@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-XOBD3EAM.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.controls.js"],
+  "sourcesContent": ["import { initByInput } from '#plots/controls.config.js'\nimport { to_svg } from '#src/client'\nimport { getSorterUi } from './matrix.sorterUi'\nimport { fillTermWrapper, get$id } from '#termsetting'\nimport { Menu, zoom, icons, svgScroll, make_radios, make_one_checkbox, GeneSetEditUI } from '#dom'\nimport { select } from 'd3-selection'\nimport { mclass, dt2label, dtsnvindel, dtcnv, dtfusionrna, dtgeneexpression, dtsv } from '#shared/common.js'\nimport { TermTypes, isNumericTerm } from '#shared/terms.js'\n\nconst tip = new Menu({ padding: '' })\n\nexport class MatrixControls {\n\tconstructor(opts, appState) {\n\t\tthis.type = 'matrixControls'\n\t\tthis.opts = opts\n\t\tthis.parent = opts.parent\n\t\tthis.overrides = {}\n\n\t\tthis.opts.holder.style('margin', '10px 10px 20px 10px').style('white-space', 'nowrap')\n\t\tconst state = this.parent.getState(appState)\n\t\tconst s = state.config.settings.matrix\n\t\tif (this.parent.setClusteringBtn)\n\t\t\tthis.parent.setClusteringBtn(this.opts.holder, (event, data) => this.callback(event, data))\n\t\tthis.setSamplesBtn(s)\n\t\tif (\n\t\t\tstate.termdbConfig?.allowedTermTypes?.includes(TermTypes.GENE_VARIANT) ||\n\t\t\tstate.termdbConfig.queries.snvindel ||\n\t\t\t(this.parent.chartType == 'hierCluster' && this.parent.config.dataType == TermTypes.GENE_EXPRESSION)\n\t\t) {\n\t\t\tthis.setGenesBtn(s)\n\t\t}\n\t\tif (s.addMutationCNVButtons && this.parent.chartType !== 'hierCluster') {\n\t\t\tthis.setMutationBtn()\n\t\t\tthis.setCNVBtn()\n\t\t}\n\t\tthis.setVariablesBtn(s)\n\t\tthis.setDimensionsBtn(s)\n\t\tthis.setLegendBtn(s)\n\t\tthis.setDownloadBtn(s)\n\t\tthis.setZoomInput()\n\t\tthis.setDragToggle({\n\t\t\tholder: this.opts.holder.append('div').style('display', 'inline-block'),\n\t\t\ttarget: this.parent.dom.seriesesG\n\t\t})\n\t\tthis.setSvgScroll(state)\n\n\t\tthis.keyboardNavHandler = async event => {\n\t\t\tif (event.target.tagName == 'BUTTON') this.keyEventTarget = event.target\n\t\t\tif (event.key == 'Escape') {\n\t\t\t\tthis.parent.app.tip.hide()\n\t\t\t} else if (event.key == 'Enter' || event.key == 'ArrowDown') {\n\t\t\t\tconst elems =\n\t\t\t\t\tevent.target.tagName == 'BUTTON'\n\t\t\t\t\t\t? this.parent.app.tip.d.node().querySelectorAll('input, select')\n\t\t\t\t\t\t: event.target.querySelectorAll('input, select')\n\t\t\t\tfor (const elem of elems) {\n\t\t\t\t\tif (elem.checkVisibility?.() || (!elem.checkVisibility && elem.getBoundingClientRect().height)) {\n\t\t\t\t\t\telem.focus()\n\t\t\t\t\t\treturn false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if ((event.key == 'Tab' && event.shiftKey) || event.key == 'Backspace' || event.key == 'ArrowUp') {\n\t\t\t\tthis.keyEventTarget.focus()\n\t\t\t\treturn false\n\t\t\t} //else if (event.keyShift && el)\n\t\t}\n\n\t\tthis.btns = this.opts.holder\n\t\t\t.selectAll(':scope>button')\n\t\t\t.filter(d => d && d.label)\n\t\t\t.on(`keyup.matrix-${this.parent.id}`, this.keyboardNavHandler)\n\t}\n\n\tsetSamplesBtn(s) {\n\t\tconst l = s.controlLabels\n\t\tconst controls = this\n\t\tconst parent = this.parent\n\t\tconst rows = [\n\t\t\t{\n\t\t\t\tlabel: `Maximum # ${l.Samples}`,\n\t\t\t\ttitle: `Limit the number of displayed ${l.samples}`,\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tsettingsKey: 'maxSample',\n\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\treturn plot.chartType == 'hierCluster' ? 'none' : 'table-row'\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Sort ${l.Sample} Groups`,\n\t\t\t\ttitle: `Set how to sort ${l.sample} groups`,\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tsettingsKey: 'sortSampleGrpsBy',\n\t\t\t\toptions: [\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Predefined or Group Name',\n\t\t\t\t\t\tvalue: 'name',\n\t\t\t\t\t\ttitle: `Sort by group name`\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: `${l.Sample} Count`,\n\t\t\t\t\t\tvalue: 'sampleCount',\n\t\t\t\t\t\ttitle: `Sort by the number of samples in the group`\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: `Hits`,\n\t\t\t\t\t\tvalue: 'hits',\n\t\t\t\t\t\ttitle: `Sort by the total number of variants for every ${l.sample} in the group`\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\treturn plot.divideBy && !plot.hierCluster ? 