@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-Q4FZUHZW.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/matrix/matrix.interactivity.js"],
-  "sourcesContent": ["import { select, pointer } from 'd3-selection'\nimport { format as d3format } from 'd3-format'\nimport { fillTermWrapper, termsettingInit } from '#termsetting'\nimport { icons, newSandboxDiv, Menu, renderTable, table2col, renderCnvConfig } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { TermTypes, isNumericTerm } from '#shared/terms.js'\nimport {\n\tmclass,\n\tdt2label,\n\tdtsnvindel,\n\tdtcnv,\n\tdtgeneexpression,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance\n} from '#shared/common.js'\nimport { rgb2hex } from '#src/client'\nimport { getSamplelstTW, getFilter, addNewGroup } from '../../mass/groups.js'\nimport { TwBase } from '#tw/TwBase'\n\nlet inputIndex = 0\nconst svgIcons = {\n\texternalLink: '' //`<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"16\" width=\"16\" viewBox=\"0 0 512 512\" transform=\"scale(0.8)\" style=\"display: inline-block; position:relative; top: -2px; left:4px;\" ><!--!Font Awesome Free 6.5.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free Copyright 2023 Fonticons, Inc.--><path d=\"M320 0c-17.7 0-32 14.3-32 32s14.3 32 32 32h82.7L201.4 265.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L448 109.3V192c0 17.7 14.3 32 32 32s32-14.3 32-32V32c0-17.7-14.3-32-32-32H320zM80 32C35.8 32 0 67.8 0 112V432c0 44.2 35.8 80 80 80H400c44.2 0 80-35.8 80-80V320c0-17.7-14.3-32-32-32s-32 14.3-32 32V432c0 8.8-7.2 16-16 16H80c-8.8 0-16-7.2-16-16V112c0-8.8 7.2-16 16-16H192c17.7 0 32-14.3 32-32s-14.3-32-32-32H80z\"/></svg>`\n}\n\nexport function setInteractivity(self) {\n\tlet t\n\tself.delayedMouseoutHandler = () => {\n\t\tif (t) clearTimeout(t)\n\t\tt = setTimeout(self.mouseout, 500)\n\t}\n\tself.showCellInfo = function (event) {\n\t\tif (self.activeLabel || self.zoomArea) return\n\t\tif (event.target.__data__?.isLegendItem) {\n\t\t\t// do not show info for matrix legend\n\t\t\treturn\n\t\t}\n\t\tif (!(event.target.tagName == 'rect' || event.target.tagName == 'image')) {\n\t\t\tconst d = event.target.__data__\n\t\t\tconst grp = d?.grp\n\t\t\tif (grp?.legendData) {\n\t\t\t\tif (event.target.closest('.sjpp-matrix-series-group-label-g')) self.displaySampleGroupInfo(event, grp)\n\t\t\t} //else if (d?.isLegendItem) self.handleLegendMouseover(event, d)\n\t\t\treturn\n\t\t}\n\t\tif (event.target.tagName !== 'rect' && !self.imgBox) self.imgBox = event.target.getBoundingClientRect()\n\t\tconst d = event.target.tagName == 'rect' ? event.target.__data__ : self.getImgCell(event)\n\t\t// TODO: svg-rendered cell rects may be thin and hard to mouse over,\n\t\t// but the tooltip should still display info\n\t\tif (!d || !d.term || !d.sample) {\n\t\t\tself.dom.tip.hide()\n\t\t\tself.mouseout()\n\t\t\treturn\n\t\t}\n\n\t\tconst x = self.dimensions.xOffset + self.dimensions.seriesXoffset\n\t\tconst y = self.dimensions.yOffset\n\t\tconst s = self.settings.matrix\n\t\tconst l = s.controlLabels\n\n\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\tconst twBarh = twSpecificSettings[d.tw.$id]?.contBarH\n\t\tconst twGap = twSpecificSettings[d.tw.$id]?.contBarGap\n\n\t\tself.dom.rowBeam\n\t\t\t.attr('x', x)\n\t\t\t.attr('y', y + d.seriesY)\n\t\t\t.attr('height', twBarh ? twBarh + 2 * twGap : d.t.grp.type == 'hierCluster' ? s.clusterRowh : s.rowh)\n\t\t\t.style('display', '')\n\n\t\tself.dom.colBeam\n\t\t\t.attr('x', x + d.x)\n\t\t\t.attr('y', y)\n\t\t\t.style('display', '')\n\n\t\tself.dom.matrixCellHoverOver.clear()\n\t\tconst table = table2col({ holder: self.dom.matrixCellHoverOver.d.append('div') })\n\n\t\tif (d.term.type == 'geneVariant' && d.tw.q?.type == 'values') {\n\t\t\t{\n\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\tc1.html(l.Sample)\n\t\t\t\tc2.html(d.row._ref_.label || d.value?.sample)\n\t\t\t}\n\t\t\t{\n\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\tc1.html('Gene')\n\t\t\t\tc2.html(d.term.name)\n\t\t\t}\n\n\t\t\tconst siblingCellLabels = {}\n\t\t\tif (d.siblingCells)\n\t\t\t\tfor (const c of d.siblingCells) {\n\t\t\t\t\tif (c.$id != d.$id) continue\n\t\t\t\t\tconst v = c.value\n\t\t\t\t\tconst p = v.pairlst\n\t\t\t\t\tconst dtLabel = v.origin ? `${v.origin} ${dt2label[v.dt]}` : dt2label[v.dt]\n\t\t\t\t\t// TODO: when the same label can apply to multiple values/hits in the same matrix cell,\n\t\t\t\t\t// list that label only once but with a hit count, instead of listing that same label\n\t\t\t\t\t// as multiple table rows in the mouseover\n\t\t\t\t\tconst label = getLabel(c, v, p)\n\t\t\t\t\t/* display as two column tabel, do not display these info and do not show gradient CNV anymore\n\t\t\t\tconst info = []\n\t\t\t\tif (v.label && v.label !== c.label) info.push(v.label)\n\t\t\t\tif ('value' in v) info.push(`${s.cnvUnit}=${v.value}`)\n\t\t\t\tif (v.chr) {\n\t\t\t\t\tconst pos = v.pos ? `:${v.pos}` : v.start ? `:${v.start}-${v.stop}` : ''\n\t\t\t\t\tinfo.push(`${v.chr}${pos}`)\n\t\t\t\t}\n\t\t\t\tif (v.alt) info.push(`${v.ref}>${v.alt}`)\n\n\t\t\t\tconst tds = !info.length\n\t\t\t\t\t? `<td colspan='2' style='text-align: center'>${label}</td>`\n\t\t\t\t\t: `<td style='text-align: right'>${label}</td><td>${info.map(i => `<span>${i}</span>`).join(' ')}</td>`\n\t\t\t\t*/\n\t\t\t\t\tconst color = c.fill == v.color || v.class == 'Blank' ? '' : c.fill\n\n\t\t\t\t\tif (!siblingCellLabels[dtLabel]) {\n\t\t\t\t\t\tsiblingCellLabels[dtLabel] = [{ label, color }]\n\t\t\t\t\t} else {\n\t\t\t\t\t\tsiblingCellLabels[dtLabel].push({ label, color })\n\t\t\t\t\t}\n\t\t\t\t\t/*\n\t\t\t\tdo not use gradient CNV anymore\n\t\t\t\tif (v.dt == 4 && 'value' in v) {\n\t\t\t\t\tconst textColor = Math.abs(v.value) < 0.5 ? '#000' : '#fff'\n\t\t\t\t\trows.push(\n\t\t\t\t\t\t`<tr style='background-color: ${color}; color: ${textColor}; padding-left: 2px; padding-right: 2px'>${tds}</tr>`\n\t\t\t\t\t)\n\t\t\t\t} else {\n\t\t\t\t\trows.push(`<tr style='color: ${color}'>${tds}</tr>`)\n\t\t\t\t}\n\t\t\t\t*/\n\t\t\t\t}\n\t\t\tfor (const [dtLabel, classArray] of Object.entries(siblingCellLabels).sort((a, b) => b.length - a.length)) {\n\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\tc1.html(dtLabel)\n\t\t\t\tc2.html(`<span style=\"display:inline-block; width:12px; height:12px; background-color:${classArray[0].color}\" ></span>\n\t\t\t\t\t${classArray[0].label}`)\n\t\t\t\tfor (const classType of classArray.slice(1)) {\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.html('')\n\t\t\t\t\tc2.html(`<span style=\"display:inline-block; width:12px; height:12px; background-color:${classType.color}\" ></span>\n\t\t\t\t\t\t${classType.label}`)\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t{\n\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\tc1.html(l.Sample)\n\t\t\t\tc2.html(d.row._ref_.label)\n\t\t\t}\n\n\t\t\tlet survivalInfo\n\t\t\tif (d.term.type == TermTypes.SURVIVAL && d.exitCodeKey) {\n\t\t\t\tsurvivalInfo = d.term.values?.[d.exitCodeKey]?.label || d.exitCodeKey\n\t\t\t}\n\n\t\t\tif (survivalInfo || d.convertedValueLabel || d.label || d.label === 0) {\n\t\t\t\t// show term value row only when not undefined\n\t\t\t\tif (d.term.type == TermTypes.GENE_EXPRESSION) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Gene')\n\t\t\t\t\t\tc2.html(d.term.gene)\n\t\t\t\t\t}\n\t\t\t\t\t{\n\t\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t\t(d.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous') || d.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\t\td.fill == '#fff' || d.fill == 'transparent' ? '' : d.fill\n\t\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Gene Expression')\n\t\t\t\t\t\tc2.html(\n\t\t\t\t\t\t\t`${colorSquare} ${d.convertedValueLabel || d.label}${\n\t\t\t\t\t\t\t\td.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous' && d.zscoreLabel ? d.zscoreLabel : ''\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} else if (d.term.type == TermTypes.METABOLITE_INTENSITY) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Metabolite')\n\t\t\t\t\t\tc2.html(d.term.name)\n\t\t\t\t\t}\n\t\t\t\t\t{\n\t\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t\t(d.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous') || d.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\t\td.fill == '#fff' || d.fill == 'transparent' ? '' : d.fill\n\t\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Metabolite Intensity')\n\t\t\t\t\t\tc2.html(\n\t\t\t\t\t\t\t`${colorSquare} ${d.convertedValueLabel || d.label}${\n\t\t\t\t\t\t\t\td.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous' && d.zscoreLabel ? d.zscoreLabel : ''\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} else if (d.term.type == TermTypes.PROTEOME_ABUNDANCE) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('gene')\n\t\t\t\t\t\tc2.html(d.term.name)\n\t\t\t\t\t}\n\t\t\t\t\t{\n\t\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t\t(d.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous') || d.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\t\td.fill == '#fff' || d.fill == 'transparent' ? '' : d.fill\n\t\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Protein Abundance')\n\t\t\t\t\t\tc2.html(\n\t\t\t\t\t\t\t`${colorSquare} ${d.convertedValueLabel || d.label}${\n\t\t\t\t\t\t\t\td.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous' && d.zscoreLabel ? d.zscoreLabel : ''\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} else if (d.term.type == TermTypes.SURVIVAL) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html(d.term.name)\n\t\t\t\t\t\tc2.html(`<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\td.fill == '#fff' || d.fill == 'transparent' ? '' : d.fill\n\t\t\t\t\t\t}\" ></span>\n\t\t\t\t\t\t\t${survivalInfo || d.label}`)\n\t\t\t\t\t}\n\n\t\t\t\t\tconst timeToEventKey =\n\t\t\t\t\t\t'Time to Event: ' +\n\t\t\t\t\t\t(d.timeToEventKey\n\t\t\t\t\t\t\t? d.timeToEventKey + (d.term.unit ? ` ${d.term.unit}` : '')\n\t\t\t\t\t\t\t: (d.convertedValueLabel || d.label) +\n\t\t\t\t\t\t\t  (d.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous' && d.zscoreLabel ? d.zscoreLabel : ''))\n\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('')\n\t\t\t\t\t\tc2.html(timeToEventKey)\n\t\t\t\t\t}\n\t\t\t\t} else if (d.term.type == TermTypes.TERM_COLLECTION) {\n\t\t\t\t\tconst renderedValues = d.row[d.$id].renderedValues\n\t\t\t\t\tconst sortedRenderedValues = renderedValues.filter(rv => rv.value !== 0).sort((a, b) => b.value - a.value)\n\n\t\t\t\t\tfor (const renderedValue of sortedRenderedValues) {\n\t\t\t\t\t\tconst colorSquare = `<span style=\"display:inline-block; width:12px; height:12px; background-color:${renderedValue.color}\"></span>`\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html(`${colorSquare} ${renderedValue.label}`)\n\t\t\t\t\t\tc2.html(`${renderedValue.value.toFixed(2)}%`)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t(d.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous') || d.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\td.fill == '#fff' || d.fill == 'transparent' ? '' : d.fill\n\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.html(d.term.name)\n\t\t\t\t\tc2.html(\n\t\t\t\t\t\t`${colorSquare} ${d.convertedValueLabel || d.label}${\n\t\t\t\t\t\t\td.tw?.q?.convert2ZScore && d.tw.q.mode == 'continuous' && d.zscoreLabel ? d.zscoreLabel : ''\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\tself.dom.matrixCellHoverOver.show2(event.clientX, event.clientY)\n\t\tself.dom.mainG.on('mouseout', self.mouseout)\n\t}\n\n\tself.getImgCell = function (event) {\n\t\tif (!self.imgBox) {\n\t\t\tif (event.target.tagName == 'image') self.imgBox = event.target.getBoundingClientRect()\n\t\t\telse return\n\t\t}\n\t\t//const [x,y] = pointer(event, event.target)\n\t\tconst y = event.clientY - self.imgBox.y - event.target.clientTop\n\t\tconst d = event.target.__data__.find(series => series.hoverY0 <= y && y <= series.hoverY1)\n\t\tif (!d) return\n\t\tconst { xMin, dx } = self.dimensions\n\t\tconst x2 = event.clientX - self.imgBox.x - event.target.clientLeft + xMin\n\t\tfor (const cell of d.cells) {\n\t\t\tconst min = cell.x\n\t\t\tconst max = cell.x + dx\n\t\t\tif (min <= x2 && x2 <= max) return cell\n\t\t}\n\t\treturn null\n\t}\n\n\tself.mouseout = function () {\n\t\tif (!self.activeLabel && self.dom.tip) self.dom.tip.hide()\n\t\tdelete self.imgBox\n\t\tif (self.dom.colBeam) self.dom.colBeam.style('display', 'none')\n\t\tif (self.dom.rowBeam) self.dom.rowBeam.style('display', 'none')\n\t\tif (self.dom.matrixCellHoverOver) self.dom.matrixCellHoverOver.clear()\n\t}\n\n\tself.mouseclick = async function (event, data) {\n\t\t// clicking only show actions for available genomic data; can later expand to non-genomic data and custom overrides\n\t\tconst q = self.state.termdbConfig.queries\n\t\tif (!q) return // no genomic queries\n\n\t\tif (!(q.singleSampleGenomeQuantification || q.singleSampleMutation || q.NIdata || q.DZImages)) return // only works for these queries\n\n\t\tself.dom.mainG.on('mouseout', null)\n\t\tdelete self.imgBox\n\t\tconst sampleData = data || event.target.__data__\n\n\t\tif (!sampleData) return // !!! it's undefined when dragging on the sample names\n\t\tconst s = self.config.settings.matrix\n\t\t// preliminary fix: assign string sample name for \"sample_id\", which is used by data queries below\n\t\tconst sample = {\n\t\t\tsample_id: sampleData.row._ref_.label\n\t\t}\n\t\t//when clicking a cell in SV, CNV, mutation panels\n\t\tconst geneName = sampleData.term?.type == 'geneVariant' ? sampleData.term.name : null\n\n\t\tself.dom.clickMenu.clear()\n\t\tself.dom.dendroClickMenu.clear()\n\t\tself.dom.brushMenu.clear()\n\t\tself.dom.matrixCellHoverOver.clear()\n\n\t\tif (self.dom.sampleListMenu) self.dom.sampleListMenu.destroy()\n\n\t\tif (q.singleSampleGenomeQuantification) {\n\t\t\tfor (const k in q.singleSampleGenomeQuantification) {\n\t\t\t\tconst menuDiv = self.dom.clickMenu.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.attr('data-testid', 'sjpp-ssgp-menu-btn')\n\t\t\t\t\t.text(k)\n\t\t\t\t\t.on('click', async event => {\n\t\t\t\t\t\tconst sandbox = newSandboxDiv(self.opts.plotDiv || select(self.opts.holder.node().parentNode))\n\t\t\t\t\t\tsandbox.header.text(sample.sample_id)\n\t\t\t\t\t\tawait (\n\t\t\t\t\t\t\tawait import('#plots/plot.ssgq.js')\n\t\t\t\t\t\t).plotSingleSampleGenomeQuantification(\n\t\t\t\t\t\t\tself.state.termdbConfig,\n\t\t\t\t\t\t\tself.state.vocab.dslabel,\n\t\t\t\t\t\t\tk,\n\t\t\t\t\t\t\tsample,\n\t\t\t\t\t\t\tsandbox.body.append('div').style('margin', '20px'),\n\t\t\t\t\t\t\tself.app.opts.genome,\n\t\t\t\t\t\t\tgeneName\n\t\t\t\t\t\t)\n\t\t\t\t\t\tmenuDiv.remove()\n\t\t\t\t\t\tself.dom.clickMenu.d.selectAll('*').remove()\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (q?.singleSampleMutation) {\n\t\t\tconst menuDiv = self.dom.clickMenu.d\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.attr('data-testid', 'oncoMatrix_termLabel_disco_button')\n\t\t\t\t.text('Disco plot')\n\t\t\t\t.on('click', async event => {\n\t\t\t\t\tconst sandbox = newSandboxDiv(self.opts.plotDiv || select(self.opts.holder.node().parentNode))\n\t\t\t\t\tsandbox.header.text(sample.sample_id)\n\t\t\t\t\t;(await import('#plots/plot.disco.js')).default(\n\t\t\t\t\t\tself.state.termdbConfig,\n\t\t\t\t\t\tself.state.vocab.dslabel,\n\t\t\t\t\t\tsample,\n\t\t\t\t\t\tsandbox.body,\n\t\t\t\t\t\tself.app.opts.genome\n\t\t\t\t\t)\n\t\t\t\t\tmenuDiv.remove()\n\t\t\t\t\tself.dom.clickMenu.d.selectAll('*').remove()\n\t\t\t\t})\n\t\t}\n\n\t\tif (q.DZImages) {\n\t\t\t// no longer used. replaced by wsimages\n\t\t\tconst menuDiv = self.dom.clickMenu.d\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.attr('data-testid', 'oncoMatrix_termLabel_dzi_button')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.text(`${q.DZImages.type} Images (0)`)\n\n\t\t\tconst data = await dofetch3('sampledzimages', {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: self.app.opts.genome.name,\n\t\t\t\t\tdslabel: self.state.vocab.dslabel,\n\t\t\t\t\tsample_id: sample.sample_id\n\t\t\t\t}\n\t\t\t})\n\n\t\t\tif (data.sampleDZImages?.length > 0) {\n\t\t\t\tmenuDiv.style('display', 'block')\n\t\t\t\tmenuDiv.text(`${q.DZImages.type} Images (${data.sampleDZImages.length})`)\n\t\t\t\tmenuDiv.on('click', async _ => {\n\t\t\t\t\tconst sandbox = newSandboxDiv(self.opts.plotDiv || select(self.opts.holder.node().parentNode))\n\t\t\t\t\tsandbox.header.text(sample.sample_id)\n\t\t\t\t\t;(await import('#plots/dziviewer/plot.dzi.js')).default(\n\t\t\t\t\t\tself.state.vocab.dslabel,\n\t\t\t\t\t\tsandbox.body,\n\t\t\t\t\t\tself.app.opts.genome,\n\t\t\t\t\t\tsample.sample_id,\n\t\t\t\t\t\tdata.sampleDZImages\n\t\t\t\t\t)\n\n\t\t\t\t\tmenuDiv.remove()\n\t\t\t\t\tself.dom.clickMenu.d.selectAll('*').remove()\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tif (q.NIdata) {\n\t\t\tfor (const [queryKey, ref] of Object.entries(q.NIdata)) {\n\t\t\t\tconst menuDiv = self.dom.clickMenu.