\t\t\tif (!Number.isNaN(m)) values.push(m)\n\t\t\tconst l = Number(lst[CIlow]),\n\t\t\t\th = Number(lst[CIhigh])\n\t\t\tif (!Number.isNaN(l) && !Number.isNaN(h)) {\n\t\t\t\t// if either low/high is NA, do not use\n\t\t\t\t// this prevent the case of low=NA, high=3e+41 (somehow high is extremely large value)\n\t\t\t\tvalues.push(l)\n\t\t\t\tvalues.push(h)\n\t\t\t}\n\t\t}\n\t\tfunction get_scale(values) {\n\t\t\tif (self.config.regressionType == 'logistic') {\n\t\t\t\t// apply log to odds ratio\n\t\t\t\t// iterate to find a non-0 value\n\t\t\t\tlet i = 0\n\t\t\t\twhile (values[i] <= 0) {\n\t\t\t\t\ti++\n\t\t\t\t}\n\t\t\t\tif (i >= values.length || values[i] <= 0) {\n\t\t\t\t\t// no valid value, won't build scale\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst min = values[i]\n\t\t\t\tconst max = values[values.length - 1]\n\t\t\t\treturn scaleLog()\n\t\t\t\t\t.domain([Math.max(min, capMin), Math.min(max, capMax)])\n\t\t\t\t\t.range([0, width])\n\t\t\t\t\t.nice()\n\t\t\t}\n\t\t\tif (self.config.regressionType == 'linear' || self.config.regressionType == 'cox') {\n\t\t\t\treturn scaleLinear()\n\t\t\t\t\t.domain([Math.max(values[0], capMin), Math.min(values[values.length - 1], capMax)])\n\t\t\t\t\t.range([0, width])\n\t\t\t}\n\t\t\tthrow 'unknown type'\n\t\t}\n\t}\n}\n\nfunction fillTdName(td, name) {\n\tif (name.length < 40) {\n\t\ttd.text(name)\n\t} else {\n\t\ttd.text(name.substring(0, 35) + ' ...').attr('aria-label', name)\n\t}\n}\nfunction fillCoefficientTermname(tw, td) {\n\t// fill column 1 <td> using term name\n\tfillTdName(td, tw.term.name || tid)\n\t// fill refGrp or effect allele, if applicable\n\tconst hasRefGrp = 'refGrp' in tw && tw.refGrp != refGrp_NA && tw.q.mode != 'spline'\n\tif (hasRefGrp || tw.effectAllele) {\n\t\t// has refGrp or effect allele\n\t\t// display beneath term name\n\t\tconst bottomDiv = td\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpcb-coef-variable-bottom')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('margin-top', '2px')\n\t\t\t.style('font-size', '.8em')\n\n\t\tlet label\n\t\tif (hasRefGrp) {\n\t\t\tlabel = tw.term.values && tw.term.values[tw.refGrp] ? tw.term.values[tw.refGrp].label : tw.refGrp\n\t\t} else {\n\t\t\tlabel = tw.effectAllele\n\t\t}\n\n\t\tbottomDiv\n\t\t\t.append('div')\n\t\t\t.style('padding', '1px 5px')\n\t\t\t.style('border', '1px solid #aaa')\n\t\t\t.style('border-radius', '10px')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.text(hasRefGrp ? 'REF' : 'EFFECT ALLELE')\n\n\t\tbottomDiv.append('div').style('padding', '1px 3px').text(label)\n\t}\n}\n\nfunction make_mds3_variants(tw, resultLst, regressionType) {\n\t/* return a list of variants as mds3 client-side custom data\n\ttw:\n\t\tterm:\n\t\t\tsnps[ {} ]\n\t\t\t\tsnpid\n\t\t\t\tmlst[]\n\t\t\t\t\telement: {alt/class/dt/mname}\n\t\tq{}\n\t\t\tsnp2effAle:{}\n\n\tresultLst: [{data,id},{data,id},...]\n\t*/\n\tconst mlst = []\n\tfor (const snp of tw.term.snps) {\n\t\tconst m = {\n\t\t\tchr: snp.chr,\n\t\t\tpos: snp.pos,\n\t\t\tssm_id: snp.snpid // needed for highlighting dot\n\t\t}\n\t\tmlst.push(m)\n\t\t// decide class/mname for this based on effect allele\n\t\tconst effAle = tw.q.snp2effAle[snp.snpid]\n\t\tconst m2 = snp.mlst.find(i => i.alt == effAle)\n\t\tif (m2) {\n\t\t\t// eff ale is an alt allele, transfer its class to m\n\t\t\tObject.assign(m, m2)\n\t\t} else {\n\t\t\t// eff allele is not an alterative allele!