'table-row' : 'none'\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `${l.Sample} Group Label Character Limit`,\n\t\t\t\ttitle: `Truncate the ${l.sample} group label if it exceeds this maximum number of characters`,\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tsettingsKey: 'sampleGrpLabelMaxChars',\n\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\treturn plot.divideBy && !plot.hierCluster ? 'table-row' : 'none'\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `${l.Sample} Label Character Limit`,\n\t\t\t\ttitle: `Truncate the ${l.sample} label if it exceeds this maximum number of characters`,\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tsettingsKey: 'collabelmaxchars'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Toggle sample labels`,\n\t\t\t\ttitle: `Do not automatically show sample labels based on column width`,\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tsettingsKey: 'sampleLabelsToggle',\n\t\t\t\tstyles: { display: 'inline-block' },\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: `Based on column width`, value: 'auto' },\n\t\t\t\t\t{ label: 'Always hide', value: 'hide' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Group ${l.Samples} By`,\n\t\t\t\ttitle: `Select a variable with discrete values to group ${l.samples}`,\n\t\t\t\ttype: 'term',\n\t\t\t\tchartType: 'matrix',\n\t\t\t\tconfigKey: 'divideBy',\n\t\t\t\tvocabApi: this.opts.app.vocabApi,\n\t\t\t\tstate: {\n\t\t\t\t\tvocab: this.opts.vocab\n\t\t\t\t\t//activeCohort: appState.activeCohort\n\t\t\t\t},\n\t\t\t\tprocessInput: async tw => {\n\t\t\t\t\tif (tw?.term && isNumericTerm(tw.term)) {\n\t\t\t\t\t\t// any numeric term should be discrete when used as divideBy term\n\t\t\t\t\t\t// tw is missing when dividedBy term deleted\n\t\t\t\t\t\ttw.q = { ...tw.q, mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t\tif (tw) await fillTermWrapper(tw, this.opts.app.vocabApi)\n\t\t\t\t\treturn tw\n\t\t\t\t},\n\t\t\t\tprocessConfig: config => {\n\t\t\t\t\tif (this.parent.chartType == 'hierCluster' && config['divideBy']) {\n\t\t\t\t\t\tconfig.settings = {\n\t\t\t\t\t\t\thierCluster: {\n\t\t\t\t\t\t\t\tyDendrogramHeight: 0,\n\t\t\t\t\t\t\t\tclusterSamples: false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (this.parent.config.divideBy)\n\t\t\t\t\t\tconfig.legendValueFilter = this.parent.mayRemoveTvsEntry(this.parent.config.divideBy)\n\t\t\t\t},\n\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t// hierCluster hides the groupBy, so no need to consider gene expression term type\n\t\t\t\t\tconst currentGeneNames = this.parent.termOrder\n\t\t\t\t\t\t.filter(t => t.tw.term.type === 'geneVariant')\n\t\t\t\t\t\t.map(t =>\n\t\t\t\t\t\t\tt.tw.term.chr ? `${t.tw.term.chr}:${t.tw.term.start}-${t.tw.term.stop}` : t.tw.term.gene || t.tw.term.name\n\t\t\t\t\t\t) // TODO term.gene replaces term.name\n\t\t\t\t\tif (currentGeneNames.length) return { currentGeneNames }\n\t\t\t\t\treturn {}\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\trows.push({\n\t\t\tlabel: `Sort ${l.Sample} Priority`,\n\t\t\ttitle: `Set how to sort ${l.samples}`,\n\t\t\ttype: 'custom',\n\t\t\t// the \"input\" argument is created by controls\n\t\t\tinit(input) {\n\t\t\t\tconst m = parent.config.settings.matrix\n\t\t\t\tif (!controls.activeTab) controls.activeTab = 'basic'\n\t\t\t\tinput.dom.inputTd.style('padding', '5px')\n\t\t\t\t// **** !!! TODO: use dom/toggleButtons to create tabbed sections !!!\n\t\t\t\tconst btnsDiv = input.dom.inputTd.append('div').style('margin-bottom', '5px')\n\t\t\t\tconst basicBtn = btnsDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('padding-right', '5px')\n\t\t\t\t\t.style('border-right', '2px solid black')\n\t\t\t\t\t.style('text-decoration', controls.activeTab == 'basic' ? 