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text('Neuro Image: ' + queryKey)\n\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\tself.dom.clickMenu.clear()\n\n\t\t\t\t\t\tconst config = {\n\t\t\t\t\t\t\tchartType: 'brainImaging',\n\t\t\t\t\t\t\tqueryKey,\n\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\tbrainImaging: {\n\t\t\t\t\t\t\t\t\tbrainImageL: ref.parameters.l,\n\t\t\t\t\t\t\t\t\tbrainImageF: ref.parameters.f,\n\t\t\t\t\t\t\t\t\tbrainImageT: ref.parameters.t\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tselectedSampleFileNames: [sample.sample_id + '.nii']\n\t\t\t\t\t\t}\n\t\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\t\tconfig\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tconst l = self.settings.matrix.controlLabels\n\t\tconst table = table2col({ holder: self.dom.clickMenu.d.append('div').append('span') })\n\n\t\tconst templates = self.state.termdbConfig.urlTemplates\n\t\tif (templates?.sample) {\n\t\t\tconst name = sampleData[templates.sample.namekey] || sampleData.sample || sampleData.row.sample\n\t\t\tconst [c1, c2] = table.addRow()\n\t\t\tc1.html(l.Sample)\n\t\t\tc2.html(\n\t\t\t\t`<a href=\"${templates.sample.base}${name}\" target=\"_blank\">${sampleData.row._ref_.label} ${svgIcons.externalLink}</a>`\n\t\t\t)\n\t\t} else {\n\t\t\tconst [c1, c2] = table.addRow()\n\t\t\tc1.html(l.Sample)\n\t\t\tc2.html(sampleData.row._ref_.label || sampleData.value.sample)\n\t\t}\n\t\tif (sampleData.term?.type == 'geneVariant' && sampleData.tw.q?.type == 'values') {\n\t\t\tif (sampleData.value) {\n\t\t\t\tif (templates?.gene) {\n\t\t\t\t\tconst name = self.data.refs.byTermId[sampleData.tw.$id][templates.gene.namekey]\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.html('Gene')\n\t\t\t\t\tc2.html(\n\t\t\t\t\t\t`<a href=\"${templates.gene.base}${name}\" target=\"_blank\">${sampleData.tw.term.name} ${svgIcons.externalLink}</a>`\n\t\t\t\t\t)\n\t\t\t\t} else {\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.html('Gene')\n\t\t\t\t\tc2.html(sampleData.term.name)\n\t\t\t\t}\n\n\t\t\t\tconst siblingCellLabels = {}\n\t\t\t\tfor (const c of sampleData.siblingCells) {\n\t\t\t\t\tif (c.$id != sampleData.$id) continue\n\t\t\t\t\tconst v = c.value\n\t\t\t\t\tconst p = v.pairlst\n\t\t\t\t\tconst dtLabel = v.origin ? `${v.origin} ${dt2label[v.dt]}` : dt2label[v.dt]\n\t\t\t\t\tconst label = getLabel(c, v, p)\n\t\t\t\t\tconst color = c.fill == v.color || v.class == 'Blank' ? '' : c.fill\n\n\t\t\t\t\tif (!siblingCellLabels[dtLabel]) {\n\t\t\t\t\t\tsiblingCellLabels[dtLabel] = [{ label, color }]\n\t\t\t\t\t} else {\n\t\t\t\t\t\tsiblingCellLabels[dtLabel].push({ label, color })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tfor (const [dtLabel, classArray] of Object.entries(siblingCellLabels).sort((a, b) => b.length - a.length)) {\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.html(dtLabel)\n\t\t\t\t\tc2.html(`<span style=\"display:inline-block; width:12px; height:12px; background-color:${classArray[0].color}\" ></span>\n\t\t\t\t\t\t${classArray[0].label}`)\n\t\t\t\t\tfor (const classType of classArray.slice(1)) {\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('')\n\t\t\t\t\t\tc2.html(`<span style=\"display:inline-block; width:12px; height:12px; background-color:${classType.color}\" ></span>\n\t\t\t\t\t\t\t${classType.label}`)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (sampleData.term) {\n\t\t\tlet survivalInfo\n\t\t\tif (sampleData.term.type == TermTypes.SURVIVAL && sampleData.exitCodeKey) {\n\t\t\t\tsurvivalInfo = sampleData.term.values?.[sampleData.exitCodeKey]?.label || sampleData.exitCodeKey\n\t\t\t}\n\n\t\t\tif (survivalInfo || sampleData.convertedValueLabel || sampleData.label || sampleData.label === 0) {\n\t\t\t\t// show term value row only when not undefined\n\t\t\t\tif (sampleData.term.type == TermTypes.GENE_EXPRESSION) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Gene')\n\t\t\t\t\t\tc2.html(sampleData.term.name)\n\t\t\t\t\t}\n\t\t\t\t\t{\n\t\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t\t(sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous') ||\n\t\t\t\t\t\t\tsampleData.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\t\tsampleData.fill == '#fff' || sampleData.fill == 'transparent' ? '' : sampleData.fill\n\t\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Gene Expression')\n\t\t\t\t\t\tc2.html(\n\t\t\t\t\t\t\t`${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${\n\t\t\t\t\t\t\t\tsampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous' && sampleData.zscoreLabel\n\t\t\t\t\t\t\t\t\t? sampleData.zscoreLabel\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} else if (sampleData.term.type == TermTypes.METABOLITE_INTENSITY) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Metabolite')\n\t\t\t\t\t\tc2.html(sampleData.term.name)\n\t\t\t\t\t}\n\t\t\t\t\t{\n\t\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t\t(sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous') ||\n\t\t\t\t\t\t\tsampleData.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\t\tsampleData.fill == '#fff' || sampleData.fill == 'transparent' ? '' : sampleData.fill\n\t\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Metabolite Intensity')\n\t\t\t\t\t\tc2.html(\n\t\t\t\t\t\t\t`${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${\n\t\t\t\t\t\t\t\tsampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous' && sampleData.zscoreLabel\n\t\t\t\t\t\t\t\t\t? sampleData.zscoreLabel\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} else if (sampleData.term.type == TermTypes.PROTEOME_ABUNDANCE) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Gene')\n\t\t\t\t\t\tc2.html(sampleData.term.name)\n\t\t\t\t\t}\n\t\t\t\t\t{\n\t\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t\t(sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous') ||\n\t\t\t\t\t\t\tsampleData.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\t\tsampleData.fill == '#fff' || sampleData.fill == 'transparent' ? '' : sampleData.fill\n\t\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('Protein Abundance')\n\t\t\t\t\t\tc2.html(\n\t\t\t\t\t\t\t`${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${\n\t\t\t\t\t\t\t\tsampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous' && sampleData.zscoreLabel\n\t\t\t\t\t\t\t\t\t? sampleData.zscoreLabel\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} else if (sampleData.term.type == TermTypes.SURVIVAL) {\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html(sampleData.term.name)\n\t\t\t\t\t\tc2.html(`<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\tsampleData.fill == '#fff' || sampleData.fill == 'transparent' ? '' : sampleData.fill\n\t\t\t\t\t\t}\" ></span>\n\t\t\t\t\t\t\t${survivalInfo || sampleData.label}`)\n\t\t\t\t\t}\n\t\t\t\t\tconst timeToEventKey =\n\t\t\t\t\t\t'Time to Event: ' +\n\t\t\t\t\t\t(sampleData.timeToEventKey\n\t\t\t\t\t\t\t? sampleData.timeToEventKey + (sampleData.term.unit ? ` ${sampleData.term.unit}` : '')\n\t\t\t\t\t\t\t: (sampleData.convertedValueLabel || sampleData.label) +\n\t\t\t\t\t\t\t  (sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous' && sampleData.zscoreLabel\n\t\t\t\t\t\t\t\t\t? sampleData.zscoreLabel\n\t\t\t\t\t\t\t\t\t: ''))\n\t\t\t\t\t{\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html('')\n\t\t\t\t\t\tc2.html(timeToEventKey)\n\t\t\t\t\t}\n\t\t\t\t} else if (sampleData.term.type == TermTypes.TERM_COLLECTION) {\n\t\t\t\t\tconst renderedValues = sampleData.row[sampleData.$id].renderedValues\n\t\t\t\t\tconst sortedRenderedValues = renderedValues.filter(rv => rv.value !== 0).sort((a, b) => b.value - a.value)\n\n\t\t\t\t\tfor (const renderedValue of sortedRenderedValues) {\n\t\t\t\t\t\tconst colorSquare = `<span style=\"display:inline-block; width:12px; height:12px; background-color:${renderedValue.color}\"></span>`\n\t\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\t\tc1.html(`${colorSquare} ${renderedValue.label}`)\n\t\t\t\t\t\tc2.html(`${renderedValue.value.toFixed(2)}%`)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tconst colorSquare =\n\t\t\t\t\t\t(sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous') ||\n\t\t\t\t\t\tsampleData.tw.q.mode !== 'continuous'\n\t\t\t\t\t\t\t? `<span style=\"display:inline-block; width:12px; height:12px; background-color:${\n\t\t\t\t\t\t\t\t\tsampleData.fill == '#fff' || sampleData.fill == 'transparent' ? '' : sampleData.fill\n\t\t\t\t\t\t\t  }\" ></span>`\n\t\t\t\t\t\t\t: ''\n\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.html(sampleData.term.name)\n\t\t\t\t\tc2.html(\n\t\t\t\t\t\t`${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${\n\t\t\t\t\t\t\tsampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == 'continuous' && sampleData.zscoreLabel\n\t\t\t\t\t\t\t\t? sampleData.zscoreLabel\n\t\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}\n\t\tself.dom.clickMenu.show(event.clientX, event.clientY, false, true)\n\t}\n\n\tself.legendClick = function () {}\n\n\tself.svgMousemove = function (event) {\n\t\tif (!self.dragged) return\n\t\tconst s = self.config.settings.matrix\n\t\tconst d = self.dragged\n\t\tconst x2 = !s.transpose ? d.x : d.x - d.clientX + event.clientX\n\t\tconst y2 = !s.transpose ? d.y - d.clientY + event.clientY : d.y\n\t\td.clone.attr('transform', `translate(${x2},${y2})`)\n\t}\n\n\tself.svgMouseup = function (event) {\n\t\tif (!self.dragged) return\n\t\tself.dragged.clone.remove()\n\t\tdelete self.dragged\n\t\tdelete self.clicked\n\t}\n\n\tself.getVisibleCenterCell = function (dx) {\n\t\t//const s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tif (d.seriesXoffset <= 0 && d.mainw >= d.zoomedMainW) {\n\t\t\treturn self.sampleOrder[Math.floor(self.sampleOrder.length / 2)]\n\t\t}\n\t\tconst w = 0.5 * d.mainw - d.seriesXoffset - dx\n\t\tconst i = Math.round(w / d.dx)\n\t\treturn self.sampleOrder[i]\n\t}\n\n\t//setSampleActions(self)\n\tsetTermActions(self)\n\tsetTermGroupActions(self)\n\tsetSampleGroupActions(self)\n\tsetZoomPanActions(self)\n\tsetResizeHandler(self)\n\tsetLengendActions(self)\n\tsetMutationSelectionActions(self)\n}\n\nfunction setResizeHandler(self) {\n\tlet resizeId\n\tselect(window).on(`resize.sjpp-${self.id}`, () => {\n\t\tif (resizeId) clearTimeout(resizeId)\n\t\tif (self.dimensions && self.layout) resizeId = setTimeout(resize, 200)\n\t})\n\n\tfunction resize() {\n\t\t// !!! this.abortCtl.abort()\n\t\tif (self.dimensions && self.layout) self.main()\n\t}\n}\n\nfunction setTermActions(self) {\n\tsetLabelDragEvents(self, 'term')\n\n\tself.setPill = function (appState) {\n\t\t// will reuse a pill instance to show term edit menu\n\t\tself.pill = termsettingInit({\n\t\t\ttip: self.customTipApi,\n\t\t\tmenuOptions: 'all',\n\t\t\tmenuLayout: 'horizontal',\n\t\t\tvocabApi: self.app.vocabApi,\n\t\t\tvocab: appState.vocab,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\tnumericEditMenuVersion: ['discrete', 'continuous'],\n\t\t\tusecase: { target: 'matrix' },\n\n\t\t\tgetBodyParams: () => {\n\t\t\t\tconst currentGeneNames = []\n\t\t\t\tfor (const g of self.config.termgroups) {\n\t\t\t\t\t// only consider hierCluster group for hierCluster plot\n\t\t\t\t\tif (self.chartType == 'hierCluster' && g.type != 'hierCluster') continue\n\n\t\t\t\t\tfor (const t of g.lst) {\n\t\t\t\t\t\tif (t.term.chr) {\n\t\t\t\t\t\t\tcurrentGeneNames.push(`${t.term.chr}:${t.term.start}-${t.term.stop}`)\n\t\t\t\t\t\t} else if (t.term.gene) {\n\t\t\t\t\t\t\tcurrentGeneNames.push(t.term.gene)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (currentGeneNames.length) return { currentGeneNames }\n\t\t\t\treturn {}\n\t\t\t},\n\n\t\t\t//holder: {}, //self.dom.inputTd.append('div'),\n\t\t\t//debug: opts.debug,\n\t\t\trenderAs: 'none',\n\t\t\tcallback: tw => {\n\t\t\t\t// data is object with only one needed attribute: q, never is null\n\t\t\t\tif (tw && !tw.q) throw 'data.q{} missing from pill callback'\n\t\t\t\tconst t = self.activeLabel || self.lastactiveLabel\n\t\t\t\tif (tw) {\n\t\t\t\t\t// users could modify the term label, need to update tw.label to the latest label\n\t\t\t\t\ttw.label = t.tw.label\n\t\t\t\t\tif (t && t.tw) tw.$id = t.tw.$id\n\t\t\t\t\tconst legendValueFilter = self.mayRemoveTvsEntry(tw)\n\t\t\t\t\tself.pill.main(Object.assign({ filter: self.state.filter }, tw))\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\t\t\tid: self.opts.id,\n\t\t\t\t\t\tedits: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex, 'lst', t.lstIndex],\n\t\t\t\t\t\t\t\tvalue: tw\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tnestedKeys: ['legendValueFilter'],\n\t\t\t\t\t\t\t\tvalue: legendValueFilter\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} else {\n\t\t\t\t\tself.removeTerm()\n\t\t\t\t}\n\t\t\t\tself.dom.tip.hide()\n\t\t\t}\n\t\t})\n\t}\n\n\tself.getMenuOptions = function (t) {\n\t\treturn self.config.chartType == 'hierCluster' && t.grp.type === 'hierCluster'\n\t\t\t? '{remove,}'\n\t\t\t: t.tw.term.type == 'geneVariant'\n\t\t\t? '{edit,replace,remove}'\n\t\t\t: t.tw.term.type == 'termCollection'\n\t\t\t? '{edit,replace,remove}'\n\t\t\t: '*'\n\t}\n\n\tself.showTermMenu = async function (event) {\n\t\tconst t = event.target.__data__\n\t\tif (!t || !t.tw || !t.grp) return\n\t\tconst s = self.settings.matrix\n\t\tconst l = s.controlLabels\n\t\tself.activeLabel = t\n\t\tself.dom.menutop.style('display', '').selectAll('*').remove()\n\t\tself.dom.menubody.style('padding', 0).selectAll('*').remove()\n\n\t\t// display loading... upon clicking a term row label\n\t\tconst termMenuWaitDiv = self.dom.menutop.append('div').style('display', 'block').text('Loading...')\n\t\tself.dom.tip.show(event.clientX - 20, event.clientY - 20)\n\n\t\tconst pillArg = Object.assign(\n\t\t\t{ menuOptions: self.getMenuOptions(t), filter: self.state.filter },\n\t\t\tt.tw ? t.tw : { term: null, q: null }\n\t\t)\n\n\t\tmayAddEditMsg(pillArg, t)\n\n\t\tawait self.pill.main(pillArg)\n\n\t\ttermMenuWaitDiv.remove()\n\n\t\tself.dom.shortcutDiv = self.dom.menutop.append('div').style('z-index', 10000)\n\t\tself.showShortcuts(t, self.dom.shortcutDiv)\n\t\tself.dom.twMenuDiv = self.dom.menutop.append('div')\n\t\tconst labelEditDiv = self.dom.twMenuDiv.append('div').style('text-align', 'center')\n\t\tif (t.tw?.term?.type) labelEditDiv.append('span').text(`${l.Term} `)\n\n\t\tconst twlabel = t.tw.label || t.tw.term.name\n\t\tconst vartype =\n\t\t\tt.tw.term.type == 'geneVariant' || t.tw.term.type == TermTypes.GENE_EXPRESSION\n\t\t\t\t? 'gene'\n\t\t\t\t: t.tw.term.type == TermTypes.METABOLITE_INTENSITY\n\t\t\t\t? 'metabolite'\n\t\t\t\t: t.tw.term.type == TermTypes.PROTEOME_ABUNDANCE\n\t\t\t\t? 'protein'\n\t\t\t\t: 'variable'\n\n\t\tif (t.tw?.term?.type)\n\t\t\tself.dom.twLabelInput = labelEditDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'text')\n\t\t\t\t.attr('size', twlabel.length + 3)\n\t\t\t\t.attr('aria-label', `Type to edit the ${vartype} label`)\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.property('value', twlabel)\n\t\t\t\t.on('input', () => {\n\t\t\t\t\tconst value = self.dom.twLabelInput.property('value')\n\t\t\t\t\tself.dom.twLabelInput.attr('size', value.length + 3)\n\t\t\t\t\tself.dom.twLabelEditBtn.style('display', value.trim() === twlabel ? 'none' : 'inline')\n\t\t\t\t})\n\n\t\tif (t.tw?.term?.type)\n\t\t\tself.dom.twLabelEditBtn = labelEditDiv\n\t\t\t\t.append('button')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.html('submit')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (twlabel != self.dom.twLabelInput.property('value').trim()) self.updateTermLabel()\n\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t})\n\n\t\tif (vartype == 'gene') {\n\t\t\t// is gene, may show extra button for quick data access\n\t\t\tif (t.tw.term.type == 'geneVariant') {\n\t\t\t\t// lollipop btn for plotting gene-level mut data\n\t\t\t\tself.dom.gbButton = labelEditDiv\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t.html('Lollipop')\n\t\t\t\t\t.attr('data-testid', 'oncoMatrix_cell_lollipop_button')\n\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\tawait self.launchGB(t)\n\t\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t\t})\n\t\t\t}\n\t\t\t// might add new btn to support other type, e.g. boxplot for geneexp\n\t\t}\n\n\t\t// Add gene summary button\n\t\tif (self.state.termdbConfig.urlTemplates?.gene && vartype == 'gene') {\n\t\t\tconst templates = self.state.termdbConfig.urlTemplates\n\t\t\tself.dom.geneSummaryLink = labelEditDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('color', 'rgb(0, 0, 238)')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t.html(`${templates.gene.defaultText || ''}${svgIcons.externalLink}`)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tconst name = self.data.refs.byTermId[t.tw.$id][templates.gene.namekey]\n\t\t\t\t\twindow.open(`${templates.gene.base}${name}`, '_blank')\n\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t})\n\t\t}\n\n\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\tif (!twSpecificSettings[t.tw.$id]) twSpecificSettings[t.tw.$id] = {}\n\t\tconst twSettings = twSpecificSettings[t.tw.$id]\n\n\t\tconst rowHeightColorEditDiv = self.dom.twMenuDiv.append('div').style('text-align', 'center')\n\t\tif (t.grp?.type !== 'hierCluster' && t.tw?.q?.mode == 'continuous') {\n\t\t\trowHeightColorEditDiv.append('span').text('Row Height')\n\t\t\tself.dom.twRowheightInput = rowHeightColorEditDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'number')\n\t\t\t\t.attr('aria-label', `edit the row height`)\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('width', '60px')\n\t\t\t\t.property('value', twSettings.contBarH)\n\t\t\t\t.on('keyup', async event => {\n\t\t\t\t\tif (event.code != 'Enter') return\n\t\t\t\t\tconst newBarh = parseFloat(self.dom.twRowheightInput.node().value)\n\t\t\t\t\ttwSettings.contBarH = newBarh\n\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.opts.id,\n\t\t\t\t\t\tconfig: { settings: { matrix: { twSpecificSettings } } }\n\t\t\t\t\t})\n\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t})\n\t\t}\n\n\t\tif (\n\t\t\tt.grp?.type !