\n\t\t\t// just use the class of the first alt allele\n\t\t\tObject.assign(m, snp.mlst[0])\n\t\t}\n\n\t\t// set default values as missing, to be able to show all variants in track\n\t\t// overwrite with real values if found in result\n\t\tm.regressionPvalue = 'NA'\n\t\tm.mlpv = 0 // display the dot at the bottom\n\n\t\tconst thisresult = resultLst.find(i => i.id == snp.snpid)\n\t\tif (!thisresult) {\n\t\t\t// missing result for this variant, caused by variable-skipping in R\n\t\t\tm.regressionResult = {\n\t\t\t\tdata: {\n\t\t\t\t\terr: ['No result for this variant at ' + snp.snpid]\n\t\t\t\t}\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\t\t// reg result is found for this snp; can call displayResult_oneset\n\t\tm.regressionResult = thisresult // for displaying via click_snvindel()\n\n\t\tconst d = thisresult.data\n\t\tif (!d) throw '.data{} missing'\n\n\t\tif (d.type3) {\n\t\t\t/* result has type3 section, this variant has AF>cutoff and used for model-fitting\n\t\t\tshow this variant as a dot, do not set .shape = 'filledTriangle'\n\t\t\tfind p-value in regression results\n\t\t\t*/\n\t\t\tconst v = getSnpPvalueFromRegressionResults(d, snp.snpid)\n\t\t\tif (v == undefined) {\n\t\t\t\t// no valid pvalue from regression results\n\t\t\t} else {\n\t\t\t\t// has valid pvalue from regression results\n\t\t\t\tm.regressionPvalue = v\n\t\t\t\tm.mlpv = -Math.log10(v)\n\t\t\t}\n\n\t\t\t// assign estimate, for tooltip display\n\t\t\tif (!d.coefficients || !d.coefficients.terms) throw '.data.coefficients.terms{} missing'\n\t\t\tconst r = d.coefficients.terms[snp.snpid]\n\t\t\tif (!r) throw 'snp missing from data.coefficients.terms{}'\n\t\t\tif (Array.isArray(r.fields)) {\n\t\t\t\t// has fields[], snp is used as additive/dominant/recessive\n\t\t\t\tm.regressionEstimate = regressionType == 'cox' ? r.fields[2] : r.fields[0]\n\t\t\t} else if (r.categories) {\n\t\t\t\t// has categories{}: {C/T: Array(6), T/T: Array(6)}\n\t\t\t\t// snp is used by genotype\n\t\t\t\tconst lst = []\n\t\t\t\tfor (const gt in r.categories) {\n\t\t\t\t\tlst.push(gt + ':' + regressionType == 'cox' ? r.categories[gt][2] : r.categories[gt][0])\n\t\t\t\t}\n\t\t\t\tm.regressionEstimate = ' ' + lst.join(' ')\n\t\t\t} else {\n\t\t\t\tthrow 'unknown way to get snp estimates from coefficients table'\n\t\t\t}\n\t\t} else if (d.fisher) {\n\t\t\t/* { pvalue:float, table:[] }\n\t\t\tthis variant is tested by fisher, show as triangle\n\t\t\t*/\n\t\t\tm.regressionPvalue = d.fisher.pvalue\n\t\t\tm.mlpv = -Math.log10(d.fisher.pvalue)\n\t\t\tm.shape = 'filledTriangle'\n\t\t} else if (d.wilcoxon) {\n\t\t\t/* { pvalue:float }\n\t\t\tthis variant is tested by wilcoxon, show as triangle\n\t\t\t*/\n\t\t\tm.regressionPvalue = d.wilcoxon.pvalue\n\t\t\tm.mlpv = -Math.log10(d.wilcoxon.pvalue)\n\t\t\tm.shape = 'filledTriangle'\n\t\t} else if (d.cuminc) {\n\t\t\t/* { pvalue:float }\n\t\t\tthis variant is tested by cuminc, show as triangle\n\t\t\t*/\n\t\t\tm.regressionPvalue = d.cuminc.pvalue\n\t\t\tm.mlpv = -Math.log10(d.cuminc.pvalue)\n\t\t\tm.shape = 'filledTriangle'\n\t\t} else {\n\t\t\t// none of above. is monomorphic, show as