'underline' : '')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.html('Basic')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tcontrols.activeTab = 'basic'\n\t\t\t\t\t\tbasicBtn.style('text-decoration', 'underline')\n\t\t\t\t\t\tadvancedBtn.style('text-decoration', '')\n\t\t\t\t\t\tbasicDiv.style('display', '')\n\t\t\t\t\t\tadvancedDiv.style('display', 'none')\n\t\t\t\t\t})\n\t\t\t\tconst advancedBtn = btnsDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t\t.style('text-decoration', controls.activeTab == 'advanced' ? 'underline' : '')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.html('Advanced')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tcontrols.activeTab = 'advanced'\n\t\t\t\t\t\tbasicBtn.style('text-decoration', '')\n\t\t\t\t\t\tadvancedBtn.style('text-decoration', 'underline')\n\t\t\t\t\t\tbasicDiv.style('display', 'none')\n\t\t\t\t\t\tadvancedDiv.style('display', '')\n\t\t\t\t\t})\n\n\t\t\t\tconst basicDiv = input.dom.inputTd.append('div').style('display', controls.activeTab == 'basic' ? '' : 'none')\n\t\t\t\tconst ssmDiv = basicDiv.append('div')\n\t\t\t\tssmDiv.append('span').html('SSM')\n\t\t\t\tconst { inputs } = make_radios({\n\t\t\t\t\t// holder, options, callback, styles\n\t\t\t\t\tholder: ssmDiv.append('span'),\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'by consequence', value: 'consequence', checked: m.sortByMutation === 'consequence' },\n\t\t\t\t\t\t{ label: 'by presence', value: 'presence', checked: m.sortByMutation === 'presence' }\n\t\t\t\t\t],\n\t\t\t\t\tstyles: {\n\t\t\t\t\t\tdisplay: 'inline-block'\n\t\t\t\t\t},\n\t\t\t\t\tcallback: sortByMutation => {\n\t\t\t\t\t\tconst sortOptions = parent.config.settings.matrix.sortOptions\n\t\t\t\t\t\tconst activeOption = sortOptions.a\n\t\t\t\t\t\tconst mutTb = activeOption.sortPriority[0].tiebreakers[1]\n\t\t\t\t\t\tmutTb.disabled = !sortByMutation\n\t\t\t\t\t\tmutTb.isOrdered = sortByMutation === 'consequence'\n\n\t\t\t\t\t\tparent.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: parent.id,\n\t\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t\t\t\tsortByMutation, // needed to show the correct status for checkbox, but actual sorting behavior\n\t\t\t\t\t\t\t\t\t\tsortOptions // is based on sortOptions.a[*].tiebreaker[*][disabled, isOrdered]\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t})\n\n\t\t\t\tinputs.style('margin', '2px 0 0 2px').style('vertical-align', 'top')\n\t\t\t\tconst cnvDiv = basicDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', m.showMatrixCNV != 'none' && !m.allMatrixCNVHidden ? 'block' : 'none')\n\n\t\t\t\tcnvDiv.append('span').html('CNV')\n\t\t\t\t// holder, labeltext, callback, checked, divstyle\n\t\t\t\tconst checkbox = make_one_checkbox({\n\t\t\t\t\tholder: cnvDiv.append('span'),\n\t\t\t\t\tdivstyle: { display: 'inline-block' },\n\t\t\t\t\tchecked: m.sortByCNV,\n\t\t\t\t\tlabeltext: 'sort by CNV',\n\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\tconst sortByCNV = checkbox.property('checked')\n\t\t\t\t\t\tconst sortOptions = parent.config.settings.matrix.sortOptions\n\t\t\t\t\t\tconst activeOption = sortOptions.a\n\t\t\t\t\t\tconst cnvTb = activeOption.sortPriority[0].tiebreakers[2]\n\t\t\t\t\t\tcnvTb.disabled = !sortByCNV\n\t\t\t\t\t\tcnvTb.isOrdered = sortByCNV\n\n\t\t\t\t\t\tparent.