== 'hierCluster' &&\n\t\t\tt.tw?.q?.mode == 'continuous' &&\n\t\t\tt.tw.term.type != 'survival' &&\n\t\t\tt.tw.term.type != 'termCollection' &&\n\t\t\tt.tw.q.convert2ZScore != true\n\t\t) {\n\t\t\trowHeightColorEditDiv.append('span').text('Bar Color')\n\n\t\t\tself.dom.twRowColorInput = rowHeightColorEditDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('aria-label', `change the bar color`)\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.attr('value', twSettings.contBarColor)\n\t\t\t\t.on('change', async () => {\n\t\t\t\t\tconst color = self.dom.twRowColorInput.node().value\n\t\t\t\t\ttwSettings.contBarColor = color\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.opts.id,\n\t\t\t\t\t\tconfig: { settings: { matrix: { twSpecificSettings } } }\n\t\t\t\t\t})\n\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t})\n\t\t}\n\n\t\tif (self.config.settings.matrix.maxSample && t.counts.samples && t.allCounts.samples) {\n\t\t\tself.dom.twMenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('margin', '5px')\n\t\t\t\t.text(`#${l.samples}: ${t.counts.samples} rendered, ${t.allCounts.samples - t.counts.samples} not rendered`)\n\t\t}\n\n\t\tself.dom.twMenuBar = self.dom.twMenuDiv.append('div').style('text-align', 'center')\n\t\t//menuBtnsDiv.on('click', () => menuBtnsDiv.style('display', 'none'))\n\t\t// must remember event target since it's cleared after async-await\n\t\tconst clickedElem = event.target\n\t\tself.pill.showMenu(event, clickedElem, self.dom.twMenuBar)\n\n\t\tself.dom.grpMenuDiv = self.dom.menutop.append('div').style('margin-top', '10px')\n\t\t//self.showTermGroupInputs(self.dom.grpMenuDiv)\n\t\t//self.dom.tip.showunder(clickedElem)\n\t\t//self.dom.tip.show(event.clientX - 20, event.clientY - 20)\n\t}\n\n\tself.launchGB = t => {\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'genomeBrowser',\n\t\t\t\tsnvindel: { shown: true },\n\t\t\t\tgeneSearchResult: { geneSymbol: t.tw.term.name }\n\t\t\t}\n\t\t})\n\t}\n\n\tself.updateTermLabel = () => {\n\t\tconst value = self.dom.twLabelInput.property('value').trim()\n\t\tconst t = self.activeLabel\n\t\tif (t.tw.label === value) return\n\t\tt.tw.label = value\n\t\tt.grp.lst[t.lstIndex] = t.tw\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_nestedEdits',\n\t\t\tid: self.opts.id,\n\t\t\tedits: [\n\t\t\t\t{\n\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex],\n\t\t\t\t\tvalue: t.grp\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t}\n\n\tself.showShortcuts = (t, div) => {\n\t\tconst l = self.settings.matrix.controlLabels\n\t\tdiv.style('text-align', 'center')\n\t\t//div.append('span').html('Shortcuts: ')\n\n\t\t// sorting icons\n\t\tconst vartype =\n\t\t\tt.tw.term.type == 'geneVariant' || t.tw.term.type == TermTypes.GENE_EXPRESSION\n\t\t\t\t? 'gene'\n\t\t\t\t: t.tw.term.type == TermTypes.METABOLITE_INTENSITY\n\t\t\t\t? 'metabolite'\n\t\t\t\t: t.tw.term.type == TermTypes.PROTEOME_ABUNDANCE\n\t\t\t\t? 'protein'\n\t\t\t\t: 'variable'\n\t\tconst sortRevertable = self.type != 'hierCluster' && t.tw.sortSamples?.priority !== undefined\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.selectAll('div')\n\t\t\t.data(\n\t\t\t\t[\n\t\t\t\t\t{\n\t\t\t\t\t\ticon: 'corner',\n\t\t\t\t\t\ttitle: `Sort ${l.samples} against this ${vartype}, and position this ${vartype} at the top left corner`,\n\t\t\t\t\t\tdisabled:\n\t\t\t\t\t\t\tt.grp.lst.length < 1 || (t.index === 0 && t.tw.sortSamples?.priority === 0) || self.type == 'hierCluster',\n\t\t\t\t\t\thandler: self.sortSamplesAgainstCornerTerm\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\ticon: 'left',\n\t\t\t\t\t\ttitle: `Sort ${l.samples} against this ${vartype}`,\n\t\t\t\t\t\t// should not disable sorting when hierCluster has top dendrogram\n\t\t\t\t\t\tdisabled: t.tw.sortSamples?.priority === 0 && !self.config.settings.hierCluster?.clusterSamples,\n\t\t\t\t\t\tfill: sortRevertable ? 'rgba(200,100,100,0.5)' : '',\n\t\t\t\t\t\thandler: sortRevertable ? self.unsortSamplesAgainstTerm : self.sortSamplesAgainstTerm\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\thtml: '&nbsp;|&nbsp;'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\ticon: 'up',\n\t\t\t\t\t\ttitle: `Move this ${vartype} up`,\n\t\t\t\t\t\tdisabled: t.index === 0 || self.type == 'hierCluster',\n\t\t\t\t\t\thandler: self.moveTermUp\n\t\t\t\t\t},\n\n\t\t\t\t\t{\n\t\t\t\t\t\ticon: 'down',\n\t\t\t\t\t\ttitle: `Move this ${vartype} down`,\n\t\t\t\t\t\tdisabled: t.index === t.grp.lst.length - 1 || self.type == 'hierCluster',\n\t\t\t\t\t\thandler: self.moveTermDown\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\td => d.icon\n\t\t\t)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.each(function (d) {\n\t\t\t\tconst elem = select(this)\n\t\t\t\tif (d.icon) icons[d.icon](elem, d)\n\t\t\t\telse elem.html(d.html)\n\t\t\t})\n\t}\n\n\tself.sortSamplesAgainstCornerTerm = event => {\n\t\tevent.stopPropagation()\n\t\tconst t = self.activeLabel\n\t\tconst termgroups = JSON.parse(JSON.stringify(self.termGroups))\n\t\tconst grp = termgroups[t.grpIndex]\n\t\tconst [tcopy, sorterTerms] = self.getSorterTerms(t)\n\t\tconst removed = grp.lst.splice(t.lstIndex, 1)\n\t\tgrp.lst.unshift(tcopy)\n\t\tgrp.sortTermsBy = 'asListed'\n\n\t\tfor (const g of termgroups) {\n\t\t\tif (g == grp) {\n\t\t\t\tfor (const [priority, tw] of g.lst.entries()) {\n\t\t\t\t\t// the `by: 'values'` may be overridden by self.config.settings.matrix.sortPriority, if available\n\t\t\t\t\tif (!tw.sortSamples) tw.sortSamples = { priority, by: 'values' }\n\t\t\t\t\ttw.sortSamples.priority = priority\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tfor (const tw of g.lst) {\n\t\t\t\t\tif (!tw.sortSamples) continue\n\t\t\t\t\ttw.sortSamples.priority = sorterTerms.findIndex(t => t.tw?.$id === tw.$id) + grp.lst.length\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.opts.id,\n\t\t\tconfig: {\n\t\t\t\ttermgroups,\n\t\t\t\tsettings: {\n\t\t\t\t\tmatrix: {\n\t\t\t\t\t\tsortTermsBy: 'asListed'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.sortSamplesAgainstTerm = event => {\n\t\tevent?.stopPropagation()\n\t\tconst t = self.activeLabel\n\t\tconst [tcopy] = self.getSorterTerms(t)\n\t\tif (t.grp.type == 'hierCluster') tcopy.sortSamples.by = 'values'\n\t\tconst termgroups = self.termGroups\n\t\ttermgroups[t.grpIndex].lst[t.lstIndex] = tcopy\n\t\tfor (const g of termgroups) {\n\t\t\tfor (const tw of g.lst) {\n\t\t\t\tif (!tw.sortSamples) continue\n\t\t\t\tif (tw.$id === t.tw.$id) {\n\t\t\t\t\ttw.sortSamples.priority = 0\n\t\t\t\t} else tw.sortSamples.priority += 1\n\t\t\t}\n\t\t}\n\n\t\tif (self.chartType == 'hierCluster') {\n\t\t\t// remove top dendrogram after sortting samples in hierCluster\n\t\t\tself.config.settings.hierCluster.clusterSamples = false\n\t\t\tself.config.settings.hierCluster.yDendrogramHeight = 0\n\t\t}\n\n\t\tself.config.termgroups = termgroups\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.opts.id,\n\t\t\tconfig: self.config\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.unsortSamplesAgainstTerm = (event, d) => {\n\t\tevent.stopPropagation()\n\t\tconst t = self.activeLabel || d.data.t\n\t\tconst [tcopy] = self.getSorterTerms(t)\n\t\tconst termgroups = self.termGroups\n\t\ttermgroups[t.grpIndex].lst[t.lstIndex] = tcopy\n\t\tfor (const g of termgroups) {\n\t\t\tfor (const tw of g.lst) {\n\t\t\t\tif (!tw.sortSamples) continue\n\t\t\t\tif (tw.$id === t.tw.$id) {\n\t\t\t\t\tdelete tw.sortSamples //.priority\n\t\t\t\t} else if ('sortSamples' in tw && 'priority' in tw.sortSamples) {\n\t\t\t\t\tif (tw.sortSamples.priority > t.sortSamples?.priority) tw.sortSamples.priority -= 1\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.opts.id,\n\t\t\tconfig: {\n\t\t\t\ttermgroups\n\t\t\t}\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.moveTermUp = event => {\n\t\tevent.stopPropagation()\n\t\tconst t = self.activeLabel\n\t\tconst grp = self.termGroups[t.grpIndex]\n\t\tgrp.lst.splice(t.lstIndex, 1)\n\t\tgrp.lst.splice(t.lstIndex - 1, 0, t.tw)\n\t\tgrp.sortTermsBy = 'asListed'\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_nestedEdits',\n\t\t\tid: self.opts.id,\n\t\t\tedits: [\n\t\t\t\t{\n\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex],\n\t\t\t\t\tvalue: grp\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tnestedKeys: ['settings', 'matrix', 'sortTermsBy'],\n\t\t\t\t\tvalue: 'asListed'\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.moveTermDown = event => {\n\t\tevent.stopPropagation()\n\t\tconst t = self.activeLabel\n\t\tconst grp = self.termGroups[t.grpIndex]\n\t\tgrp.lst.splice(t.lstIndex, 1)\n\t\tgrp.lst.splice(t.lstIndex + 1, 0, t.tw)\n\t\tgrp.sortTermsBy = 'asListed'\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_nestedEdits',\n\t\t\tid: self.opts.id,\n\t\t\tedits: [\n\t\t\t\t{\n\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex],\n\t\t\t\t\tvalue: grp\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tnestedKeys: ['settings', 'matrix', 'sortTermsBy'],\n\t\t\t\t\tvalue: 'asListed'\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.showTermEditMenu = async () => {\n\t\tself.dom.menubody.selectAll('*').remove()\n\t\tconst t = self.activeLabel\n\t\tconst s = self.config.settings.matrix\n\t\tconst l = s.controlLabels\n\n\t\tif (t.tw.term.type == 'geneVariant') {\n\t\t\tconst div = self.dom.menubody.append('div')\n\t\t\tconst label = div.append('label')\n\t\t\tlabel.append('span').html(`Minimum # ${l.samples} to be visible`)\n\n\t\t\tconst minNumSamples = 'minNumSamples' in t.tw ? t.tw.minNumSamples : ''\n\t\t\tconst input = label\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'number')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.style('width', '50px')\n\t\t\t\t.property('value', minNumSamples)\n\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.append('button')\n\t\t\t\t.html('Submit')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst value = input.property('value')\n\t\t\t\t\tif (value === minNumSamples) return\n\t\t\t\t\tif (value === '') {\n\t\t\t\t\t\tdelete t.tw.minNumSamples\n\t\t\t\t\t} else {\n\t\t\t\t\t\tt.tw.minNumSamples = Number(value)\n\t\t\t\t\t}\n\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\t\t\tid: self.opts.id,\n\t\t\t\t\t\tedits: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex, 'lst', t.lstIndex],\n\t\t\t\t\t\t\t\tvalue: t.tw\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\tself.dom.tip.hide()\n\t\t\t\t})\n\t\t} else {\n\t\t\tawait self.pill.main(\n\t\t\t\tObject.assign({ menuOptions: self.getMenuOptions(t), filter: self.state.filter }, self.activeLabel.tw)\n\t\t\t)\n\t\t\tself.pill.showMenu()\n\t\t}\n\t}\n\n\tself.showMoveMenu = async () => {\n\t\tself.dom.menubody.selectAll('*').remove()\n\t\tself.termBeingMoved = self.activeLabel\n\t\tconst div = self.dom.menubody.append('div')\n\t\tdiv.append('span').html('Click on another label')\n\t\tself.makeInsertPosRadios(div)\n\t}\n\n\tself.showTermInsertMenu = () => {\n\t\t//self.dom.tip.clear()\n\t\t//self.dom.menutop = self.dom.tip.d.append('div')\n\t\tself.dom.menubody.selectAll('*').remove()\n\n\t\tself.dom.editbtns = self.dom.menubody.append('div')\n\t\tself.dom.editbody = self.dom.menubody.append('div')\n\n\t\tif (self.activeLabel.grp.type == 'hierCluster') {\n\t\t\t// for hierCluster term group, only allow to add current hierCluster term to current group\n\t\t\tself.showDictTermSelection(self.dom.editbody)\n\t\t\treturn\n\t\t}\n\n\t\tconst grpNameDiv = self.dom.editbtns.append('div').style('margin', '10px 5px')\n\t\tgrpNameDiv.append('label').html(`Insert genes or variables in `)\n\t\tself.dom.grpNameSelect = grpNameDiv.append('select').on('change', () => {\n\t\t\tconst value = self.dom.grpNameSelect.property('value')\n\t\t\tself.dom.grpNameTextInput\n\t\t\t\t.property('disabled', value == 'current')\n\t\t\t\t.property('value', value == 'current' ? self.activeLabel.grp.name : newGrpName)\n\t\t})\n\t\tself.dom.grpNameSelect\n\t\t\t.selectAll('option')\n\t\t\t.data([\n\t\t\t\t{ label: 'current', value: 'current', selected: true },\n\t\t\t\t{ label: 'new', value: 'new' }\n\t\t\t])\n\t\t\t.enter()\n\t\t\t.append('option')\n\t\t\t.attr('selected', d => d.selected)\n\t\t\t.html(d => d.label)\n\n\t\tgrpNameDiv.append('span').html('&nbsp;group: &nbsp;')\n\n\t\tlet newGrpName = ''\n\t\tself.dom.grpNameTextInput = grpNameDiv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'text')\n\t\t\t.property('disabled', true)\n\t\t\t.property('value', self.activeLabel.grp.name)\n\t\t\t.on('change', () => {\n\t\t\t\tconst name = self.dom.grpNameTextInput.property('value')\n\t\t\t\tif (name == self.activeLabel.grp.name) {\n\t\t\t\t} else {\n\t\t\t\t\tnewGrpName = self.dom.grpNameTextInput.property('value')\n\t\t\t\t}\n\t\t\t})\n\n\t\tself.makeInsertPosRadios(self.dom.editbtns)\n\n\t\t//const termSrcDiv = self.dom.editbtns.append('div')\n\t\t//termSrcDiv.append('span').html('Source&nbsp;')\n\t\tself.showDictTermSelection(self.dom.editbody)\n\t}\n\n\tself.makeInsertPosRadios = function (div) {\n\t\tconst insertPosInput = div\n\t\t\t.append('div') /*.style('display', 'inline-block')*/\n\t\t\t.style('margin', '10px 5px')\n\t\tinsertPosInput.append('div').style('display', 'inline-block').style('padding-right', '10px').html('Insert&nbsp')\n\n\t\tconst insertRadiosDiv = insertPosInput.append('div').style('display', 'inline-block')\n\n\t\tself.insertRadioId = `sjpp-matrix-${self.id}-insert-pos`\n\t\tconst aboveLabel = insertRadiosDiv.append('label')\n\t\taboveLabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'radio')\n\t\t\t.attr('value', 'above')\n\t\t\t.property('checked', true)\n\t\t\t.attr('name', self.insertRadioId)\n\t\taboveLabel.append('span').html('above')\n\n\t\tinsertRadiosDiv.append('span').html('&nbsp;&nbsp')\n\n\t\tconst belowLabel = insertRadiosDiv.append('label')\n\t\tbelowLabel.append('input').attr('type', 'radio').attr('value', 'below').attr('name', self.insertRadioId)\n\t\tbelowLabel.append('span').html('&nbsp;below')\n\t}\n\n\tself.showDictTermSelection = async holder => {\n\t\t//self.dom.dictTermBtn.style('text-decoration', 'underline')\n\t\t//self.dom.textTermBtn.style('text-decoration', '')\n\n\t\tconst usecase = { target: 'matrix', detail: 'termgroups' }\n\t\tif (self.chartType == 'hierCluster') {\n\t\t\tif (\n\t\t\t\tself.config.dataType == TermTypes.METABOLITE_INTENSITY &&\n\t\t\t\t(!self.activeLabel || self.activeLabel.grp.type == 'hierCluster')\n\t\t\t) {\n\t\t\t\tusecase.target = TermTypes.METABOLITE_INTENSITY\n\t\t\t\tusecase.detail = 'term'\n\t\t\t} else if (\n\t\t\t\tself.config.dataType == TermTypes.PROTEOME_ABUNDANCE &&\n\t\t\t\t(!self.activeLabel || self.activeLabel.grp.type == 'hierCluster')\n\t\t\t) {\n\t\t\t\tusecase.target = TermTypes.PROTEOME_ABUNDANCE\n\t\t\t\tusecase.detail = 'term'\n\t\t\t} else {\n\t\t\t\tusecase.target = self.activeLabel.tw.term.type\n\t\t\t\tusecase.detail = 'term'\n\t\t\t}\n\t\t}\n\t\tconst termdb = await import('#termdb/app')\n\t\tholder.selectAll('*').remove()\n\t\ttermdb.appInit({\n\t\t\tholder: holder.append('div'),\n\t\t\tvocabApi: self.app.vocabApi,\n\t\t\tstate: {\n\t\t\t\tvocab: self.state.vocab,\n\t\t\t\tactiveCohort: self.activeCohort,\n\t\t\t\tnav: {\n\t\t\t\t\theader_mode: 'search_only'\n\t\t\t\t},\n\t\t\t\ttree: {\n\t\t\t\t\tusecase\n\t\t\t\t},\n\t\t\t\t...(!self.activeLabel || self.activeLabel.grp.type == 'hierCluster'\n\t\t\t\t\t? { selectedTerms: self.hcTermGroup.lst.map(t => t.term) }\n\t\t\t\t\t: {})\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tsubmit_lst\n\t\t\t},\n\t\t\tsearch: {\n\t\t\t\thandleGeneVariant: term => submit_lst([term])\n\t\t\t}\n\t\t})\n\t}\n\n\tasync function submit_lst(termlst) {\n\t\tconst newterms = await Promise.all(\n\t\t\ttermlst.map(async _term => {\n\t\t\t\tconst term = structuredClone(_term)\n\t\t\t\tconst tw = 'id' in term ? { id: term.id, term } : { term }\n\t\t\t\tawait fillTermWrapper(tw, self.app.vocabApi)\n\t\t\t\treturn tw\n\t\t\t})\n\t\t)\n\t\tconst t = self.activeLabel\n\t\tconst termgroups = self.termGroups\n\n\t\tconst isMetaboliteIntensityCBut = self.config.dataType == TermTypes.METABOLITE_INTENSITY && !t\n\t\tconst isProteomeAbundanceCBut = self.config.dataType == TermTypes.PROTEOME_ABUNDANCE && !t\n\t\tif (isMetaboliteIntensityCBut || isProteomeAbundanceCBut || t.grp.type == 'hierCluster') {\n\t\t\tconst grp = isMetaboliteIntensityCBut || isProteomeAbundanceCBut ? termgroups[0] : termgroups[t.grpIndex]\n\t\t\t// for hiercluster group, use selected terms as new group.lst\n\t\t\tgrp.lst.splice(0, grp.lst.length, ...newterms)\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\tid: self.opts.id,\n\t\t\t\tedits: [\n\t\t\t\t\t{\n\t\t\t\t\t\tnestedKeys: ['termgroups', isMetaboliteIntensityCBut || isProteomeAbundanceCBut ? 0 : t.grpIndex, 'lst'],\n\t\t\t\t\t\tvalue: grp.lst\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t})\n\t\t} else if (self.dom.grpNameSelect.property('value') == 'current') {\n\t\t\tconst pos = self.insertRadioId && select(`input[name='${self.insertRadioId}']:checked`)?.property('value')\n\t\t\tconst grp = termgroups[t.grpIndex]\n\t\t\tconst i = pos == 'above' ? t.lstIndex : t.lstIndex + 1\n\t\t\t// remove this element\n\t\t\tgrp.lst.splice(i, 0, ...newterms)\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\tid: self.opts.id,\n\t\t\t\tedits: [\n\t\t\t\t\t{\n\t\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex, 'lst'],\n\t\t\t\t\t\tvalue: grp.lst\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t})\n\t\t} else {\n\t\t\tconst pos = self.insertRadioId && select(`input[name='${self.insertRadioId}']:checked`)?.property('value')\n\t\t\tconst i = pos == 'above' ? t.grpIndex : t.grpIndex + 1\n\t\t\ttermgroups.splice(i, 0, {\n\t\t\t\tname: self.dom.grpNameTextInput.property('value'),\n\t\t\t\tlst: newterms\n\t\t\t})\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.opts.id,\n\t\t\t\tconfig: { termgroups }\n\t\t\t})\n\t\t}\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.showSortMenu = () => {\n\t\t/*\n\t\t\tsort rows and samples by:\n\t\t\t- #hits\n\n\t\t\tsort samples by #hits against\n\t\t\t- draggable divs of term names\n\n\n\t\t\t-- OR --\n\n\t\t\t[ ] move this row [above || below] [all rows || term names]\n\n\t\t\t[ ] sort samples against this term:\n\t\t\t\t\t// by: *hits _values _mutation class\n\t\t\t\t\t// priority: *first _last _order# [ ]\n\n\t\t\tApply\n\t\t*/\n\n\t\tconst t = self.activeLabel\n\t\tself.dom.menubody.selectAll('*').remove()\n\n\t\tself.dom.menubody.append('div').style('margin-top', '10px').style('text-align', 'center').html(t.tw.term.name)\n\n\t\tself.moveInput = undefined\n\t\t//if (t.grp.lst.length > 1) self.showTermMoveOptions(t)\n\t\tself.showSortOptions(t)\n\t}\n\n\tself.showTermMoveOptions = t => {\n\t\tconst moveDiv = self.dom.menubody.append('div').style('margin-top', '10px')\n\n\t\tconst moveLabel = moveDiv.append('label')\n\t\tself.moveInput = moveLabel.append('input').attr('type', 'checkbox').style('text-align', 'center')\n\n\t\tmoveLabel.append('span').html(`&nbsp;move this row&nbsp;`)\n\n\t\tconst movePos = moveDiv.append('select')\n\t\tmovePos\n\t\t\t.selectAll('option')\n\t\t\t.data([\n\t\t\t\t{ label: 'before', value: 0 },\n\t\t\t\t{ label: 'after', value: 1 }\n\t\t\t])\n\t\t\t.enter()\n\t\t\t.append('option')\n\t\t\t.attr('value', d => d.value)\n\t\t\t.html(d => d.label)\n\n\t\tmoveDiv.append('span').html('&nbsp;')\n\n\t\tconst otherTermsInGrp = t.grp.lst\n\t\t\t.filter(tw => tw.