hollow circle\n\t\t\tm.shape = 'emptyCircle'\n\t\t}\n\t}\n\treturn mlst\n}\n\nasync function createGenomebrowser(self, input, resultLst) {\n\t// create block instance that harbors the mds3 track for showing variants from the snplocus term\n\t// input is the snplocus Input instance\n\tconst arg = {\n\t\tholder: self.dom.snplocusBlockDiv,\n\t\tgenome: self.parent.genomeObj,\n\t\tchr: input.term.q.chr,\n\t\tstart: input.term.q.start,\n\t\tstop: input.term.q.stop,\n\t\tnobox: true,\n\t\ttklst: [],\n\t\tonCoordinateChange: async rglst => {\n\t\t\t// at the mds3 track, clear highlights added before\n\t\t\t// so that nothing is highlighted by default in updated data\n\t\t\tfor (const t of self.snplocusBlock.tklst) {\n\t\t\t\tif (t.type == 'mds3') delete t.skewer.hlssmid\n\t\t\t}\n\n\t\t\tconst { chr, start, stop } = rglst[0]\n\t\t\t// temporary tw as override for pill.runCallback()\n\t\t\tconst overrideTw = {\n\t\t\t\tterm: {\n\t\t\t\t\tid: input.term.term.id,\n\t\t\t\t\ttype: 'snplocus'\n\t\t\t\t},\n\t\t\t\tq: JSON.parse(JSON.stringify(input.term.q))\n\t\t\t}\n\t\t\toverrideTw.q.chr = chr\n\t\t\toverrideTw.q.start = start\n\t\t\toverrideTw.q.stop = stop\n\t\t\t// call fillTW of snplocus.js to recompute tw.term.snps[] and cache file\n\t\t\tconst _ = await import('../termsetting/handlers/snplocus')\n\t\t\tawait _.fillTW(overrideTw, self.app.vocabApi)\n\t\t\t/*\n\t\t\tupdated term info (term.snps[] and q.cacheid etc) are now in overrideTw\n\t\t\tcall pill.runCallback() with this override\n\t\t\twhich in turn calls editConfig() and\n\t\t\tdispatch action and write the updated tw into state;\n\t\t\tstate change will trigger pill.main()\n\t\t\tto propagate updated data to termsetting instance\n\n\t\t\t* Note *\n\t\t\tit is incorrect to call pill.main() or inputs.editConfig() here\n\n\t\t\taction dispatch will contain hasUnsubmittedEdits=true,\n\t\t\teffect of which is to hide result UI and require user to click submit button to rerun analysis\n\t\t\tset a single-use flag to nullify it so results.js can automatically run analysis\n\t\t\tso user can continuously look at genome browser\n\t\t\twithout break/interruption to user experience\n\t\t\t*/\n\t\t\tself.hasUnsubmittedEdits_nullify_singleuse = true\n\t\t\tinput.pill.runCallback(overrideTw)\n\t\t}\n\t}\n\n\t// add mds3 tk\n\targ.tklst.push({\n\t\ttype: 'mds3', // tkt.mds3\n\t\tname: 'Variants',\n\t\tskewerModes: [\n\t\t\t{\n\t\t\t\ttype: 'numeric',\n\t\t\t\tbyAttribute: 'mlpv', // corresponds to the \"mlpv\" attribute in m{}, can be anything\n\t\t\t\tlabel: '-log10 p-value',\n\t\t\t\tinuse: true,\n\t\t\t\ttooltipPrintValue: m => getMtooltipValues(m, self.config.regressionType)\n\t\t\t}\n\t\t],\n\t\tcustom_variants: make_mds3_variants(input.term, resultLst, self.config.regressionType),\n\t\tlegend: {\n\t\t\tcustomShapeLabels: {\n\t\t\t\tfilledCircle: 'common variants analyzed by model-fitting',\n\t\t\t\tfilledTriangle:\n\t\t\t\t\t'rare variants analyzed by ' +\n\t\t\t\t\t(self.config.regressionType == 'linear'\n\t\t\t\t\t\t? 