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: parent.id,\n\t\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t\t\t\tsortByCNV, // needed to show the correct status for checkbox, but actual sorting behavior\n\t\t\t\t\t\t\t\t\t\tsortOptions // is based on sortOptions.a[*].tiebreaker[*][disabled, isOrdered]\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t})\n\n\t\t\t\tconst advancedDiv = input.dom.inputTd\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', controls.activeTab == 'advanced' ? '' : 'none')\n\t\t\t\tinput.dom.row.on('mouseover', function () {\n\t\t\t\t\tthis.style.backgroundColor = '#fff'\n\t\t\t\t\tthis.style.textShadow = 'none'\n\t\t\t\t})\n\n\t\t\t\tif (!controls.sorterUi) {\n\t\t\t\t\tcontrols.sorterUi = getSorterUi({\n\t\t\t\t\t\tcontrols: this,\n\t\t\t\t\t\tholder: advancedDiv,\n\t\t\t\t\t\ttip: this.parent.app.tip\n\t\t\t\t\t})\n\t\t\t\t} else {\n\t\t\t\t\tcontrols.sorterUi.main(this.parent.config.settings.matrix, { holder: advancedDiv })\n\t\t\t\t}\n\n\t\t\t\treturn {\n\t\t\t\t\tmain: plot => {\n\t\t\t\t\t\tconst s = plot.settings.matrix\n\t\t\t\t\t\t// ssm\n\t\t\t\t\t\tinputs.property('checked', d => d.value == s.sortByMutation)\n\t\t\t\t\t\t// cnv\n\t\t\t\t\t\tcheckbox.property('checked', s.sortByCNV)\n\t\t\t\t\t\tcnvDiv.style('display', s.showMatrixCNV != 'none' && !s.allMatrixCNVHidden ? 'block' : 'none')\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t//.property('disabled', d => d.disabled)\n\t\t\t.datum({\n\t\t\t\tlabel: l.Samples || `Samples`,\n\t\t\t\tgetCount: () =>\n\t\t\t\t\t'sampleCount' in this.overrides ? this.overrides.sampleCount : this.parent.sampleOrder?.length || 0,\n\t\t\t\trows,\n\t\t\t\tcustomInputs: this.updateSamplesControls\n\t\t\t})\n\t\t\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\tsetGenesBtn(s) {\n\t\tconst l = s.controlLabels\n\t\tconst renderStyleOptions = [\n\t\t\t{\n\t\t\t\tlabel: `&nbsp;Stacked <span style=\"font-size:.7em;color:#555;\">Show stacked rectangles in the same matrix cell to render variants for the same ${l.sample} and gene</span>`,\n\t\t\t\tvalue: '',\n\t\t\t\ttitle: `Show stacked rectangles in the same matrix cell to render variants for the same ${l.sample} and gene`\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `&nbsp;OncoPrint <span style=\"font-size:.7em;color:#555;\">Show overlapping rectangles in the same matrix cell to render variants for the same ${l.sample} and gene</span>`,\n\t\t\t\tvalue: 'oncoprint',\n\t\t\t\ttitle: `Show overlapping rectangles in the same matrix cell to render variants for the same ${l.sample} and gene`\n\t\t\t}\n\t\t]\n\t\tif (s.addMutationCNVButtons && this.parent.chartType !== 'hierCluster')\n\t\t\trenderStyleOptions.unshift({\n\t\t\t\tlabel: `&nbsp;Single <span style=\"font-size:.7em;color:#555;\">Show a single rectangle in a matrix cell to render the most severe variant (truncating > indels > missense > synonymous) for the same ${l.sample} and gene</span>`,\n\t\t\t\tvalue: 'single',\n\t\t\t\ttitle: `Show a single rectangle in a matrix cell to render the most severe variant (truncating > indels > missense > synonymous) for the same ${l.sample} and gene`\n\t\t\t})\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t//.property('disabled', d => d.disabled)\n\t\t\t.datum({\n\t\t\t\tlabel: 'Genes',\n\t\t\t\tgetCount: () =>\n\t\t\t\t\tthis.parent.termOrder?.filter(\n\t\t\t\t\t\tt => t.tw.term.type == TermTypes.GENE_VARIANT || t.tw.term.type == TermTypes.GENE_EXPRESSION\n\t\t\t\t\t).length || 0,\n\t\t\t\tcustomInputs: this.addGeneInputs,\n\t\t\t\trows: [\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: `Display ${l.Sample} Counts for Gene`,\n\t\t\t\t\t\ttitle: `Include the ${l.sample} count in the gene label`,\n\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'samplecount4gene',\n\t\t\t\t\t\tstyles: { display: 'inline-block' },\n\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t{ label: 'Absolute', value: 'abs' },\n\t\t\t\t\t\t\t{ label: `Percent`, value: 'pct' },\n\t\t\t\t\t\t\t{ label: `None`, value: '' }\n\t\t\t\t\t\t],\n\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\treturn this.parent.termOrder?.filter(t => t.tw.term.type == 'geneVariant').length ? 'table-row' : 'none'\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t// TODO: implement this contol option\n\t\t\t\t\t// {\n\t\t\t\t\t// \tlabel: `Exclude From ${l.Sample} Displayed Counts`,\n\t\t\t\t\t// \ttitle: `Do not include these variations/mutations when counting samples for a gene.