$id != t.tw.$id)\n\t\t\t.map(tw => {\n\t\t\t\treturn { label: tw.term.name, value: tw.$id }\n\t\t\t})\n\t\tconst moveTarget = moveDiv.append('select')\n\t\tmoveTarget\n\t\t\t.selectAll('option')\n\t\t\t.data([{ label: 'all', value: '*' }, ...otherTermsInGrp])\n\t\t\t.enter()\n\t\t\t.append('option')\n\t\t\t.attr('value', d => d.value)\n\t\t\t.html(d => d.label)\n\t}\n\n\tself.showSortOptions = t => {\n\t\tconst sortColDiv = self.dom.menubody.append('div').style('margin-top', '10px')\n\t\tconst sortColLabel = sortColDiv.append('label')\n\t\tconst sortColInput = sortColLabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.property('checked', true)\n\t\t\t.style('text-align', 'center')\n\n\t\tconst l = self.settings.matrix.controlLabels\n\t\tsortColLabel.append('span').html(`&nbsp;sort ${l.samples} against (in order of priority):`)\n\n\t\tconst tcopy = self.showSorterTerms(sortColDiv, t)\n\n\t\tself.dom.menubody\n\t\t\t.append('button')\n\t\t\t.html('Apply')\n\t\t\t.on('click', () => {\n\t\t\t\tconst matrix = JSON.parse(JSON.stringify(self.config.settings.matrix)) || {}\n\t\t\t\tdelete tcopy.div\n\t\t\t\tdelete tcopy.up\n\t\t\t\tdelete tcopy.down\n\t\t\t\tdelete tcopy.delete\n\n\t\t\t\t//if (self.moveInput.property('checked')) {}\n\n\t\t\t\tif (sortColInput.property('checked') || self.moveInput?.property('checked')) {\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\t\t\tid: self.opts.id,\n\t\t\t\t\t\tedits: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex, 'lst', t.lstIndex],\n\t\t\t\t\t\t\t\tvalue: tcopy\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tself.dom.tip.hide()\n\t\t\t})\n\t}\n\n\tself.showSorterTerms = (sortColDiv, t) => {\n\t\tconst [tcopy, sorterTerms] = self.getSorterTerms(t)\n\t\tconst s = self.settings.matrix\n\t\tconst l = s.controlLabels\n\t\tsortColDiv\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px')\n\t\t\t.style('padding', '5px 10px')\n\t\t\t.selectAll('div')\n\t\t\t.data(sorterTerms, s => s.$id)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.style('width', 'fit-content')\n\t\t\t.style('margin', '3px')\n\t\t\t.style('cursor', 'default')\n\t\t\t.style('padding', '3px 10px')\n\t\t\t.style('border-radius', '5px')\n\t\t\t.style('color', 'black')\n\t\t\t.style('background-color', 'rgb(238, 238, 238)')\n\t\t\t.each(function (st, i) {\n\t\t\t\tst.sortSamples.priority = i\n\t\t\t\tst.div = select(this)\n\t\t\t\tconst label = st.$id == 'sample' ? `${l.Sample} name` : st.term.name\n\t\t\t\tst.div.append('span').style('margin-right', '10px').html(label)\n\t\t\t\tst.up = st.div\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.html(' &#9650; ')\n\t\t\t\t\t.style('display', i === 0 ? 'none' : 'inline')\n\t\t\t\t\t.style('color', '#555')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.parentNode.insertBefore(this, this.previousSibling)\n\t\t\t\t\t\tsorterTerms.splice(st.priority, 1)\n\t\t\t\t\t\tsorterTerms.splice(st.priority - 1, 0, st)\n\t\t\t\t\t\tupdateSorterDivStyles()\n\t\t\t\t\t})\n\n\t\t\t\tst.down = st.div\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.html(' &#9660; ')\n\t\t\t\t\t.style('display', i < sorterTerms.length - 1 ? 'inline' : 'none')\n\t\t\t\t\t.style('color', '#555')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.parentNode.insertBefore(this, this.nextSibling.nextSibling)\n\t\t\t\t\t\tsorterTerms.splice(st.priority, 1)\n\t\t\t\t\t\tsorterTerms.splice(st.priority + 1, 0, st)\n\t\t\t\t\t\tupdateSorterDivStyles()\n\t\t\t\t\t})\n\n\t\t\t\tst.delete = st.div\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.html(' &#10005; ')\n\t\t\t\t\t.style('display', 'inline')\n\t\t\t\t\t.style('color', 'rgb(255, 100, 100)')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tst.div.remove()\n\t\t\t\t\t\tsorterTerms.splice(st.priority, 1)\n\t\t\t\t\t\tupdateSorterDivStyles()\n\t\t\t\t\t})\n\t\t\t})\n\n\t\tfunction updateSorterDivStyles() {\n\t\t\tfor (const [i, st] of sorterTerms.entries()) {\n\t\t\t\tst.priority = i\n\t\t\t\tst.up.style('display', st.priority > 0 ? 'inline' : 'none')\n\t\t\t\tst.down.style('display', st.priority < sorterTerms.length - 1 ? 'inline' : 'none')\n\t\t\t}\n\t\t}\n\n\t\treturn tcopy\n\t}\n\n\tself.getSorterTerms = t => {\n\t\tconst sorterTerms = [\n\t\t\t...self.termOrder\n\t\t\t\t.filter(t => t.tw.sortSamples)\n\t\t\t\t.map(t => JSON.parse(JSON.stringify(t.tw)))\n\t\t\t\t.sort((a, b) => a.sortSamples.priority - b.sortSamples.priority),\n\t\t\t...self.config.settings.matrix.sortSamplesTieBreakers.map(st => JSON.parse(JSON.stringify(st)))\n\t\t]\n\n\t\tconst s = self.settings.matrix\n\t\tconst activeOption = s.sortOptions[s.sortSamplesBy]\n\t\tif (!activeOption) {\n\t\t\tthrow `unsupported s.sortSamplesBy='${s.sortSamplesBy}'`\n\t\t}\n\t\tconst matchingSortSamples = activeOption.sortPriority?.find(o => o.types.includes(t.tw?.term?.type))?.tiebreakers[0]\n\t\tconst sortSamples = matchingSortSamples\n\t\t\t? {} // will let matrix.sort fill-in based on the first matching tiebreaker\n\t\t\t: t.tw?.term?.type == 'geneVariant' && t.tw?.q?.type == 'values'\n\t\t\t? {\n\t\t\t\t\tby: 'class',\n\t\t\t\t\torder: [\n\t\t\t\t\t\t'Fuserna',\n\t\t\t\t\t\t'CNV_homozygous_deletion',\n\t\t\t\t\t\t'CNV_amplification',\n\t\t\t\t\t\t'CNV_loss',\n\t\t\t\t\t\t'CNV_amp',\n\t\t\t\t\t\t'CNV_loh',\n\t\t\t\t\t\t// truncating\n\t\t\t\t\t\t'F',\n\t\t\t\t\t\t'N',\n\t\t\t\t\t\t// indel\n\t\t\t\t\t\t'D',\n\t\t\t\t\t\t'I',\n\t\t\t\t\t\t// point\n\t\t\t\t\t\t'M',\n\t\t\t\t\t\t'P',\n\t\t\t\t\t\t'L',\n\t\t\t\t\t\t// noncoding\n\t\t\t\t\t\t'Utr3',\n\t\t\t\t\t\t'Utr5',\n\t\t\t\t\t\t'S',\n\t\t\t\t\t\t'Intron',\n\t\t\t\t\t\t'WT',\n\t\t\t\t\t\t'Blank'\n\t\t\t\t\t]\n\t\t\t  }\n\t\t\t: { by: 'values' }\n\n\t\tconst i = sorterTerms.findIndex(st => st.$id === t.tw?.$id)\n\t\tconst tcopy = JSON.parse(JSON.stringify(t.tw || {}))\n\t\t// will let the matrix.sorter code fill-in the sortSamples with tiebreakers\n\t\ttcopy.sortSamples = sortSamples\n\t\tif (i == -1) {\n\t\t\tsorterTerms.unshift(tcopy)\n\t\t} else {\n\t\t\tif (sortSamples.order) tcopy.sortSamples.order = sortSamples.order\n\t\t}\n\n\t\treturn [tcopy, sorterTerms]\n\t}\n\n\tself.removeTerm = () => {\n\t\tconst t = self.activeLabel\n\t\tconst legendValueFilter = self.mayRemoveTvsEntry(t.tw)\n\t\tconst termgroups = self.termGroups\n\t\tconst grp = termgroups[t.grpIndex]\n\t\t// remove this element\n\t\tgrp.lst.splice(t.lstIndex, 1)\n\t\tif (grp.lst.length) {\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\tid: self.opts.id,\n\t\t\t\tedits: [\n\t\t\t\t\t{\n\t\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex, 'lst'],\n\t\t\t\t\t\tvalue: grp.lst\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tnestedKeys: ['legendValueFilter'],\n\t\t\t\t\t\tvalue: legendValueFilter\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t})\n\t\t} else {\n\t\t\t// remove this now-empty group\n\t\t\ttermgroups.splice(t.grpIndex, 1)\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.opts.id,\n\t\t\t\tconfig: {\n\t\t\t\t\ttermgroups,\n\t\t\t\t\tlegendValueFilter\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.removeTermGroup = () => {\n\t\tconst t = self.activeLabel\n\t\tconst termgroups = self.termGroups\n\t\ttermgroups.splice(t.grpIndex, 1)\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.opts.id,\n\t\t\tconfig: { termgroups }\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.mayRemoveTvsEntry = tw => {\n\t\tif (!self.config.legendValueFilter?.lst.length) return self.config.legendValueFilter\n\t\tconst lst = structuredClone(self.config.legendValueFilter.lst)\n\t\tconst items = lst.filter(\n\t\t\tf =>\n\t\t\t\tf.tvs?.term.type === tw?.term.type &&\n\t\t\t\t((('id' in f.tvs.term || 'id' in tw.term) && f.tvs.term.id === tw.term.id) || f.tvs.term.name === tw.term.name)\n\t\t)\n\t\tif (!items.length) return self.config.legendValueFilter\n\t\telse {\n\t\t\tfor (const t of items) {\n\t\t\t\tconst tvs = t.tvs\n\t\t\t\tif (tvs.term.type != tw.term.type) continue\n\t\t\t\tif (('id' in tvs.term || 'id' in tw.term) && tvs.term.id !== tw.term.id) continue\n\t\t\t\telse if (tvs.term.name != tw.term.name) continue\n\t\t\t\t// always remove a legendValueFilter.lst entry that corresponds to an edited term\n\t\t\t\t// TODO: may improve the logic to not remove a tvs entry when the tw edits are not data related, such as for colors\n\t\t\t\tconst i = lst.findIndex(t => t === tvs)\n\t\t\t\tlst.splice(i, 1)\n\t\t\t}\n\t\t}\n\t\treturn { in: true, join: 'and', type: 'tvslst', lst }\n\t}\n}\n\nfunction setSampleGroupActions(self) {\n\tself.showSampleGroupMenu = function (event) {\n\t\tconst d = event.target.__data__\n\t\tif (!d) return\n\t\tself.activeLabel = d\n\t\tself.dom.menutop.selectAll('*').remove()\n\t\tself.dom.menubody.style('padding', 0).selectAll('*').remove()\n\n\t\tconst options = JSON.parse(JSON.stringify(self.config.menuOpts?.sampleGroup || [])).map(d => {\n\t\t\td.callback = self[d.callback]\n\t\t\treturn d\n\t\t})\n\t\tconst menuOptions = [...options, { label: 'Delete', callback: self.removeSampleGroup }]\n\n\t\tself.dom.menutop\n\t\t\t.append('div')\n\t\t\t.selectAll(':scope>.sja_menuoption')\n\t\t\t.data(menuOptions)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.style('display', 'block')\n\t\t\t.html(d => d.label)\n\t\t\t.on('click', (event, d) => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\td.callback(d)\n\t\t\t})\n\n\t\tself.dom.tip.showunder(event.target)\n\t}\n\n\tself.showNewChartMenu = () => {\n\t\tself.dom.menubody.selectAll('*').remove()\n\t}\n\n\tself.launchSurvivalPlot = async menuOpt => {\n\t\tself.dom.menubody.selectAll('*').remove()\n\t\tself.dom.menubody\n\t\t\t.append('div')\n\t\t\t.style('padding-top', '10px')\n\t\t\t.html(`Use \"<b>${self.config.divideBy.term.name}</b>\" to`)\n\n\t\tconst radioDiv = self.dom.menubody.append('div').style('padding', '0 10px')\n\n\t\tconst radioName = 'sjpp-matrix-surv-termnum-' + inputIndex++\n\t\tconst label1 = radioDiv.append('label')\n\t\tlabel1\n\t\t\t.append('input')\n\t\t\t.attr('type', 'radio')\n\t\t\t.attr('name', radioName)\n\t\t\t.attr('value', 'term2')\n\t\t\t.property('checked', true)\n\t\tlabel1.append('span').html(' overlay')\n\n\t\tconst label2 = radioDiv.append('label').style('margin-left', '10px')\n\t\tlabel2.append('input').attr('type', 'radio').attr('name', radioName).attr('value', 'term0')\n\t\tlabel2.append('span').html(' divide')\n\n\t\tself.dom.menubody.append('div').style('padding-bottom', '10px').html(`the selected survival variable below:`)\n\n\t\tconst termdb = await import('#termdb/app')\n\t\ttermdb.appInit({\n\t\t\tholder: self.dom.menubody.append('div'),\n\t\t\tvocabApi: self.app.vocabApi,\n\t\t\tstate: {\n\t\t\t\tvocab: self.state.vocab,\n\t\t\t\tactiveCohort: self.state.activeCohort,\n\t\t\t\tnav: {\n\t\t\t\t\theader_mode: 'search_only'\n\t\t\t\t},\n\t\t\t\ttree: { usecase: { target: 'survival', detail: 'term' } }\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tclick_term: term => {\n\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t\tconst termNum = radioDiv.select(`input[name='${radioName}']:checked`).property('value')\n\t\t\t\t\tself.dom.menubody.selectAll('*').remove()\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\tterm,\n\t\t\t\t\t\t[termNum]: JSON.parse(JSON.stringify(self.config.divideBy)),\n\t\t\t\t\t\tinsertBefore: self.id\n\t\t\t\t\t}\n\n\t\t\t\t\tif (menuOpt.config) {\n\t\t\t\t\t\tObject.assign(config, menuOpt.config)\n\t\t\t\t\t}\n\t\t\t\t\tself.app.dispatch({ type: 'plot_create', config })\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tself.removeSampleGroup = () => {\n\t\t// this should not happen, but making sure\n\t\tif (!self.config.divideBy) return\n\n\t\tconst tw = self.activeLabel.grp.tw\n\t\tconst term = tw.term\n\t\tif (term.type == 'categorical' || term.type == 'survival') {\n\t\t\tterm.$id = tw.$id\n\t\t\tconst filterGrpIndex = self.config.legendValueFilter.lst.findIndex(l => l.legendGrpName == tw.term.id)\n\t\t\tif (filterGrpIndex == -1) {\n\t\t\t\tconst filterNew = {\n\t\t\t\t\tlegendGrpName: tw.term.id,\n\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\ttvs: {\n\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\tterm,\n\t\t\t\t\t\tvalues: [{ key: self.activeLabel.grp.id }]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t\t} else {\n\t\t\t\t// the filter for the categorical or survival term exist, but the current legend key is not there.\n\t\t\t\tself.config.legendValueFilter.lst[filterGrpIndex].tvs.values.push({ key: self.activeLabel.grp.id })\n\t\t\t}\n\t\t} else if (isNumericTerm(term)) {\n\t\t\tterm.$id = tw.$id\n\t\t\tconst filterNew = {\n\t\t\t\tlegendGrpName: tw.term.id || tw.term.name,\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: {\n\t\t\t\t\tisnot: true,\n\t\t\t\t\tterm,\n\t\t\t\t\tranges: [self.data.refs.byTermId[tw.$id].bins.find(b => self.activeLabel.grp.id == b.name)]\n\t\t\t\t}\n\t\t\t}\n\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t}\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: { legendValueFilter: self.config.legendValueFilter }\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.showDeletedSampleGroups = () => {\n\t\t// this should not happen, but making sure\n\t\tif (!self.config.divideBy) return\n\n\t\tconst tw = self.activeLabel?.grp?.tw || self.config.divideBy\n\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\tl => l.legendGrpName !== tw.term.id && l.legendGrpName != tw.term.name\n\t\t)\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: { legendValueFilter: self.config.legendValueFilter }\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\n\tself.displaySampleGroupInfo = (event, grp) => {\n\t\tconst l = self.settings.matrix.controlLabels\n\t\tconst n = grp.lst.length\n\t\tself.dom.menutop.selectAll('*').remove()\n\t\tself.dom.menubody.selectAll('*').remove()\n\t\tself.dom.menubody\n\t\t\t.append('div')\n\t\t\t.style('text-align', 'center')\n\t\t\t.html(`<b>${grp.name}</b> (${n} ${n < 2 ? l.sample : l.samples})`)\n\t\tconst div = self.dom.menubody.append('div').style('max-width', '400px').style('padding', '5px')\n\t\tfor (const key in event.target.__data__.grp.legendData) {\n\t\t\tconst g = event.target.__data__.grp.legendData[key]\n\t\t\tdiv.append('div').style('padding-top', '10px').html(`<b>${g.name}</b>`)\n\t\t\tconst t = div.append('table')\n\t\t\tfor (const i of g.items) {\n\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t// icon\n\t\t\t\ttr.append('td')\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t.style('background-color', i.color)\n\t\t\t\t\t.style('border', `1px soloid ${i.stroke}`)\n\t\t\t\ttr.append('td').html(i.text)\n\t\t\t}\n\t\t}\n\t\tself.dom.tip.show(event.clientX, event.clientY)\n\t}\n\n\t// TODO: may use this later to sort legend, mouseover items by count\n\tself.legendItemSorter = (a, b) => {\n\t\tif (a.order && b.order) return a.order - b.order\n\t\tif (Number.isFinite(a.order) || b.order == -1) return -1\n\t\tif (Number.isFinite(b.order) || a.order == -1) return 1\n\t\tif (a.count) return b.count - a.count\n\t\tif (Number.isFinite(a.count)) return -1\n\t\tif (Number.isFinite(b.count)) return 1\n\t\treturn 0\n\t}\n\n\tself.handleLegendItemClick = d => {\n\t\tconst dvt = structuredClone(self.config.divideBy || {})\n\t\tconst id = 'id' in dvt ? dvt.id : dvt.name\n\t\tif (d.termid == id) {\n\t\t\tif (!dvt.exclude) dvt.exclude = []\n\t\t\tconst i = dvt.exclude?.indexOf(d.key)\n\t\t\tif (i == -1) dvt.exclude.push(d.key)\n\t\t\telse dvt.exclude.splice(i, 1)\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tdivideBy: dvt\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tself.handleLegendMouseover = (event, d) => {\n\t\tconst dvt = structuredClone(self.config.divideBy || {})\n\t\tconst id = 'id' in dvt ? dvt.id : dvt.name\n\t\tif (d.termid == id) {\n\t\t\tself.dom.menutop.selectAll('*').remove()\n\t\t\tself.dom.menubody.selectAll('*').remove()\n\t\t\tself.dom.menubody.html(`Click to ${d.isExcluded ? 'show' : 'hide'}`)\n\t\t\tself.dom.tip.show(event.clientX, event.clientY)\n\t\t}\n\t}\n}\n\nfunction setTermGroupActions(self) {\n\tsetLabelDragEvents(self, 'termGrp')\n\n\tself.showTermGroupMenu = function (event) {\n\t\tconst d = event.target.tagName.toLowerCase() == 'tspan' ? event.target.parentNode.__data__ : event.target.