'Wilcoxon rank sum test'\n\t\t\t\t\t\t: self.config.regressionType == 'logistic'\n\t\t\t\t\t\t? \"Fisher's exact test\"\n\t\t\t\t\t\t: 'Cumulative incidence test'),\n\t\t\t\temptyCircle: 'monomorphic variants skipped'\n\t\t\t}\n\t\t},\n\t\tclick_snvindel: async m => {\n\t\t\t// displayResult_oneset() will modify m.regressionResult.data\n\t\t\t// during rendering, so need to input clone of data\n\t\t\tself.displayResult_oneset(structuredClone(m.regressionResult.data))\n\t\t\tawait mayCheckLD(m, input, self)\n\t\t\tconst result_y = self.dom.oneSetResultDiv.node().getBoundingClientRect().top + window.scrollY\n\t\t\tconst nav_height = document.querySelector('.sjpp-nav').getBoundingClientRect().height\n\t\t\twindow.scroll({ behavior: 'smooth', top: result_y - nav_height })\n\t\t}\n\t})\n\n\tfirst_genetrack_tolist(self.parent.genomeObj, arg.tklst)\n\tconst _ = await import('../src/block')\n\treturn new _.Block(arg)\n}\n\nasync function updateMds3Tk(self, input, resultLst) {\n\t// browser is already created\n\t// find the mds3 track\n\tconst tk = self.snplocusBlock.tklst.find(i => i.type == 'mds3')\n\t// apply new sets of variants and results to track and render\n\ttk.custom_variants = make_mds3_variants(input.term, resultLst, self.config.regressionType)\n\t// if user changes position using termsetting ui,\n\t// input.term.q{} will hold different chr/start/stop than block\n\t// and block will need to update coord\n\tconst r = self.snplocusBlock.rglst[0]\n\tif (r.chr == input.term.q.chr && r.start == input.term.q.start && r.stop == input.term.q.stop) {\n\t\t// coord is the same between input and block\n\t\t// only need to rerender tk\n\t\ttk.load()\n\t} else {\n\t\tawait self.snplocusBlock.jump_1basedcoordinate(input.term.q)\n\t}\n\tself.snplocusBlock.cloakOff()\n}\n\nconst LDcolor0 = '#2E6594',\n\tLDcolor1 = '#ff0000',\n\tLDcolorScale = interpolateRgb(LDcolor0, LDcolor1)\n\nasync function mayCheckLD(m, input, self) {\n\t/*\n\tm: the mutation data object for the clicked dot in mds3 tk\n\t\t{chr, pos, ref, alt}\n\tinput: the snplocus Input instance\n\tself: result instance\n\t*/\n\tif (!input.term.q.restrictAncestry) {\n\t\t// requires restrictAncestry\n\t\t// may also support ld overlay without specifying an ancestry\n\t\treturn\n\t}\n\tconst tk = self.snplocusBlock.tklst.find(i => i.type == 'mds3')\n\tif (!tk || !tk.skewer || !tk.skewer.nmg) return\n\n\t// clear old result\n\tfor (const m of tk.custom_variants) delete m.regressionR2\n\n\tconst wait = self.dom.LDresultDiv.append('span').text('Loading LD data...')\n\n\ttry {\n\t\tconst data = await self.app.vocabApi.getLDdata(input.term.q.restrictAncestry.name, m)\n\t\tif (data.error) throw data.error\n\n\t\tif (data.nodata || !data.lst || data.lst.length == 0) {\n\t\t\t// either dataset does not have ld tracks, or no ld track found by name\n\t\t\t// or no ld data retrieved using given variant\n\t\t\t// restore color in case dots have been colored by ld in a prior click\n\t\t\twait.text('No LD data')\n\t\t\ttk.skewer.nmg.selectAll('.sja_aa_disk_fill').attr('fill', m => (m.shapeCircle ? 