`,\n\t\t\t\t\t// \ttype: 'text',\n\t\t\t\t\t// \tchartType: 'matrix',\n\t\t\t\t\t// \tsettingsKey: 'geneVariantCountSamplesSkipMclass',\n\t\t\t\t\t// \tprocessInput: tw => {},\n\t\t\t\t\t// },\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Genomic Alterations Rendering',\n\t\t\t\t\t\ttitle: `Set how to indicate a ${l.sample}'s applicable variant types in the same matrix cell`,\n\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'cellEncoding',\n\t\t\t\t\t\toptions: renderStyleOptions,\n\t\t\t\t\t\tstyles: { padding: '5px 0px', margin: 0 },\n\t\t\t\t\t\tlabelDisplay: 'block',\n\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\treturn this.parent.termOrder?.filter(t => t.tw.term.type == 'geneVariant').length ? 'table-row' : 'none'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tcallback: this.parent.geneStyleControlCallback\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Sort Genes',\n\t\t\t\t\t\ttitle: 'Set how to order the genes as rows',\n\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'sortTermsBy',\n\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t{ label: 'By Input Data Order', value: 'asListed' },\n\t\t\t\t\t\t\t{ label: `By ${l.sample} Count`, value: 'sampleCount' }\n\t\t\t\t\t\t],\n\t\t\t\t\t\tstyles: { padding: 0, 'padding-right': '10px', margin: 0, display: 'inline-block' },\n\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\treturn this.parent.termOrder?.filter(t => t.tw.term.type == 'geneVariant').length ? 'table-row' : 'none'\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\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\tsetVariablesBtn(s) {\n\t\tconst l = s.controlLabels\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t.datum({\n\t\t\t\tlabel: s.controlLabels.Terms || `Variables`,\n\t\t\t\t//getCount: () => this.parent.termOrder.filter(t => t.tw.term.type != 'geneVariant').length.length,\n\t\t\t\trows: [\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: `Row Group Label Max Length`,\n\t\t\t\t\t\ttitle: `Truncate the row group label if it exceeds this maximum number of characters`,\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'termGrpLabelMaxChars'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: `Row Label Max Length`,\n\t\t\t\t\t\ttitle: `Truncate the row label if it exceeds this maximum number of characters`,\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'rowlabelmaxchars'\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\tcustomInputs: this.appendDictInputs\n\t\t\t})\n\t\t\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\tsetDimensionsBtn(s) {\n\t\tconst l = s.controlLabels\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t.datum({\n\t\t\t\tlabel: 'Cell Layout',\n\t\t\t\ttables: [\n\t\t\t\t\t{\n\t\t\t\t\t\trows: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Grid',\n\t\t\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t\t\t'Show grid lines, which creates borders around each matrix cells. ' +\n\t\t\t\t\t\t\t\t\t' Note that grid lines are hidden when the auto-computed width <= 2, or when either the column and row spacing is set to 0.',\n\t\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\t\tboxLabel: 'show',\n\t\t\t\t\t\t\t\t// v===true means property('checked') and convert to recognized 'rect' value for dispatch\n\t\t\t\t\t\t\t\t// otherwise, compared value to 'rect' to set the current value of the checkbox\n\t\t\t\t\t\t\t\t// note: the non-boolean showGrid values allow keeping the hidden value='pattern' option for benchmark tests\n\t\t\t\t\t\t\t\tprocessInput: v => (v === true ? 