__data__\n\t\tif (!d) return\n\t\tself.activeLabel = d\n\t\tself.dom.menutop.style('display', '').selectAll('*').remove()\n\t\tself.showTermGroupInputs(self.dom.menutop.append('div'))\n\t\tself.dom.tip.showunder(event.target)\n\t}\n\n\tself.showTermGroupInputs = function (div) {\n\t\tconst holder = div\n\t\tconst labelEditDiv = holder.append('div').style('text-align', 'center')\n\t\tlabelEditDiv.append('span').text('Group ')\n\n\t\tself.dom.grpNameInput = labelEditDiv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'text')\n\t\t\t.attr('size', (self.activeLabel.grp.name?.length || 0) + 5)\n\t\t\t.style('padding', '1px 5px')\n\t\t\t.style('text-align', 'center')\n\t\t\t.property('value', self.activeLabel.grp.name)\n\t\t\t.on('input', () => {\n\t\t\t\tconst value = self.dom.grpNameInput.property('value')\n\t\t\t\tself.dom.grpNameInput.attr('size', value.length + 5)\n\t\t\t\tself.dom.grpEditBtn.style('display', value === self.activeLabel.grp.name ? 'none' : '')\n\t\t\t})\n\t\t//.on('change', self.updateTermGrpName)\n\n\t\tself.dom.grpEditBtn = labelEditDiv\n\t\t\t.append('button')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-left', '5px')\n\t\t\t.html('submit')\n\t\t\t.on('click', () => {\n\t\t\t\tself.updateTermGrpName()\n\t\t\t\tself.dom.tip.hide()\n\t\t\t})\n\n\t\tself.dom.menubody.style('padding', 0).selectAll('*').remove()\n\n\t\tconst menuOptions = [{ label: 'Add Rows', callback: self.showTermInsertMenu }]\n\t\t// try to maintain a familiar button order\n\t\tif (self.chartType != 'hierCluster') {\n\t\t\tmenuOptions.push(\n\t\t\t\t{ label: 'Edit', callback: self.showTermGroupEditMenu }\n\t\t\t\t//{ label: 'Sort', callback: self.showSortMenu },\n\t\t\t)\n\t\t}\n\t\tif (self.activeLabel.grp.type != 'hierCluster') {\n\t\t\tmenuOptions.push({ label: 'Delete', callback: self.removeTermGroup })\n\t\t}\n\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.style('text-align', 'center')\n\t\t\t.selectAll(':scope>.sja_menuoption')\n\t\t\t.data(menuOptions)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.html(d => d.label)\n\t\t\t.on('click', (event, d) => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tself.dom.menutop.style('display', 'none')\n\t\t\t\td.callback(d)\n\t\t\t})\n\t}\n\n\tself.updateTermGrpName = () => {\n\t\tconst value = self.dom.grpNameInput.property('value')\n\t\tconst t = self.activeLabel\n\t\tif (t.grp.name === value) return\n\t\tt.grp.name = value\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_nestedEdits',\n\t\t\tid: self.opts.id,\n\t\t\tedits: [\n\t\t\t\t{\n\t\t\t\t\tnestedKeys: ['termgroups', t.grpIndex],\n\t\t\t\t\tvalue: t.grp\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t}\n\n\tself.showTermGroupEditMenu = async () => {\n\t\tself.dom.menubody.selectAll('*').remove()\n\n\t\tconst menu = self.dom.menubody.append('div').style('padding', '5px')\n\t\tmenu.append('div').style('width', '100%').style('font-weight', 600).html('Group options')\n\n\t\tconst label = menu.append('div').append('label')\n\t\tconst l = self.settings.matrix.controlLabels\n\t\tlabel\n\t\t\t.append('span')\n\t\t\t.html(\n\t\t\t\t`Minimum # of mutated ${l.samples} for the ${l.term.charAt(0).toLowerCase() + l.term.slice(1)} to be visible `\n\t\t\t)\n\t\t\t.attr('aria-label', `May be overridden by a row-specific minNumSamples`)\n\t\tconst minNumSampleInput = label\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('margin-left', '5px')\n\t\t\t.style('width', '50px')\n\t\t\t.property('value', self.activeLabel.grp.settings?.minNumSamples || 0)\n\n\t\tmenu\n\t\t\t.append('div')\n\t\t\t.append('button')\n\t\t\t.html('Submit')\n\t\t\t.on('click', () => {\n\t\t\t\tconst settings = self.activeLabel.grp.settings || {}\n\t\t\t\tsettings.minNumSamples = minNumSampleInput.property('value')\n\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tedits: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tnestedKeys: ['termgroups', self.activeLabel.grpIndex, 'settings'],\n\t\t\t\t\t\t\tvalue: settings\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\tself.removeTermGroup = () => {\n\t\tconst termgroups = self.termGroups\n\t\ttermgroups.splice(self.activeLabel.grpIndex, 1)\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: {\n\t\t\t\ttermgroups\n\t\t\t}\n\t\t})\n\t\tself.dom.tip.hide()\n\t}\n\tconst labelParentSelectors = ['series', 'series-group', 'term', 'term-group']\n\t\t.map(d => `.sjpp-matrix-${d}-label-g`)\n\t\t.join(',')\n\tself.enableTextHighlight = event => {\n\t\tselect(event.target.closest(labelParentSelectors))\n\t\t\t.selectAll('.sjpp-matrix-label text')\n\t\t\t//.selectAll('text')\n\t\t\t.style('-webkit-user-select', 'auto')\n\t\t\t.style('-moz-user-select', 'auto')\n\t\t\t.style('-ms-user-select', 'auto')\n\t\t\t.style('user-select', 'auto')\n\n\t\tselect('body').on('mouseup.sjppMatrixLabelText', self.disableTextHighlight)\n\t}\n\n\tself.disableTextHighlight = event => {\n\t\tselect(event.target.closest(labelParentSelectors))\n\t\t\t.selectAll('.sjpp-matrix-label text')\n\t\t\t.style('-webkit-user-select', 'none')\n\t\t\t.style('-moz-user-select', 'none')\n\t\t\t.style('-ms-user-select', 'none')\n\t\t\t.style('user-select', 'none')\n\n\t\tselect('body').on('mouseup.sjppMatrixLabelText', null)\n\t}\n}\n\n// prefix = \"term\" | \"termGrp\"\nfunction setLabelDragEvents(self, prefix) {\n\tself[`${prefix}LabelMousedown`] = (event, d) => {\n\t\tself.clicked = { event, d }\n\t}\n\n\tself[`${prefix}LabelMouseover`] = (event, t) => {\n\t\tif (prefix == 'term' && event.target.__data__?.tw && event.target.__data__.grp) {\n\t\t\tif (event.target.__data__.grp.type == 'hierCluster') {\n\t\t\t\t// do allow to be dragged/dropped and do not show term label hover over tooltip for hier cluster\n\t\t\t\treturn\n\t\t\t}\n\t\t\t//show counts in each subgroup when hover over term label\n\t\t\tif (self.activeLabel || self.zoomArea) {\n\t\t\t\t// when an edit menu is open or when users are selecting a portion of matrix to zoom\n\t\t\t\treturn\n\t\t\t}\n\t\t\tself.dom.menutop.selectAll('*').remove()\n\t\t\tself.dom.menubody.selectAll('*').remove()\n\t\t\tconst groupName = event.target.__data__.grp.name\n\t\t\tconst termName = event.target.__data__.tw.term.name\n\n\t\t\t//Add subGroup name\n\t\t\tconst titleDiv = self.dom.menubody\n\t\t\t\t.append('div')\n\t\t\t\t.style('text-align', 'left')\n\t\t\t\t.style('font-size', '1.1em')\n\t\t\t\t.html(groupName ? `<b>${groupName}: ${termName}</b>` : `<b>${termName}</b>`)\n\n\t\t\tconst div = self.dom.menubody.append('div').style('max-width', '400px')\n\n\t\t\tconst data = event.target.__data__\n\n\t\t\tif (data.tw.term.type == 'geneVariant' && data.tw.q?.type == 'values') {\n\t\t\t\t// for geneVariant term, when groupsetting is <not?> used, use subGroupCounts to\n\t\t\t\t// show number of counted samples (WT and Blank are not counted)\n\t\t\t\t// and number of each class in the subGroup\n\n\t\t\t\t//Sum of not tested samples in all group\n\t\t\t\tconst notTestedSum = Object.values(data.counts.subGroupCounts).reduce(\n\t\t\t\t\t(sum, curr) => sum + curr.samplesNotTested,\n\t\t\t\t\t0\n\t\t\t\t)\n\n\t\t\t\t//Add number of tested samples\n\t\t\t\ttitleDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('text-align', 'left')\n\t\t\t\t\t.style('font-size', '0.9em')\n\t\t\t\t\t.html(`(tested ${self.samples.length - notTestedSum} of ${self.samples.length})`)\n\n\t\t\t\tfor (const [grpName, counts] of Object.entries(data.counts.subGroupCounts)) {\n\t\t\t\t\tconst groupSampleTotal = self.sampleGroups.find(g => g.name == grpName).lst.length\n\t\t\t\t\tconst mRate =\n\t\t\t\t\t\tgroupSampleTotal - counts.samplesNotTested\n\t\t\t\t\t\t\t? counts.samplesTotal / (groupSampleTotal - counts.samplesNotTested)\n\t\t\t\t\t\t\t: 0\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('padding-top', '10px')\n\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\tgrpName\n\t\t\t\t\t\t\t\t? `<b>${grpName}</b>: Mutated samples (${counts.samplesTotal} of ${\n\t\t\t\t\t\t\t\t\t\tgroupSampleTotal - counts.samplesNotTested\n\t\t\t\t\t\t\t\t  }, ${d3format('.1%')(mRate)})`\n\t\t\t\t\t\t\t\t: `<b>Mutated samples (${counts.samplesTotal} of ${\n\t\t\t\t\t\t\t\t\t\tgroupSampleTotal - counts.samplesNotTested\n\t\t\t\t\t\t\t\t  }, ${d3format('.1%')(mRate)})`\n\t\t\t\t\t\t)\n\t\t\t\t\tconst t = div.append('table').style('margin-left', '15px')\n\t\t\t\t\tfor (const [classType, num] of Object.entries(counts.classes).sort((a, b) => b[1] - a[1])) {\n\t\t\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t\t\t// icon\n\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t\t\t.style('background-color', mclass[classType].color)\n\t\t\t\t\t\ttr.append('td').html(`${mclass[classType].label}: ${num}`)\n\t\t\t\t\t}\n\t\t\t\t\tif (counts.notTestedClasses) {\n\t\t\t\t\t\tdiv.append('div').style('margin-left', '15px').style('padding-top', '12px').html('<b> Not counted:</b>')\n\t\t\t\t\t\tconst t = div.append('table').style('margin-left', '15px')\n\t\t\t\t\t\tfor (const [classType, num] of Object.entries(counts.notTestedClasses).sort((a, b) => b[1] - a[1])) {\n\t\t\t\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t\t\t\t// icon\n\t\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t\t\t\t.style('background-color', mclass[classType].color)\n\t\t\t\t\t\t\ttr.append('td').html(`${mclass[classType].label}: ${num}`)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (!self.config.divideBy) {\n\t\t\t\t// non-geneVariant term, when matrix is not divided into multiple subGorups\n\t\t\t\tconst termLegend = self.legendData.find(t => t.name == data.tw.term.name)\n\t\t\t\tif (termLegend && termLegend.items) {\n\t\t\t\t\t// when legend data is available\n\t\t\t\t\tconst t = div.append('table')\n\t\t\t\t\tfor (const classType of termLegend.items) {\n\t\t\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t\t\t// icon\n\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t\t\t.style('background-color', classType.color)\n\t\t\t\t\t\ttr.append('td').html(`${classType.key}: ${classType.count}`)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// when legend data is not available, use subGroupCounts\n\t\t\t\t\tfor (const [grpName, counts] of Object.entries(data.counts.subGroupCounts)) {\n\t\t\t\t\t\tconst groupSampleTotal = self.sampleGroups.find(g => g.name == grpName).totalCountedValues\n\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('padding-top', '10px')\n\t\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\t\tgrpName !== ''\n\t\t\t\t\t\t\t\t\t? `<b>${grpName}</b>: ${counts.samplesTotal} of ${groupSampleTotal}`\n\t\t\t\t\t\t\t\t\t: `<b>${counts.samplesTotal} of ${groupSampleTotal}`\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\tconst t = div.append('table').style('margin-left', '15px')\n\t\t\t\t\t\tfor (const [classType, num] of Object.entries(counts.classes).sort((a, b) => b[1] - a[1])) {\n\t\t\t\t\t\t\tconst classColor = data.tw.term.values?.[classType]?.color\n\t\t\t\t\t\t\tif (!classColor) continue\n\t\t\t\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t\t\t\t// icon\n\t\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t\t\t\t.style('background-color', classColor)\n\t\t\t\t\t\t\ttr.append('td').html(`${classType}: ${num}`)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// non-geneVariant term, when matrix is divided into multiple subGorups\n\t\t\t\tfor (const [grpName, counts] of Object.entries(data.counts.subGroupCounts)) {\n\t\t\t\t\tconst groupSampleTotal = self.sampleGroups.find(g => g.name == grpName).totalCountedValues\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('padding-top', '10px')\n\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\tgrpName !== ''\n\t\t\t\t\t\t\t\t? `<b>${grpName}</b>: ${counts.samplesTotal} of ${groupSampleTotal}`\n\t\t\t\t\t\t\t\t: `<b>${counts.samplesTotal} of ${groupSampleTotal}`\n\t\t\t\t\t\t)\n\t\t\t\t\tconst subGrp = self.sampleGroups.find(g => g.name == grpName)\n\t\t\t\t\tconst termLegend = subGrp.legendData.find(t => t.name == data.tw.term.name)\n\n\t\t\t\t\tif (termLegend && termLegend.items) {\n\t\t\t\t\t\t// when legend data is available\n\t\t\t\t\t\tconst t = div.append('table').style('margin-left', '15px')\n\t\t\t\t\t\tfor (const classType of termLegend.items) {\n\t\t\t\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t\t\t\t// icon\n\t\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t\t\t\t.style('background-color', classType.color)\n\t\t\t\t\t\t\ttr.append('td').html(`${classType.key}: ${classType.count}`)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// when legend data is not available, use subGroupCounts\n\t\t\t\t\t\tconst t = div.append('table').style('margin-left', '15px')\n\t\t\t\t\t\tfor (const [classType, num] of Object.entries(counts.classes).sort((a, b) => b[1] - a[1])) {\n\t\t\t\t\t\t\tconst classColor = data.tw.term.values?.[classType]?.color\n\t\t\t\t\t\t\tif (!classColor) continue\n\t\t\t\t\t\t\tconst tr = t.append('tr')\n\t\t\t\t\t\t\t// icon\n\t\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('width', '12px')\n\t\t\t\t\t\t\t\t.style('height', '12px')\n\t\t\t\t\t\t\t\t.style('background-color', classColor)\n\t\t\t\t\t\t\ttr.append('td').html(`${classType}: ${num}`)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tself.dom.tip.show(event.clientX, event.clientY)\n\t\t}\n\t\t//const cls = event.target.className?.baseVal || event.target.parentNode.className?.baseVal || ''\n\t\tif (event.target.innerHTML.includes('grouped by')) return\n\t\tif (event.target.tagName === 'text') {\n\t\t\tselect(event.target).style('fill', 'blue')\n\t\t}\n\t\tif (!self.dragged) return\n\t\t// TODO: why is the element-bound __data__ (t) not provided as a second argument by d3??\n\t\tself.hovered = event.target.__data__\n\t}\n\n\tself[`${prefix}LabelMouseout`] = event => {\n\t\tselect(event.target).style('fill', '')\n\t\t//if (!this.dragged) return\n\t}\n\n\tself[`${prefix}LabelMousemove`] = (event, data) => {\n\t\tconst s = self.config.settings.matrix\n\t\tif (self.clicked && !self.dragged) {\n\t\t\tself.dom[`${prefix}LabelG`]\n\t\t\t\t.selectAll('text')\n\t\t\t\t.style('-webkit-user-select', 'none')\n\t\t\t\t.style('-moz-user-select', 'none')\n\t\t\t\t.style('-ms-user-select', 'none')\n\t\t\t\t.style('user-select', 'none')\n\n\t\t\tconst label = self.clicked.event.target.closest('.sjpp-matrix-label')\n\t\t\tconst t = label?.__data__\n\t\t\tif (!t) return\n\t\t\tif (self.type == 'hierCluster' && t.tw && t.grp?.name == self.config.settings.hierCluster?.termGroupName) return\n\t\t\t// TODO: use a native or D3 transform accessor\n\t\t\tconst [x, y] = select(label).attr('transform').split('translate(')[1].split(')')[0].split(',').map(Number)\n\t\t\tconst node = label.cloneNode(true)\n\t\t\tself.dom[`${prefix}LabelG`].node().prepend(node)\n\t\t\tself.dragged = {\n\t\t\t\torig: label,\n\t\t\t\tclone: select(node).style('cursor', 'move').style('pointer-events', 'none'),\n\t\t\t\tnode,\n\t\t\t\tx,\n\t\t\t\ty,\n\t\t\t\tclientX: event.clientX,\n\t\t\t\tclientY: event.clientY\n\t\t\t}\n\t\t\tself.dragged.clone.selectAll('text').style('fill', 'red')\n\t\t}\n\t\tif (!self.dragged) return\n\t\tconst d = self.dragged\n\t\tconst x2 = !s.transpose ? d.x : d.x - d.clientX + event.clientX\n\t\tconst y2 = !s.transpose ? d.y - d.clientY + event.clientY : d.y\n\t\td.clone.attr('transform', `translate(${x2},${y2})`)\n\t}\n\n\tself[`${prefix}LabelMouseup`] = event => {\n\t\tdelete self.clicked\n\t\tconst s = self.config.settings.matrix\n\t\tif (self.dragged) {\n\t\t\tself.dragged.clone.remove()\n\t\t\t//self.dragged.bgrect.remove()\n\t\t\tif (self.hovered) {\n\t\t\t\t// reposition the dragged row/column\n\t\t\t\tconst d = self.dragged\n\t\t\t\tconst t = d.orig.__data__\n\t\t\t\tconst h = self.hovered\n\n\t\t\t\tif (prefix == 'termGrp') {\n\t\t\t\t\tconst grp = self.config.termgroups.splice(t.grpIndex, 1)[0]\n\t\t\t\t\tself.config.termgroups.splice(h.grpIndex, 0, grp)\n\t\t\t\t} else {\n\t\t\t\t\t// NOTE: currently, the rendered order does not have to match the termgroup.lst order\n\t\t\t\t\t// ??? actually resort termgroup.lst to reflect the current term order ???\n\t\t\t\t\tfor (const grp of self.config.termgroups) {\n\t\t\t\t\t\tgrp.lst.sort((a, b) => {\n\t\t\t\t\t\t\tconst a1 = self.termOrder.find(t => t.tw.$id === a.$id)\n\t\t\t\t\t\t\tconst b1 = self.termOrder.find(t => t.tw.$id === b.$id)\n\t\t\t\t\t\t\tif (!a1 && !b1) return 0\n\t\t\t\t\t\t\tif (!a1) return 1\n\t\t\t\t\t\t\tif (!b1) return -1\n\t\t\t\t\t\t\treturn a1.totalIndex - b1.totalIndex\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\n\t\t\t\t\tconst tw = self.config.termgroups[t.grpIndex].lst.splice(t.index, 1)[0]\n\t\t\t\t\tself.config.termgroups[h.grpIndex].lst.splice(h.index, 0, t.tw)\n\t\t\t\t\t// if the \"source\" term group was emptied, then remove that group\n\t\t\t\t\tif (!self.config.termgroups[t.grpIndex].lst.length) self.config.termgroups.splice(t.grpIndex, 1)\n\t\t\t\t}\n\n\t\t\t\tconst sortKey = prefix == 'term' ? 'sortTermsBy' : 'sortTermGroupsBy'\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\ttermgroups: self.config.termgroups,\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t\t[sortKey]: 'asListed'\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\n\t\t\tself.dom[`${prefix}LabelG`]\n\t\t\t\t.selectAll('text')\n\t\t\t\t.style('fill', '')\n\t\t\t\t.style('-webkit-user-select', '')\n\t\t\t\t.style('-moz-user-select', '')\n\t\t\t\t.style('-ms-user-select', '')\n\t\t\t\t.style('user-select', '')\n\n\t\t\tdelete self.dragged\n\t\t} else if (prefix == 'term') {\n\t\t\tself.showTermMenu(event)\n\t\t} else {\n\t\t\tself.showTermGroupMenu(event)\n\t\t}\n\t}\n}\n\nfunction setZoomPanActions(self) {\n\tself.resetInteractions = function () {\n\t\tif (self.zoomArea) {\n\t\t\tself.zoomArea.remove()\n\t\t\tdelete self.zoomArea\n\t\t\t//self.dom.seriesesG.on('mouseup.zoom', null)\n\t\t\tselect('body').on('mouseup.matrixZoom', null)\n\t\t}\n\t\tdelete self.clickedSeriesCell\n\t}\n\n\tself.seriesesGMousedown = function (event) {\n\t\tevent.stopPropagation()\n\t\tself.resetInteractions()\n\t\tconst startCell = self.getCellByPos(event)\n\t\tif (!startCell) return\n\t\tself.clickedSeriesCell = { event, startCell }\n\t\tif (self.settings.matrix.mouseMode == 'pan') {\n\t\t\tself.seriesesGdragInit()\n\t\t} else {\n\t\t\tself.zoomPointer = pointer(event, self.dom.seriesesG.node())\n\t\t\tself.dom.seriesesG\n\t\t\t\t.on('mousemove', self.seriesesGoutlineZoom)\n\t\t\t\t.on('mouseup', self.seriesesGtriggerZoom)\n\t\t\t\t.on('contextmenu', self.resetInteractions)\n\t\t}\n\t\tself.dom.mainG\n\t\t\t.selectAll('text')\n\t\t\t.style('-webkit-user-select', 'none')\n\t\t\t.style('-moz-user-select', 'none')\n\t\t\t.style('-ms-user-select', 'none')\n\t\t\t.style('user-select', 'none')\n\t}\n\n\tself.getCellByPos = function (event) {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tif (event.target.tagName == 'rect') {\n\t\t\tif (event.target.