'none' : tk.color4disc(m)))\n\t\t\treturn\n\t\t}\n\t\ttk.skewer.nmg.selectAll('.sja_aa_disk_fill').attr('fill', m2 => {\n\t\t\tif (m2.pos == m.pos && m2.ref == m.ref && m2.alt == m.alt) {\n\t\t\t\t// same as m\n\t\t\t\treturn LDcolor1\n\t\t\t}\n\t\t\tfor (const i of data.lst) {\n\t\t\t\tif (i.pos == m2.pos && i.alleles == m2.ref + '.' + m2.alt) {\n\t\t\t\t\t// matched, record new result for displaying in hover tooltip\n\t\t\t\t\tm2.regressionR2 = i.r2\n\t\t\t\t\treturn LDcolorScale(i.r2)\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn LDcolorScale(0)\n\t\t})\n\n\t\twait.html(input.term.q.restrictAncestry.name + ' LD r<sup>2</sup>')\n\t\tshowLDlegend(self.dom.LDresultDiv, LDcolorScale)\n\t} catch (e) {\n\t\twait.text('Error: ' + (e.message || e))\n\t}\n}\n\nexport function showLDlegend(div, colorScale) {\n\tconst colorbardiv = div.append('span').style('margin-left', '10px')\n\tconst colorlst = []\n\tfor (let i = 0; i <= 1; i += 0.1) {\n\t\tcolorlst.push(colorScale(i))\n\t}\n\n\tconst axisheight = 20\n\tconst barheight = 15\n\tconst xpad = 10\n\tconst axiswidth = 150\n\n\t/** ColorScale component requires the color and data array to be the same\n\t * length. This data array is purely to fulfill that requirement.*/\n\tconst domain = colorlst.map((d, i) => i / (colorlst.length - 1))\n\n\tnew ColorScale({\n\t\tholder: colorbardiv,\n\t\tdomain,\n\t\ttopTicks: true,\n\t\twidth: xpad * 2 + axiswidth,\n\t\theight: axisheight + barheight,\n\t\tbarheight,\n\t\tbarwidth: axiswidth,\n\t\tfontSize: 12,\n\t\tcolors: colorlst,\n\t\tposition: `${xpad},${axisheight}`,\n\t\ttickSize: 6\n\t})\n}\n\nfunction getMtooltipValues(m, regressionType) {\n\tconst lst = [{ k: 'p-value', v: m.regressionPvalue }]\n\tif (m.regressionResult.AFstr) {\n\t\tlst.push({ k: 'AF', v: m.regressionResult.AFstr })\n\t}\n\tif (m.regressionEstimate) {\n\t\tif (regressionType == 'linear') lst.push({ k: 'beta', v: m.regressionEstimate })\n\t\telse if (regressionType == 'logistic') lst.push({ k: 'odds ratio', v: m.regressionEstimate })\n\t\telse if (regressionType == 'cox') lst.push({ k: 'hazard ratio', v: m.regressionEstimate })\n\t\telse throw 'unknown regression type'\n\t}\n\tif (m.regressionR2) {\n\t\tlst.push({ k: 'LD r2', v: m.regressionR2 })\n\t}\n\treturn lst\n}\n\nfunction getSnpPvalueFromRegressionResults(d, snpid) {\n\tlet str\n\tif (d.totalSnpEffect) {\n\t\t// snp has interactions\n\t\t// use p-value from total snp effect table\n\t\tstr = d.totalSnpEffect.lst[d.totalSnpEffect.lst.length - 1]\n\t} else {\n\t\t// snp has no interactions\n\t\t// use p-value from type3 stats table\n\t\tif (!d.type3.terms) throw '.data{type3:{terms}} missing'\n\t\tif (!d.type3.terms[snpid]) throw snpid + ' missing in type3.terms{}'\n\t\tif (!Array.isArray(d.type3.terms[snpid])) throw `type3.terms[${snp.snpid}] not array`\n\t\tstr = d.type3.terms[snpid][d.type3.terms[snpid].length - 1]\n\t}\n\tconst v = Number(str) // p-value string can be 'NA'\n\tif (Number.isFinite(v)) {\n\t\treturn v\n\t}\n\treturn undefined\n}\n\nfunction fillColumn2coefficientsTable(div, tw, categoryKey) {\n\tif (categoryKey) {\n\t\tdiv.text(tw && tw.term.values && tw.term.values[categoryKey] ? tw.term.values[categoryKey].label : categoryKey)\n\t\treturn\n\t}\n\t// the term doesn't have category, so indicate helpful status\n\tdiv.style('opacity', 0.3) // also gray out text to differentiate it from a category\n\tif ('geneticModel' in tw.q) {\n\t\tconst v = tw.q.geneticModel\n\t\tdiv.text(v == 0 ? '(additive)' : v == 1 ? '(dominant)' : '(recessive)')\n\t\treturn\n\t}\n\tif (tw.q.mode) {\n\t\tdiv.text('(' + tw.q.mode + ')')\n\t\treturn\n\t}\n}\n"],
+  "mappings": 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+}