__data__?.sample) return event.target.__data__\n\t\t\tif (event.target.__data__?.xg) {\n\t\t\t\tconst width = event.clientX - event.target.getBoundingClientRect().x + d.seriesXoffset\n\t\t\t\tconst i = Math.floor(width / d.dx)\n\t\t\t\treturn self.sampleOrder[i]\n\t\t\t}\n\t\t}\n\t\tif (event.target.tagName == 'image' && s.useCanvas) {\n\t\t\treturn self.getImgCell(event)\n\t\t}\n\t}\n\n\tself.seriesesGdragInit = function () {\n\t\t//self.dom.seriesesG.on('mousemove', self.seriesesGdrag).on('mouseup', self.seriesesGcancelDrag)\n\t\tselect('body')\n\t\t\t.on('mousemove.sjppMatrixDrag', self.seriesesGdrag)\n\t\t\t.on('mouseup.sjppMatrixDrag', self.seriesesGcancelDrag)\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst c = self.clickedSeriesCell\n\t\tc.dxPad = 20 // to show edge that limits drag, and to \"bounce back\" on mouseup\n\t\t//const pos = d.seriesXoffset s.zoomCenterPct * d.mainw /// d.mainw\n\t\tc.dxMax = -d.seriesXoffset\n\t\tc.dxMaxPad = c.dxMax + c.dxPad\n\t\tc.dxMin = d.mainw - d.zoomedMainW - d.seriesXoffset\n\t\tc.dxMinPad = c.dxMin - c.dxPad\n\t\tconst halfw = 0.5 * d.mainw\n\t\tc.center = {\n\t\t\tmax: halfw + (d.zoomedMainW - d.mainw),\n\t\t\tmin: halfw\n\t\t}\n\t}\n\n\tself.seriesesGdrag = function (event) {\n\t\tconst s = self.settings.matrix\n\t\tconst c = self.clickedSeriesCell\n\t\tconst d = self.dimensions\n\t\tconst dx = event.clientX - c.event.clientX\n\t\tif (Math.abs(dx) < 1) return\n\t\tif (dx < c.dxMinPad || dx > c.dxMaxPad) return\n\t\tself.clickedSeriesCell.dx = dx\n\t\tself.translateElems(dx, d, s, c)\n\t}\n\n\tself.translateElems = function (dx, d, s, c) {\n\t\tself.dom.seriesesG.attr('transform', `translate(${d.xOffset + d.seriesXoffset + dx},${d.yOffset})`)\n\t\tself.layout.top.attr.adjustBoxTransform(dx)\n\t\tself.layout.btm.attr.adjustBoxTransform(dx)\n\t\tconst computedCenter = s.zoomCenterPct * d.mainw - d.seriesXoffset - dx\n\t\tself.controlsRenderer.svgScrollApi.update({ zoomCenter: computedCenter })\n\t}\n\n\tself.seriesesGcancelDrag = function (event) {\n\t\tselect('body').on('mousemove.sjppMatrixDrag', null).on('mouseup.sjppMatrixDrag', null)\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst cc = self.clickedSeriesCell\n\t\tconst _dx = event.clientX - cc.event.clientX\n\t\tconst dx = Math.min(cc.dxMax, Math.max(_dx, cc.dxMin))\n\t\tif (Math.abs(_dx) < 1 || Math.abs(dx) < 1) {\n\t\t\tself.translateElems(0, d, s, cc)\n\t\t\treturn\n\t\t}\n\t\tself.translateElems(dx, d, s, cc)\n\t\tconst c = self.getVisibleCenterCell(dx)\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tmatrix: {\n\t\t\t\t\t\tzoomCenterPct: 0.5,\n\t\t\t\t\t\tzoomIndex: c.totalIndex,\n\t\t\t\t\t\tzoomGrpIndex: c.grpIndex\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tself.seriesesGoutlineZoom = function (event) {\n\t\tif (!self.clickedSeriesCell) return\n\t\tconst s = self.config.settings.matrix\n\t\tconst e = self.clickedSeriesCell.event\n\n\t\tif (self.clickedSeriesCell && !self.zoomArea) {\n\t\t\tself.zoomArea = self.dom.seriesesG.append('rect').attr('fill', 'rgba(50, 50, 50, 0.3)')\n\n\t\t\tselect('body').on('mouseup.matrixZoom', self.mouseup)\n\n\t\t\tself.dom.mainG\n\t\t\t\t.selectAll('text')\n\t\t\t\t.style('-webkit-user-select', 'none')\n\t\t\t\t.style('-moz-user-select', 'none')\n\t\t\t\t.style('-ms-user-select', 'none')\n\t\t\t\t.style('user-select', 'none')\n\t\t}\n\n\t\tconst dx = event.clientX - e.clientX\n\t\tconst dy = event.clientY - e.clientY\n\t\tconst x = dx > 0 ? self.zoomPointer[0] : self.zoomPointer[0] + dx + 3\n\t\tself.zoomWidth = Math.abs(dx)\n\t\tself.zoomArea\n\t\t\t.attr('transform', `translate(${x},0)`)\n\t\t\t.attr('width', Math.max(0, self.zoomWidth - 2))\n\t\t\t.attr('height', self.dimensions.mainh)\n\n\t\tif (!self.clickedSeriesCell.endCell) self.clickedSeriesCell.endCell = self.getCellByPos(event)\n\t}\n\n\tself.seriesesGtriggerZoom = function (event) {\n\t\tevent.stopPropagation()\n\t\tself.dom.seriesesG.on('mousemove', null).on('mouseup', null)\n\t\t//const d = event.target.__data__\n\t\tselect('body').on('mouseup.matrixZoom', null)\n\n\t\tself.dom.mainG\n\t\t\t.selectAll('text')\n\t\t\t.style('-webkit-user-select', '')\n\t\t\t.style('-moz-user-select', '')\n\t\t\t.style('-ms-user-select', '')\n\t\t\t.style('user-select', '')\n\n\t\tconst c = self.clickedSeriesCell\n\t\tconst endCell = self.getCellByPos(event)\n\t\tif (!c || !c.startCell) {\n\t\t\tself.dom.mainG.on('mouseout', null)\n\t\t\tdelete self.clickedSeriesCell\n\t\t\treturn\n\t\t} else if (!c.endCell || endCell === c.startCell) {\n\t\t\tself.dom.mainG.on('mouseout', null)\n\t\t\tself.dom.tip.hide()\n\t\t\tconst cell = event.target.tagName == 'rect' ? event.target.__data__ : c.startCell\n\t\t\tif (cell) {\n\t\t\t\tif (self.opts.cellClick) {\n\t\t\t\t\tself.opts.cellClick(\n\t\t\t\t\t\tstructuredClone({\n\t\t\t\t\t\t\tsampleData: cell.row,\n\t\t\t\t\t\t\tterm: cell.term,\n\t\t\t\t\t\t\tvalue: cell.value,\n\t\t\t\t\t\t\ts: cell.s,\n\t\t\t\t\t\t\tt: cell.t,\n\t\t\t\t\t\t\tsiblingCells: cell.siblingCells\n\t\t\t\t\t\t\t\t.filter(c => c !== cell)\n\t\t\t\t\t\t\t\t.map(c => ({\n\t\t\t\t\t\t\t\t\tterm: c.term,\n\t\t\t\t\t\t\t\t\tvalue: c.value,\n\t\t\t\t\t\t\t\t\ts: c.s,\n\t\t\t\t\t\t\t\t\tt: c.t\n\t\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} else {\n\t\t\t\t\tself.mouseclick(event, cell)\n\t\t\t\t}\n\t\t\t}\n\t\t\tdelete self.clickedSeriesCell\n\t\t\tdelete self.zoomArea\n\t\t\treturn\n\t\t}\n\n\t\tconst s = self.settings.matrix\n\t\tconst l = s.controlLabels\n\t\tc.endCell = endCell\n\t\tconst ss = self.opts.allow2selectSamples\n\n\t\tconst startCellTouched = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell\n\t\tconst endCellTouched = c.startCell.totalIndex < c.endCell.totalIndex ? c.endCell : c.startCell\n\t\tconst samplesSet = new Set()\n\t\tfor (let i = startCellTouched.totalIndex; i <= endCellTouched.totalIndex; i++) {\n\t\t\tsamplesSet.add(self.sampleOrder[i].row)\n\t\t}\n\t\tconst samples = [...samplesSet]\n\n\t\tconst optionArr = [\n\t\t\t{\n\t\t\t\tlabel: 'Zoom in',\n\t\t\t\tcallback: self.triggerZoomArea\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `List ${samples.length} ${l.samples}`,\n\t\t\t\tcallback: () => {\n\t\t\t\t\tself.resetInteractions()\n\t\t\t\t\tself.dom.tip.hide()\n\t\t\t\t\tshowTable(self, samples, event.clientX, event.clientY)\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tif (ss) {\n\t\t\toptionArr.push({\n\t\t\t\tlabel: ss.buttonText || `Select ${l.Samples}`,\n\t\t\t\tcallback: async () => {\n\t\t\t\t\tss.callback({\n\t\t\t\t\t\tsamples: await self.app.vocabApi.convertSampleId(samples, ss.attributes),\n\t\t\t\t\t\tsource: `Selected ${l.samples} from OncoMatrix`\n\t\t\t\t\t})\n\t\t\t\t\tself.zoomArea.remove()\n\t\t\t\t\tdelete self.zoomArea\n\t\t\t\t\tdelete self.clickedSeriesCell\n\t\t\t\t}\n\t\t\t})\n\t\t} else {\n\t\t\tif (self.state.nav && self.state.nav.header_mode !== 'hidden') {\n\t\t\t\tfor (const s of samples) {\n\t\t\t\t\tif (!s.sampleId) s.sampleId = s.sample\n\t\t\t\t}\n\t\t\t\toptionArr.push({\n\t\t\t\t\tlabel: 'Add to a group',\n\t\t\t\t\tcallback: async () => {\n\t\t\t\t\t\tself.resetInteractions()\n\t\t\t\t\t\tconst group = {\n\t\t\t\t\t\t\tname: 'Group',\n\t\t\t\t\t\t\titems: samples\n\t\t\t\t\t\t}\n\t\t\t\t\t\tself.addGroup(group)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tself.dom.dendroClickMenu.clear() // close the dendrogram clicking menu when brushing\n\t\tself.dom.clickMenu.clear() // close the matrix cell click menu when brushing\n\t\tself.mouseout()\n\t\tself.dom.tip.hide()\n\t\tself.dom.brushMenu.clear()\n\t\tself.dom.brushMenu.d\n\t\t\t.selectAll('div')\n\t\t\t.data(optionArr)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.style('border-radius', '0px')\n\t\t\t.html(d => d.label)\n\t\t\t.on('click', event => {\n\t\t\t\tself.dom.brushMenu.d.selectAll('*').remove()\n\t\t\t\tevent.target.__data__.callback()\n\t\t\t})\n\t\tself.dom.brushMenu.show(event.clientX, event.clientY)\n\t}\n\n\t// show the list of clicked samples as a table\n\tconst showTable = function (self, samples, x, y) {\n\t\tdelete self.clickedSeriesCell\n\t\tconst templates = self.state.termdbConfig.urlTemplates\n\t\tconst rows = templates?.sample\n\t\t\t? samples.map(c => [{ value: c._ref_.label, url: `${templates.sample.base}${c.sample}` }])\n\t\t\t: samples.map(c => [{ value: c._ref_.label }])\n\n\t\tconst columns = [{ label: self.settings.matrix.controlLabels.Samples }]\n\n\t\tif (!self.dom.sampleListMenu) self.dom.sampleListMenu = new Menu({ padding: '5px' })\n\t\telse self.dom.sampleListMenu.clear()\n\t\tconst div = self.dom.sampleListMenu.d.append('div')\n\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv,\n\t\t\tshowLines: true,\n\t\t\tmaxWidth: columns.length * '30' + 'vw',\n\t\t\tmaxHeight: '35vh',\n\t\t\tresize: true\n\t\t})\n\t\tself.dom.sampleListMenu.show(x, y)\n\t}\n\n\t// add the selected samples into a group\n\tself.addGroup = async function (group) {\n\t\tconst tw = getSamplelstTW([group])\n\t\tconst filter = getFilter(tw)\n\t\taddNewGroup(self.app, filter, self.state.groups)\n\t}\n\tself.triggerZoomArea = function () {\n\t\tif (self.zoomArea) {\n\t\t\tself.zoomArea.remove()\n\t\t\tdelete self.zoomArea\n\t\t}\n\t\tconst c = self.clickedSeriesCell\n\t\tdelete self.clickedSeriesCell\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell\n\t\tconst zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2)\n\t\tconst centerCell = self.sampleOrder[zoomIndex] || self.getImgCell(event)\n\t\tconst colw = self.computedSettings.colw || self.settings.matrix.colw\n\t\tconst maxZoomLevel = s.colwMax / colw\n\t\tconst minZoomLevel = s.colwMin / colw\n\n\t\t// 0.75 is used to add left and right padding to the zoom.\n\t\tconst tentativeZoomLevel = ((s.zoomLevel * d.mainw) / self.zoomWidth) * 0.75\n\t\tconst zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel))\n\t\tconst zoomCenter = centerCell.totalIndex * d.dx + (centerCell.grpIndex - 1) * s.colgspace + d.seriesXoffset\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tmatrix: {\n\t\t\t\t\t\tzoomLevel,\n\t\t\t\t\t\t// try to keep the center of the grey zoom rectangle in the same position before and after zoom\n\t\t\t\t\t\t// this could aslo support mouse scroll zoom in the future.\n\t\t\t\t\t\tzoomCenterPct: zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,\n\t\t\t\t\t\tzoomIndex,\n\t\t\t\t\t\tzoomGrpIndex: centerCell.grpIndex\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tself.resetInteractions()\n\t}\n}\n\nfunction setLengendActions(self) {\n\tself.legendLabelMouseover = event => {\n\t\tconst targetData = event.target.__data__\n\t\tif (\n\t\t\t!targetData ||\n\t\t\ttargetData.dt == dtgeneexpression ||\n\t\t\ttargetData.dt == dtmetaboliteintensity ||\n\t\t\ttargetData.dt == dtproteomeabundance\n\t\t) {\n\t\t\t// for gene expression don't use legend as filter\n\t\t\treturn\n\t\t}\n\t\tif (!targetData.isLegendItem && !targetData.dt) {\n\t\t\t// do not change color when its a non-genevariant legend group name\n\t\t\treturn\n\t\t}\n\t\tconst legendGrpHidden =\n\t\t\tself.config.legendGrpFilter.lst.find(\n\t\t\t\tf => f.dt?.includes(targetData.dt) && (!f.origin || f.origin == targetData.origin)\n\t\t\t) && true\n\t\tif (targetData.isLegendItem && legendGrpHidden) {\n\t\t\t// when the legend's group is hidden\n\t\t\treturn\n\t\t}\n\t\tconst term = self.termOrder.find(t => t.tw.$id == targetData.$id)\n\t\tif (term?.tw?.q?.type == 'predefined-groupset' || term?.tw?.q?.type == 'custom-groupset') {\n\t\t\t// when the term has customized groupsetting\n\t\t\treturn\n\t\t}\n\t\tif (event.target.nodeName == 'rect') select(event.target).style('cursor', 'pointer')\n\t\telse select(event.target).style('fill', 'blue').style('cursor', 'pointer')\n\t}\n\n\tself.legendLabelMouseout = event => {\n\t\t// Commenting out for reference. Borders for mouse events are not desired.\n\t\t// if (event.target.nodeName == 'rect') select(event.target).style('stroke', '#aaa')\n\t\t// else\n\t\tselect(event.target).style('fill', '')\n\t}\n\n\tself.legendLabelMouseup = event => {\n\t\tconst targetData = event.target.__data__\n\t\tif (\n\t\t\t!targetData ||\n\t\t\ttargetData.dt == dtgeneexpression ||\n\t\t\ttargetData.dt == dtmetaboliteintensity ||\n\t\t\ttargetData.dt == dtproteomeabundance\n\t\t) {\n\t\t\t// for gene expression don't use legend as filter\n\t\t\treturn\n\t\t}\n\t\tif (event.target.className.baseVal.includes('sjpp-color-scale') && targetData.dt == dtcnv) {\n\t\t\t/** Changing the cnv cutoffs are enabled from the clickable color scale menu.\n\t\t\t * Disable creating the standard matrix menu from clicking the color scale.*/\n\t\t\treturn\n\t\t}\n\t\tconst byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin\n\t\tconst menuGrp = self.dom.legendMenu.clear()\n\n\t\t// When clicking a legend group name\n\t\tif (!targetData.isLegendItem) {\n\t\t\tif (!targetData.dt) {\n\t\t\t\t// do not use as filter when its a non-genevariant legend group name\n\t\t\t\t// or when its a genevariant legend group name for hierCluster\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t//legendGrpFilterIndex is the index of the filter that is already in self.config.legendGrpFilter.lst\n\t\t\tconst legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(\n\t\t\t\tf =>\n\t\t\t\t\tf.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() &&\n\t\t\t\t\t(!byOrigin || f.origin == targetData.origin)\n\t\t\t)\n\n\t\t\t//legendFilterIndex is the index of the first filter (in this filter group being clicked) that is already in self.config.legendValueFilter.lst, if there's any\n\t\t\tconst legendFilterIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\tl =>\n\t\t\t\t\tl.legendGrpName == targetData.name &&\n\t\t\t\t\tl.tvs.values.find(v => targetData.dt.includes(v.dt) && (!byOrigin || v.origin == targetData.origin))\n\t\t\t)\n\t\t\tconst div = menuGrp.d.append('div')\n\n\t\t\t// when the legend group is not hidden\n\t\t\tif (legendGrpFilterIndex == -1) {\n\t\t\t\t// for consequences/mutations legend group\n\t\t\t\tif (targetData.dt.includes(dtsnvindel)) {\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text(`Show only truncating mutations`)\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tshowOnlyTrunc(menuGrp, targetData, self)\n\t\t\t\t\t\t})\n\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text(`Show only protein-changing mutations`)\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tshowOnlyPC(menuGrp, targetData, self)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tconst onlyGeneGroupShown =\n\t\t\t\t\tself.legendData.filter(\n\t\t\t\t\t\tl =>\n\t\t\t\t\t\t\tl.dt && !l.crossedOut && (l.name == targetData.name || l.items.find(i => !i.greyedOut && !i.crossedOut))\n\t\t\t\t\t).length <= 1\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr(\n\t\t\t\t\t\t'class',\n\t\t\t\t\t\tonlyGeneGroupShown ? 'sja_menuoption_not_interactive sja_sharp_border' : 'sja_menuoption sja_sharp_border'\n\t\t\t\t\t)\n\t\t\t\t\t.text(`Do not show ${targetData.name}`)\n\t\t\t\t\t.style('opacity', onlyGeneGroupShown ? '0.5' : '1')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (!onlyGeneGroupShown) showNone(menuGrp, targetData, self)\n\t\t\t\t\t})\n\t\t\t}\n\t\t\t// when the legend group is hidden or when a legend filter belongs to the legend group exist in legendValueFilter, show the \"show all\" option\n\t\t\tif (legendGrpFilterIndex !== -1 || legendFilterIndex !== -1) {\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text(`Show all ${targetData.name}`)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tshowAll(menuGrp, targetData, self)\n\t\t\t\t\t})\n\t\t\t}\n\n\t\t\t// // adding the option to specify criteria for a CNV alteration for numeric CNV\n\t\t\t// const cnv =\n\t\t\t// \tObject.keys(self.config.cnvCutoffs).length !== 0\n\t\t\t// \t\t? self.config.cnvCutoffs\n\t\t\t// \t\t: self.state.termdbConfig?.queries?.cnv\n\t\t\t// const keys = Object.keys(cnv)\n\t\t\t// if (\n\t\t\t// \ttargetData.dt.includes(dtcnv) &&\n\t\t\t// \tlegendGrpFilterIndex == -1 &&\n\t\t\t// \t(keys.includes('cnvGainCutoff') || keys.includes('cnvLossCutoff' || keys.includes('cnvMaxLength')))\n\t\t\t// ) {\n\t\t\t// \tconst existingCnvSetDiv = div.select('.cnv-set-div')\n\t\t\t// \tif (!existingCnvSetDiv.empty()) existingCnvSetDiv.remove()\n\n\t\t\t// \tconst cnvSetDiv = div.append('div').classed('cnv-set-div', true)\n\n\t\t\t// \t// render cnv config\n\t\t\t// \tconst arg = {\n\t\t\t// \t\tholder: cnvSetDiv,\n\t\t\t// \t\tcnvGainCutoff: cnv.cnvGainCutoff,\n\t\t\t// \t\tcnvLossCutoff: cnv.cnvLossCutoff,\n\t\t\t// \t\tcnvMaxLength: cnv.cnvMaxLength,\n\t\t\t// \t\tcallback: config => {\n\t\t\t// \t\t\tmenuGrp.hide()\n\t\t\t// \t\t\tself.config.cnvCutoffs = structuredClone(config)\n\t\t\t// \t\t\tfor (const termgroup of self.config.termgroups) {\n\t\t\t// \t\t\t\tfor (const t of termgroup.lst) {\n\t\t\t// \t\t\t\t\tif (t.term.type == 'geneVariant') {\n\t\t\t// \t\t\t\t\t\tt.q.cnvGainCutoff = config.cnvGainCutoff\n\t\t\t// \t\t\t\t\t\tt.q.cnvLossCutoff = config.cnvLossCutoff\n\t\t\t// \t\t\t\t\t\tt.q.cnvMaxLength = config.cnvMaxLength\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\tself.app.dispatch({\n\t\t\t// \t\t\t\ttype: 'plot_edit',\n\t\t\t// \t\t\t\tid: self.id,\n\t\t\t// \t\t\t\tconfig: self.config\n\t\t\t// \t\t\t})\n\t\t\t// \t\t}\n\t\t\t// \t}\n\n\t\t\t// \trenderCnvConfig(arg)\n\t\t\t// }\n\t\t\tmenuGrp.showunder(event.target)\n\t\t\treturn\n\t\t}\n\n\t\t// when clicking a legend item\n\t\tconst legendGrpHidden =\n\t\t\tself.config.legendGrpFilter.lst.find(\n\t\t\t\tf => f.dt?.includes(targetData.dt) && (!f.origin || f.origin == targetData.origin)\n\t\t\t) && true\n\t\tif (targetData.isLegendItem && legendGrpHidden) {\n\t\t\t// when the legend's group is hidden\n\t\t\treturn\n\t\t}\n\n\t\tconst term = self.terms.find(t => t.tw.$id == targetData.$id)\n\t\tif (term?.tw?.q?.type == 'predefined-groupset' || term?.tw?.q?.type == 'custom-groupset') {\n\t\t\t// when the term has customized groupsetting\n\t\t\treturn\n\t\t}\n\t\t//legendFilterIndex is the index of the filter that is already in self.config.legendValueFilter.lst\n\t\t// All the filters in self.config.legendValueFilter.lst is joined by 'and' and for all of them the isnot is true.\n\t\tlet legendFilterIndex\n\t\tif (targetData.dt) {\n\t\t\t// when its geneVariant term\n\t\t\tlegendFilterIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\tl =>\n\t\t\t\t\tl.legendGrpName == targetData.termid &&\n\t\t\t\t\tl.tvs.values.find(\n\t\t\t\t\t\tv =>\n\t\t\t\t\t\t\tv.dt == targetData.dt && (!byOrigin || v.origin == targetData.origin) && v.mclasslst[0] == targetData.key\n\t\t\t\t\t)\n\t\t\t)\n\t\t} else {\n\t\t\t// when its non-geneVariant term\n\t\t\tconst legendTerm = self.termOrder.find(to => to.tw.$id == targetData.$id)?.tw?.term\n\t\t\tif (!legendTerm) {\n\t\t\t\t// legend value filter works for the terms in self.termOrder\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (legendTerm.type == 'categorical' || legendTerm.type == 'survival') {\n\t\t\t\tlegendFilterIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\t\tl => l.legendGrpName == targetData.termid && l.tvs.values.find(v => v.key == targetData.key)\n\t\t\t\t)\n\t\t\t} else if (isNumericTerm(legendTerm)) {\n\t\t\t\tlegendFilterIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\t\tl => l.legendGrpName == targetData.termid && l.tvs.ranges.find(r => r.name == targetData.key)\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t\tconst controlLabels = self.settings.matrix.controlLabels\n\n\t\tconst div = menuGrp.d.append('div')\n\n\t\t/** targetItemData may either be the target or parent data (i.e. the original parent mclass key for a merged\n\t\t * legend item.) */\n\t\tconst addMenuOptions = targetItemData => {\n\t\t\tconst term = self.termOrder.find(t => t.tw.$id == targetItemData.$id)?.tw?.term\n\t\t\t//Add the hard filter option\n\t\t\tif (\n\t\t\t\tterm?.type !== 'termCollection' &&\n\t\t\t\t(!targetItemData.dt || self.type !== 'hierCluster' || legendFilterIndex !== -1)\n\t\t\t) {\n\t\t\t\t// Do not show the hard filter option for hierCluster geneVariant legend items.\n\n\t\t\t\t// ********* TODO  ********\n\t\t\t\t// allow to hard filter geneVariant legend for hierCluster\n\t\t\t\t// ********* TODO  ********\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text(\n\t\t\t\t\t\ttargetItemData.dt\n\t\t\t\t\t\t\t? legendFilterIndex == -1\n\t\t\t\t\t\t\t\t? `Hide ${controlLabels.samples} with ${mclass[targetItemData.key].label}`\n\t\t\t\t\t\t\t\t: `Show ${controlLabels.samples} with ${mclass[targetItemData.key].label}`\n\t\t\t\t\t\t\t: legendFilterIndex == -1\n\t\t\t\t\t\t\t? 'Hide'\n\t\t\t\t\t\t\t: 'Show'\n\t\t\t\t\t)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tmenuGrp.hide()\n\t\t\t\t\t\tif (legendFilterIndex == -1) {\n\t\t\t\t\t\t\t// when its shown and now hide it\n\t\t\t\t\t\t\tif (targetItemData.dt) {\n\t\t\t\t\t\t\t\t// for a geneVariant term\n\t\t\t\t\t\t\t\t// add a new \"hard filter\" to filter out samples that have genes' values match with the legend's origin + legend's dt + legend's class\n\t\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\t\tlegendFilterType: 'geneVariant_hard', // indicates this matrix legend filter is hard filter\n\t\t\t\t\t\t\t\t\t\tterm: { type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\t\tdt: targetItemData.dt,\n\t\t\t\t\t\t\t\t\t\t\t\torigin: targetItemData.origin,\n\t\t\t\t\t\t\t\t\t\t\t\tmclasslst: [targetItemData.key]\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t// for a non-geneVariant term\n\t\t\t\t\t\t\t\tconst term = self.termOrder.find(t => t.tw.$id == targetItemData.$id).tw.term\n\t\t\t\t\t\t\t\tif (term.type == 'categorical' || term.type == 'survival') {\n\t\t\t\t\t\t\t\t\tterm.$id = targetItemData.$id\n\t\t\t\t\t\t\t\t\tconst filterGrpIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\t\t\t\t\t\t\tl => l.legendGrpName == targetItemData.termid\n\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\tif (filterGrpIndex == -1) {\n\t\t\t\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\t\t\t\tterm,\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: targetItemData.key }]\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\t// the filter for the categorical or survival term exist, but the current legend key is not there.\n\t\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst[filterGrpIndex].tvs.values.push({ key: targetItemData.key })\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t} else if (isNumericTerm(term)) {\n\t\t\t\t\t\t\t\t\tterm.$id = targetItemData.$id\n\t\t\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\t\t\tterm,\n\t\t\t\t\t\t\t\t\t\t\tranges: [self.data.refs.byTermId[targetItemData.$id].bins.find(b => targetItemData.key == b.name)]\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// when the legend is crossed-out, either by clicking hide or by clicking another legend and show-only,\n\t\t\t\t\t\t\t// A filter to filter out the legend's dt + legend's class exist in self.config.legendValueFilter\n\t\t\t\t\t\t\t// So remove the filter that filters out the legend's dt + legend's class\n\t\t\t\t\t\t\tif (targetItemData.dt) self.config.legendValueFilter.lst.splice(legendFilterIndex, 1)\n\t\t\t\t\t\t\telse {\n\t\t\t\t\t\t\t\tconst term = self.termOrder.find(t => t.tw.$id == targetItemData.$id).tw.term\n\t\t\t\t\t\t\t\tif (term.type == 'categorical' || term.type == 'survival') {\n\t\t\t\t\t\t\t\t\tconst filterGrpIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\t\t\t\t\t\t\tl => l.legendGrpName == targetItemData.termid\n\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\tconst filterIndex = self.config.legendValueFilter.lst[filterGrpIndex].tvs.values.findIndex(\n\t\t\t\t\t\t\t\t\t\tv => v.key == targetItemData.key\n\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst[filterGrpIndex].tvs.values.splice(filterIndex, 1)\n\t\t\t\t\t\t\t\t} else self.config.legendValueFilter.lst.splice(legendFilterIndex, 1)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== 'hierCluster') {\n\t\t\t\t\t\t\tif (targetItemData.dt == dtsnvindel) {\n\t\t\t\t\t\t\t\tself.config.settings.matrix.showMatrixMutation = 'bySelection'\n\t\t\t\t\t\t\t\tconst cl = self.settings.matrix.controlLabels\n\t\t\t\t\t\t\t\tif (\n\t\t\t\t\t\t\t\t\tself.legendData.find(l => l.name == cl.Mutations)?.items?.length ==\n\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.filter(l => l.legendGrpName == cl.Mutations)?.length\n\t\t\t\t\t\t\t\t) {\n\t\t\t\t\t\t\t\t\t//when all mutation items are hidden by applying legend value filter\n\t\t\t\t\t\t\t\t\tself.config.settings.matrix.allMatrixMutationHidden = true\n\t\t\t\t\t\t\t\t} else self.config.settings.matrix.allMatrixMutationHidden = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tif (targetItemData.dt == dtcnv) {\n\t\t\t\t\t\t\t\tself.config.settings.matrix.showMatrixCNV = 'bySelection'\n\t\t\t\t\t\t\t\tif (\n\t\t\t\t\t\t\t\t\tself.legendData.find(l => l.name == 'CNV')?.items?.length ==\n\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.filter(l => l.legendGrpName == 'CNV')?.length\n\t\t\t\t\t\t\t\t) {\n\t\t\t\t\t\t\t\t\t//when all CNV items are hidden by applying legend value filter\n\t\t\t\t\t\t\t\t\tself.config.settings.matrix.allMatrixCNVHidden = true\n\t\t\t\t\t\t\t\t\tif (self.config.settings.matrix.cellEncoding == 'oncoprint')\n\t\t\t\t\t\t\t\t\t\tself.config.settings.matrix.cellEncoding = 'single'\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\tself.config.settings.matrix.allMatrixCNVHidden = false\n\t\t\t\t\t\t\t\t\tif (self.config.settings.matrix.cellEncoding !== '')\n\t\t\t\t\t\t\t\t\t\tself.config.settings.matrix.cellEncoding = 'oncoprint'\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\n\t\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\t\tconfig: self.config\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\n\t\t\tif (targetItemData.isLegendItem) {\n\t\t\t\t// Add the soft filter option only for the not already hidden geneVariant legend\n\t\t\t\tif (targetItemData.dt && legendFilterIndex == -1 && term?.type !== 'termCollection') {\n\t\t\t\t\t// only when filtering a not already hidden geneVariant legend, show the soft filter\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text(`Do not show ${mclass[targetItemData.key]?.label}`)\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tmenuGrp.hide()\n\t\t\t\t\t\t\t// add a new \"soft filter\" to filter out the legend's origin + legend's dt + legend's class\n\t\t\t\t\t\t\t// add a new \"soft filter\" to filter out samples that only have mutation match with (the legend's origin + legend's dt + legend's class) and no other mutation\n\t\t\t\t\t\t\t// and then hide the selected mutation on samples that have this selected mutation if the sample was not filtered out by this soft filter.\n\n\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\tlegendFilterType: 'geneVariant_soft', // indicates this matrix legend filter is soft filter\n\t\t\t\t\t\t\t\t\tterm: { type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\tvalues: [{ dt: targetItemData.dt, origin: targetItemData.origin, mclasslst: [targetItemData.key] }]\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\n\t\t\t\t\t\t\tif (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== 'hierCluster') {\n\t\t\t\t\t\t\t\tif (targetItemData.dt == dtsnvindel) {\n\t\t\t\t\t\t\t\t\tself.config.settings.matrix.showMatrixMutation = 'bySelection'\n\t\t\t\t\t\t\t\t\tconst cl = self.settings.matrix.controlLabels\n\t\t\t\t\t\t\t\t\tif (\n\t\t\t\t\t\t\t\t\t\tself.legendData.find(l => l.name == cl.Mutations)?.items?.length ==\n\t\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.filter(l => l.legendGrpName == cl.Mutations)?.length\n\t\t\t\t\t\t\t\t\t) {\n\t\t\t\t\t\t\t\t\t\t//when all mutation items are hidden by applying legend value filter\n\t\t\t\t\t\t\t\t\t\tself.config.settings.matrix.allMatrixMutationHidden = true\n\t\t\t\t\t\t\t\t\t} else self.config.settings.matrix.allMatrixMutationHidden = false\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (targetItemData.dt == dtcnv) {\n\t\t\t\t\t\t\t\t\tself.config.settings.matrix.showMatrixCNV = 'bySelection'\n\t\t\t\t\t\t\t\t\tif (\n\t\t\t\t\t\t\t\t\t\tself.legendData.find(l => l.name == 'CNV')?.items?.length ==\n\t\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.filter(l => l.legendGrpName == 'CNV')?.length\n\t\t\t\t\t\t\t\t\t) {\n\t\t\t\t\t\t\t\t\t\t//when all CNV items are hidden by applying legend value filter\n\t\t\t\t\t\t\t\t\t\tself.config.settings.matrix.allMatrixCNVHidden = true\n\t\t\t\t\t\t\t\t\t\tif (self.config.settings.matrix.cellEncoding == 'oncoprint')\n\t\t\t\t\t\t\t\t\t\t\tself.config.settings.matrix.cellEncoding = 'single'\n\t\t\t\t\t\t\t\t\t} else self.config.settings.matrix.allMatrixCNVHidden = false\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\t\t\tconfig: self.config\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\t//Add the show only option only for non-genevariant legend\n\t\t\t\tif (!targetItemData.dt && term?.type !== 'termCollection') {\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text('Show only')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tmenuGrp.hide()\n\t\t\t\t\t\t\tconst term = self.termOrder.find(t => t.tw.$id == targetItemData.$id)?.tw?.term\n\t\t\t\t\t\t\tconst legendGrp =\n\t\t\t\t\t\t\t\tself.legendData.find(lg => lg.name == targetItemData.termid) ||\n\t\t\t\t\t\t\t\tself.legendData.find(lg => lg.$id == targetItemData.$id)\n\n\t\t\t\t\t\t\t// reset self.config.legendValueFilter.lst to remove all the filters in the lst that's in the same legendGrp\n\t\t\t\t\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\t\t\t\t\tl => l.legendGrpName !== targetItemData.termid\n\t\t\t\t\t\t\t)\n\n\t\t\t\t\t\t\t/*\n\t\t\t\t\t\tif (targetItemData.dt) {\n\t\t\t\t\t\t\t// for a geneVariant term\n\t\t\t\t\t\t\tfor (const l of legendGrp.items) {\n\t\t\t\t\t\t\t\tif (l.dt == targetItemData.dt && (l.origin ? l.origin == targetItemData.origin : true) && l.key == targetItemData.key)\n\t\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\t\tlegendFilterType: 'geneVariant_soft', // indicates this matrix legend filter is soft filter\n\t\t\t\t\t\t\t\t\t\tterm: { type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\tvalues: [{ dt: l.dt, origin: l.origin, mclasslst: [l.key] }]\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (!self.config.legendValueFilter.lst.length) self.config.legendValueFilter.lst = [filterNew]\n\t\t\t\t\t\t\t\telse self.config.legendValueFilter.lst.push(filterNew)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tconst term = self.termOrder.find(t => t.tw.$id == targetItemData.$id).tw.term\n\t\t\t\t\t\t*/\n\n\t\t\t\t\t\t\t// for a non-geneVariant term\n\t\t\t\t\t\t\tif (term.type == 'categorical' || term.type == 'survival') {\n\t\t\t\t\t\t\t\tterm.$id = targetItemData.$id\n\t\t\t\t\t\t\t\tfor (const l of legendGrp.items) {\n\t\t\t\t\t\t\t\t\tif (l.key == targetItemData.key) continue\n\t\t\t\t\t\t\t\t\tconst filterGrpIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\t\t\t\t\t\t\t\tl => l.legendGrpName == targetItemData.termid\n\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\tif (filterGrpIndex == -1) {\n\t\t\t\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\t\t\t\tterm,\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: l.key }]\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\tself.config.legendValueFilter.lst[filterGrpIndex].tvs.values.push({ key: l.key })\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t} else if (isNumericTerm(term)) {\n\t\t\t\t\t\t\t\tterm.$id = targetItemData.$id\n\t\t\t\t\t\t\t\tfor (const l of legendGrp.items) {\n\t\t\t\t\t\t\t\t\tif (l.key == targetItemData.key) continue\n\t\t\t\t\t\t\t\t\tconst filterNew = {\n\t\t\t\t\t\t\t\t\t\tlegendGrpName: targetItemData.termid,\n\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\t\t\t\t\t\tterm,\n\t\t\t\t\t\t\t\t\t\t\tranges: [self.data.refs.byTermId[targetItemData.$id].bins.find(b => l.key == b.name)]\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tif (!self.config.legendValueFilter.lst.length) self.config.legendValueFilter.lst = [filterNew]\n\t\t\t\t\t\t\t\t\telse self.config.legendValueFilter.lst.push(filterNew)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\t\t\tconfig: self.config\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\t//Add the show all option only for non-genevariant legend\n\t\t\t\tif (!targetItemData.dt && term?.type !== 'termCollection') {\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text('Show all')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tmenuGrp.hide()\n\t\t\t\t\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\t\t\t\t\tl => l.legendGrpName !== targetItemData.termid\n\t\t\t\t\t\t\t)\n\n\t\t\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\t\t\tconfig: self.config\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\t// adding the change color option\n\t\t\t\tif (!targetData.domain) {\n\t\t\t\t\tdiv.append('span').text('Color').style('padding', '5px 10px').style('margin', '1px')\n\t\t\t\t\tself.dom.legendColorInput = div\n\t\t\t\t\t\t.append('input')\n\t\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t\t.attr('aria-label', `change the bar color`)\n\t\t\t\t\t\t.attr('value', targetData.color?.startsWith('rgb') ? rgb2hex(targetData.color) : targetData.color)\n\t\t\t\t\t\t.on('change', async () => {\n\t\t\t\t\t\t\tmenuGrp.hide()\n\t\t\t\t\t\t\tconst color = self.dom.legendColorInput.node().value\n\t\t\t\t\t\t\tif (targetData.dt) {\n\t\t\t\t\t\t\t\tif (!mclass[targetData.key].origColor) mclass[targetData.key].origColor = mclass[targetData.key].color\n\t\t\t\t\t\t\t\tmclass[targetData.key].color = color\n\t\t\t\t\t\t\t\tself.main()\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\t\t\t\t\t\tif (!twSpecificSettings[targetData.$id]) twSpecificSettings[targetData.$id] = {}\n\t\t\t\t\t\t\tconst twSettings = twSpecificSettings[targetData.$id]\n\n\t\t\t\t\t\t\tif (!twSettings[targetData.key]) twSettings[targetData.key] = {}\n\t\t\t\t\t\t\ttwSettings[targetData.key].color = color\n\n\t\t\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\t\tid: self.opts.id,\n\t\t\t\t\t\t\t\tconfig: { settings: { matrix: { twSpecificSettings } } }\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t\tif (targetData.dt && mclass[targetData.key].origColor) {\n\t\t\t\t\t\tconst resetDiv = div.append('div').style('display', 'inline-block')\n\t\t\t\t\t\tconst handler = () => {\n\t\t\t\t\t\t\tmenuGrp.hide()\n\t\t\t\t\t\t\tmclass[targetData.key].color = mclass[targetData.key].origColor\n\t\t\t\t\t\t\tdelete mclass[targetData.key].origColor\n\t\t\t\t\t\t\tself.main()\n\t\t\t\t\t\t}\n\t\t\t\t\t\ticons['restart'](resetDiv, { handler, title: 'Reset to original color' })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tmenuGrp.showunder(event.target)\n\t\t\t}\n\t\t}\n\t\tif (targetData.parents) {\n\t\t\tfor (const p of targetData.parents) {\n\t\t\t\taddMenuOptions(p)\n\t\t\t}\n\t\t} else {\n\t\t\taddMenuOptions(targetData)\n\t\t}\n\t}\n}\n\nfunction setMutationSelectionActions(self) {\n\tself.mutationSelectionActions = {\n\t\tonlyTruncating: showOnlyTrunc,\n\t\tonlyPC: showOnlyPC,\n\t\tnone: showNone,\n\t\tall: showAll,\n\t\tbySelection: showByLegendFilter\n\t}\n\tself.mutationControlCallback = mutationSelection => {\n\t\tconst menuGrp = self.dom.legendMenu.clear()\n\t\tconst targetData = self.legendData.find(l => l.dt?.includes(dtsnvindel))\n\t\tself.mutationSelectionActions[mutationSelection](menuGrp, targetData, self, 'mutation')\n\t}\n\tself.CNVControlCallback = CNVSelection => {\n\t\tconst menuGrp = self.dom.legendMenu.clear()\n\t\tconst targetData = self.legendData.find(l => l.dt?.includes(dtcnv))\n\t\tself.mutationSelectionActions[CNVSelection](menuGrp, targetData, self, 'CNV')\n\t}\n\n\tself.geneStyleControlCallback = styleSelection => {\n\t\tconst targetData = self.legendData.find(l => l.dt?.includes(dtcnv))\n\t\tif (styleSelection == '') showStackedStyle(targetData, self) //stacked style\n\t\telse if (styleSelection == 'single') showSingleStyle(targetData, self)\n\t\telse if (styleSelection == 'oncoprint') showOncoprintStyle(targetData, self)\n\t}\n}\n\nfunction showSingleStyle(targetData, self) {\n\tif (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== 'hierCluster') {\n\t\tif (targetData) {\n\t\t\t// there are CNV data\n\t\t\tconst byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin\n\n\t\t\t//legendGrpFilterIndex is the index of the filter that is already in self.config.legendGrpFilter.lst\n\t\t\tconst legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(\n\t\t\t\tf =>\n\t\t\t\t\tf.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() &&\n\t\t\t\t\t(!byOrigin || f.origin == targetData.origin)\n\t\t\t)\n\t\t\tif (legendGrpFilterIndex == -1) {\n\t\t\t\t// when the legend group is shown and now hide it\n\t\t\t\t// add a new \"legend group filter\" to filter out the legend group's origin + legend group's dt\n\t\t\t\tconst filterNew = { dt: targetData.dt }\n\t\t\t\tif (byOrigin) {\n\t\t\t\t\t// when distinguish between germline and somatic for the dt\n\t\t\t\t\tfilterNew.origin = targetData.origin\n\t\t\t\t}\n\t\t\t\t// when the legend group is hidden, need to remove the individual legend filter belongs to this legend group\n\t\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\t\tf => f.legendGrpName !== targetData.name\n\t\t\t\t)\n\t\t\t\tself.config.legendGrpFilter.lst.push(filterNew)\n\t\t\t}\n\t\t}\n\t\tself.config.settings.matrix.cellEncoding = 'single'\n\t}\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: self.config\n\t})\n}\n\nfunction showOncoprintStyle(targetData, self) {\n\tif (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== 'hierCluster') {\n\t\tif (targetData) {\n\t\t\t// there are CNV data\n\t\t\tconst byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin\n\n\t\t\t//legendGrpFilterIndex is the index of the filter that is already in self.config.legendGrpFilter.lst\n\t\t\tconst legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(\n\t\t\t\tf =>\n\t\t\t\t\tf.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() &&\n\t\t\t\t\t(!byOrigin || f.origin == targetData.origin)\n\t\t\t)\n\t\t\tif (legendGrpFilterIndex !== -1) self.config.legendGrpFilter.lst.splice(legendGrpFilterIndex, 1)\n\t\t\t// when changing to oncoPrint, need to remove the CNV legend filters\n\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\tf => f.legendGrpName !== targetData.name\n\t\t\t)\n\t\t}\n\t\tself.config.settings.matrix.showMatrixCNV = 'all'\n\t\tself.config.settings.matrix.allMatrixCNVHidden = false\n\t}\n\tself.config.settings.matrix.cellEncoding = 'oncoprint'\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: self.config\n\t})\n}\n\nfunction showStackedStyle(targetData, self) {\n\tif (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== 'hierCluster') {\n\t\tif (targetData) {\n\t\t\t// there are CNV data\n\t\t\tconst byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin\n\n\t\t\t//legendGrpFilterIndex is the index of the filter that is already in self.config.legendGrpFilter.lst\n\t\t\tconst legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(\n\t\t\t\tf =>\n\t\t\t\t\tf.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() &&\n\t\t\t\t\t(!byOrigin || f.origin == targetData.origin)\n\t\t\t)\n\t\t\tif (legendGrpFilterIndex !== -1) self.config.legendGrpFilter.lst.splice(legendGrpFilterIndex, 1)\n\t\t\t// when changing to oncoPrint, need to remove the CNV legend filters\n\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\tf => f.legendGrpName !== targetData.name\n\t\t\t)\n\t\t}\n\t}\n\n\tself.config.settings.matrix.cellEncoding = ''\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: self.config\n\t})\n}\n\nfunction showOnlyTrunc(menuGrp, targetData, self) {\n\tmenuGrp.hide()\n\t// when the legend group is not hidden and show a \"show only the truncating mutations\" option\n\t// add a new \"soft legend filter\" to for all the legends in the legend group whose mclass\n\t// is not in the truncatingM\n\n\tif (targetData) {\n\t\t// there are mutations data\n\t\t//remove the individual legend filter in the group\n\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\tf => f.legendGrpName !== targetData.name\n\t\t)\n\n\t\t// remove the grp legend filter for the group\n\t\tself.config.legendGrpFilter.lst = self.config.legendGrpFilter.lst.filter(\n\t\t\tf => !(f.dt.includes(dtsnvindel) && f.origin == targetData.origin)\n\t\t)\n\n\t\tconst truncatingM = self.config.settings.matrix.truncatingMutations\n\t\tconst controlLabels = self.config.settings.matrix.controlLabels\n\t\tfor (const [k, v] of Object.entries(mclass)) {\n\t\t\tif (truncatingM.includes(k) || v.dt != dtsnvindel) continue\n\t\t\tconst filterNew = {\n\t\t\t\tlegendGrpName: targetData.origin\n\t\t\t\t\t? `${targetData.origin[0].toUpperCase() + targetData.origin.slice(1)} ${controlLabels.Mutations}`\n\t\t\t\t\t: controlLabels.Mutations,\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: {\n\t\t\t\t\tisnot: true,\n\t\t\t\t\tlegendFilterType: 'geneVariant_soft',\n\t\t\t\t\tterm: { type: 'geneVariant' },\n\t\t\t\t\tvalues: [{ dt: dtsnvindel, origin: targetData.origin, mclasslst: [k] }]\n\t\t\t\t}\n\t\t\t}\n\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t}\n\t}\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: self.config\n\t})\n}\n\nfunction showOnlyPC(menuGrp, targetData, self) {\n\tmenuGrp.hide()\n\t// when the legend group is not hidden and show a \"show only non-truncating protein-changing mutations\" option\n\t// add a new \"soft legend filter\" for all the legends in the legend group (origin + dt) whose mclass\n\t// is not in the nonTruncatingPCM\n\n\tif (targetData) {\n\t\t// there are mutations data\n\t\t//remove the individual legend filter in the group\n\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\tf => f.legendGrpName !== targetData.name\n\t\t)\n\n\t\t// remove the grp legend filter for the group\n\t\tself.config.legendGrpFilter.lst = self.config.legendGrpFilter.lst.filter(\n\t\t\tf => !(f.dt.includes(dtsnvindel) && f.origin == targetData.origin)\n\t\t)\n\n\t\tconst proteinChangingMutations = self.config.settings.matrix.proteinChangingMutations\n\t\tconst controlLabels = self.config.settings.matrix.controlLabels\n\t\tfor (const [k, v] of Object.entries(mclass)) {\n\t\t\tif (proteinChangingMutations.includes(k) || v.dt != dtsnvindel) continue\n\t\t\tconst filterNew = {\n\t\t\t\tlegendGrpName: targetData.origin\n\t\t\t\t\t? `${targetData.origin[0].toUpperCase() + targetData.origin.slice(1)} ${controlLabels.Mutations}`\n\t\t\t\t\t: controlLabels.Mutations,\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: {\n\t\t\t\t\tisnot: true,\n\t\t\t\t\tlegendFilterType: 'geneVariant_soft',\n\t\t\t\t\tterm: { type: 'geneVariant' },\n\t\t\t\t\tvalues: [{ dt: dtsnvindel, origin: targetData.origin, mclasslst: [k] }]\n\t\t\t\t}\n\t\t\t}\n\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t}\n\t}\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: self.config\n\t})\n}\n\nfunction showNone(menuGrp, targetData, self, target) {\n\tmenuGrp.hide()\n\tif (targetData) {\n\t\t// there are data\n\t\tconst byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin\n\t\t// when the legend group is shown and now hide it\n\t\t// add a new \"legend group filter\" to filter out the legend group's origin + legend group's dt\n\n\t\t//legendGrpFilterIndex is the index of the filter that is already in self.config.legendGrpFilter.lst\n\t\tconst legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(\n\t\t\tf =>\n\t\t\t\tf.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() &&\n\t\t\t\t(!byOrigin || f.origin == targetData.origin)\n\t\t)\n\t\tif (legendGrpFilterIndex == -1) {\n\t\t\tconst filterNew = { dt: targetData.dt }\n\t\t\tif (byOrigin) {\n\t\t\t\t// when distinguish between germline and somatic for the dt\n\t\t\t\tfilterNew.origin = targetData.origin\n\t\t\t}\n\t\t\t// when the legend group is hidden, need to remove the individual legend filter belongs to this legend group\n\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\tf => f.legendGrpName !== targetData.name\n\t\t\t)\n\t\t\tself.config.legendGrpFilter.lst.push(filterNew)\n\t\t}\n\t}\n\n\tif (\n\t\tself.state.config.settings.matrix.addMutationCNVButtons &&\n\t\tself.chartType !== 'hierCluster' &&\n\t\t(target == 'CNV' || targetData?.dt?.includes(dtcnv)) &&\n\t\tself.config.settings.matrix.cellEncoding == 'oncoprint'\n\t) {\n\t\tself.config.settings.matrix.cellEncoding = 'single'\n\t}\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: self.config\n\t})\n}\n\nexport function getConfigForShowAll(self, targetData, target) {\n\tif (targetData) {\n\t\t// there are  data\n\t\tconst byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin\n\n\t\t//legendGrpFilterIndex is the index of the filter that is already in self.config.legendGrpFilter.lst\n\t\tconst legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(\n\t\t\tf =>\n\t\t\t\tf.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() &&\n\t\t\t\t(!byOrigin || f.origin == targetData.origin)\n\t\t)\n\n\t\t//legendFilterIndex is the index of the first filter (in this filter group being clicked) that is already in self.config.legendValueFilter.lst, if there's any\n\t\tconst legendFilterIndex = self.config.legendValueFilter.lst.findIndex(\n\t\t\tl =>\n\t\t\t\tl.legendGrpName == targetData.name &&\n\t\t\t\tl.tvs.values.find(v => targetData.dt.includes(v.dt) && (!byOrigin || v.origin == targetData.origin))\n\t\t)\n\n\t\tif (legendGrpFilterIndex !== -1) self.config.legendGrpFilter.lst.splice(legendGrpFilterIndex, 1)\n\t\tif (legendFilterIndex !== -1)\n\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\tf => f.legendGrpName != targetData.name\n\t\t\t)\n\t}\n\n\tconst s = self.config.settings.matrix\n\tif (\n\t\ts.addMutationCNVButtons &&\n\t\tself.chartType !== 'hierCluster' &&\n\t\t(target == 'CNV' || targetData?.dt?.includes(dtcnv)) &&\n\t\ts.cellEncoding !== ''\n\t) {\n\t\ts.cellEncoding = 'oncoprint'\n\t}\n\n\treturn self.config\n}\n\nexport function showAll(menuGrp, targetData, self, target) {\n\tmenuGrp.hide()\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: getConfigForShowAll(self, targetData, target)\n\t})\n}\n\nfunction showByLegendFilter(menuGrp, targetData, self, target) {\n\tmenuGrp.hide()\n\tconst s = self.config.settings.matrix\n\tif (!targetData) {\n\t\t//there are no mutatons data\n\t\tif (s.addMutationCNVButtons && self.chartType !== 'hierCluster' && target == 'mutation') {\n\t\t\ts.showMatrixMutation = 'bySelection'\n\t\t} else if (s.addMutationCNVButtons && self.chartType !== 'hierCluster' && target == 'CNV') {\n\t\t\ts.showMatrixCNV = 'bySelection'\n\t\t}\n\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: self.config\n\t\t})\n\t\treturn\n\t}\n\tself.app.tip.d.selectAll('.byLFClassDiv').remove()\n\tconst classDiv = self.app.tip.d.append('div').attr('class', 'byLFClassDiv')\n\n\tconst checkboxName = Math.random().toString()\n\tconst mClassDiv = classDiv\n\t\t.selectAll(':scope>div')\n\t\t.data(target == 'mutation' ? s.mutationClasses : s.CNVClasses)\n\t\t.enter()\n\t\t.append('label')\n\t\t.style('margin', '5px')\n\t\t.style('margin-left', '30px')\n\t\t.style('display', 'block')\n\t\t.each(function (d) {\n\t\t\tconst mclassDisabled = self.config.legendValueFilter.lst.find(\n\t\t\t\tf =>\n\t\t\t\t\tf.tvs.legendFilterType == 'geneVariant_hard' &&\n\t\t\t\t\tf.tvs.values[0].dt == mclass[d].dt &&\n\t\t\t\t\tf.tvs.values[0].mclasslst.includes(d)\n\t\t\t)\n\t\t\tconst mclassHidden = target == 'mutation' ? s.hiddenMutations.includes(d) : s.hiddenCNVs.includes(d)\n\n\t\t\tconst oneClassDiv = select(this).attr('class', 'sjpp_row_wrapper')\n\t\t\toneClassDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.attr('name', checkboxName)\n\t\t\t\t.property('disabled', mclassDisabled ? true : false)\n\t\t\t\t.property('checked', mclassDisabled || mclassHidden ? false : true)\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('margin-right', '3px')\n\t\t\t\t.on('change', function () {\n\t\t\t\t\tconst anyChecked = mClassDiv.selectAll(`input[type='checkbox'][name='${checkboxName}']:checked`).empty()\n\t\t\t\t\tapplyBtn.property('disabled', anyChecked)\n\t\t\t\t})\n\t\t\toneClassDiv\n\t\t\t\t.append('span')\n\t\t\t\t.style('margin-left', '3px')\n\t\t\t\t.html(mclass[d].label)\n\t\t\t\t//.style('color', d.color)\n\t\t\t\t.style('text-decoration', mclassDisabled ? 'line-through' : '')\n\t\t})\n\n\tconst applyBtn = classDiv\n\t\t.append('button')\n\t\t.property('disabled', true)\n\t\t.style('margin-top', '3px')\n\t\t.text('Apply')\n\t\t.on('click', () => {\n\t\t\tconst checkedCheckboxes = mClassDiv.selectAll(`input[type='checkbox'][name='${checkboxName}']:checked`)\n\t\t\tconst checkedItems = checkedCheckboxes.nodes().map(c => select(c).datum())\n\t\t\tmenuGrp.hide()\n\n\t\t\t//remove the individual legend filter in the group\n\t\t\tself.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(\n\t\t\t\tf => f.legendGrpName !== targetData.name || f.tvs.legendFilterType == 'geneVariant_hard'\n\t\t\t)\n\n\t\t\t// remove the grp legend filter for the group\n\t\t\tself.config.legendGrpFilter.lst = self.config.legendGrpFilter.lst.filter(\n\t\t\t\tf =>\n\t\t\t\t\t!(\n\t\t\t\t\t\t(f.dt.includes(dtsnvindel) && targetData.dt.includes(dtsnvindel)) ||\n\t\t\t\t\t\t(f.dt.includes(dtcnv) && targetData.dt.includes(dtcnv))\n\t\t\t\t\t)\n\t\t\t)\n\n\t\t\tfor (const item of target == 'mutation' ? s.mutationClasses : s.CNVClasses) {\n\t\t\t\tif (checkedItems.includes(item)) continue\n\t\t\t\t// add a new \"soft filter\" to filter out the legend's origin + legend's dt + legend's class\n\t\t\t\t// add a new \"soft filter\" to filter out samples that only have mutation match with (the legend's origin + legend's dt + legend's class) and no other mutation\n\t\t\t\t// and then hide the selected mutation on samples that have this selected mutation if the sample was not filtered out by this soft filter.\n\t\t\t\tconst filterNew = {\n\t\t\t\t\tlegendGrpName: targetData.name,\n\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\ttvs: {\n\t\t\t\t\t\tisnot: true,\n\t\t\t\t\t\tlegendFilterType: 'geneVariant_soft', // indicates this matrix legend filter is soft filter\n\t\t\t\t\t\tterm: { type: 'geneVariant' },\n\t\t\t\t\t\tvalues: [{ dt: mclass[item].dt, origin: targetData.origin, mclasslst: [item] }]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tself.config.legendValueFilter.lst.push(filterNew)\n\t\t\t}\n\n\t\t\tif (\n\t\t\t\tself.state.config.settings.matrix.addMutationCNVButtons &&\n\t\t\t\tself.chartType !== 'hierCluster' &&\n\t\t\t\t(target == 'CNV' || targetData?.dt?.includes(dtcnv))\n\t\t\t) {\n\t\t\t\tif (checkedItems.length == 0 && self.config.settings.matrix.cellEncoding == 'oncoprint') {\n\t\t\t\t\t//when all CNV items are hidden by applying legend value filter\n\t\t\t\t\tself.config.settings.matrix.cellEncoding = 'single'\n\t\t\t\t} else if (checkedItems.length > 0 && self.config.settings.matrix.cellEncoding == 'single') {\n\t\t\t\t\tself.config.settings.matrix.cellEncoding = 'oncoprint'\n\t\t\t\t}\n\t\t\t}\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: self.config\n\t\t\t})\n\t\t})\n}\n\n//used by self.showCellInfo and self.mouseclick to get appropriate label\nfunction getLabel(c, v, p) {\n\tlet fusionLabel\n\tif (p)\n\t\tfusionLabel =\n\t\t\tp[0].a.name && p[0].b.name\n\t\t\t\t? p[0].a.name + '::' + p[0].b.name\n\t\t\t\t: p[0].a.name\n\t\t\t\t? p[0].a.name + '::' + '?'\n\t\t\t\t: p[0].b.name\n\t\t\t\t? '?' + '::' + p[0].b.name\n\t\t\t\t: ''\n\tconst label =\n\t\tc.t.grp.type == 'hierCluster'\n\t\t\t? v.value\n\t\t\t: v && v.dt == dtcnv && v.value\n\t\t\t? `${mclass[v.class].label} (${v.value.toFixed(2)})`\n\t\t\t: p\n\t\t\t? fusionLabel\n\t\t\t: v.mname\n\t\t\t? `${v.mname} ${mclass[v.class].label}`\n\t\t\t: mclass[v.class].label\n\n\treturn label\n}\n\n// if group value filter is defined, then cannot reliably edit term\n// notify user in edit menu\nfunction mayAddEditMsg(arg, t) {\n\tif (!t.grp.valueFilter) return\n\tconst editMsg =\n\t\t'Cannot edit variable because group value filter is in use.<br>Please add new variable/variable group to enable editing.'\n\targ.editMsg = editMsg\n}\n"],
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