'rect' : v === 'rect'),\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'showGrid',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center'\n\t\t\t\t\t\t\t\t// for testing/benchmarking\n\t\t\t\t\t\t\t\t// type: 'radio',\n\t\t\t\t\t\t\t\t// options: [\n\t\t\t\t\t\t\t\t// \t{\n\t\t\t\t\t\t\t\t// \t\tlabel: 'hide',\n\t\t\t\t\t\t\t\t// \t\tvalue: ''\n\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// \t\tlabel: 'lines',\n\t\t\t\t\t\t\t\t// \t\tvalue: 'pattern' // needs debugging for when s.rowh or d.colw does not apply to all rows\n\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// \t\tlabel: 'rect',\n\t\t\t\t\t\t\t\t// \t\tvalue: 'rect'\n\t\t\t\t\t\t\t\t// \t}\n\t\t\t\t\t\t\t\t// ]\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Outline Color',\n\t\t\t\t\t\t\t\ttitle: 'Set a border color for the whole matrix',\n\t\t\t\t\t\t\t\ttype: 'color',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'outlineStroke',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center'\n\t\t\t\t\t\t\t\t//getDisplayStyle: plot => this.parent.settings.matrix.showGrid ? '' : 'none'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Beam Color',\n\t\t\t\t\t\t\t\ttitle: 'Set a color for the beam highlighter',\n\t\t\t\t\t\t\t\ttype: 'color',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'beamStroke',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center'\n\t\t\t\t\t\t\t\t//getDisplayStyle: plot => this.parent.settings.matrix.showGrid ? '' : 'none'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Grid Line Color',\n\t\t\t\t\t\t\t\ttitle: 'Set the grid color, equivalent to applying the same border color for each matrix cell',\n\t\t\t\t\t\t\t\ttype: 'color',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'gridStroke',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center'\n\t\t\t\t\t\t\t\t//getDisplayStyle: plot => this.parent.settings.matrix.showGrid ? '' : 'none'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Background Color',\n\t\t\t\t\t\t\t\ttitle: `Set the background color when there are no alterations or annotation data for a ${l.sample}`,\n\t\t\t\t\t\t\t\ttype: 'color',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'cellbg',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: `Use Canvas If # ${l.sample} Exceeds`,\n\t\t\t\t\t\t\t\ttitle: `Switch from SVG to canvas rendering when the number of ${l.samples} exceeds this number`,\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'svgCanvasSwitch',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\twidth: 60,\n\t\t\t\t\t\t\t\tmin: 0,\n\t\t\t\t\t\t\t\tmax: 10000,\n\t\t\t\t\t\t\t\tstep: 1\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Canvas Min. Pixel Width',\n\t\t\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t\t\t'Set a minimum pixel width for a matrix cell when using canvas, may affect the perceived sharpness of the canvas image',\n\t\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\t\tboxLabel: 'apply',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'useMinPixelWidth',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tgetDisplayStyle: () => (this.parent.settings.matrix.useCanvas ? '' : 'none')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\theader: ['Cells', 'Columns', 'Rows'],\n\t\t\t\t\t\trows: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Row Height',\n\t\t\t\t\t\t\t\ttitle: 'Set the height of a matrix row',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [{ label: 'N/A' }, { settingsKey: 'rowh', min: 8, max: 30, step: 1 }],\n\t\t\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\t\t\treturn plot.chartType == 'hierCluster' ? 'none' : 'table-row'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Min Col. Width',\n\t\t\t\t\t\t\t\ttitle: 'Set the minimum width of the auto-computed matrix column width',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [{ settingsKey: 'colwMin', min: 0.1, max: 16, step: 0.2 }, { label: 'N/A' }]\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Max Col. Width',\n\t\t\t\t\t\t\t\ttitle: 'Set the maximum width of the auto-computed matrix column width',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [{ settingsKey: 'colwMax', min: 1, max: 24, step: 0.2 }, { label: 'N/A' }]\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Spacing',\n\t\t\t\t\t\t\t\ttitle: 'Set the column spacing. Note that this will be set to 0 when the auto-computed width < 2.',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'colspace', min: 0, max: 20, step: 1 },\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'rowspace', min: 0, max: 20, step: 1 }\n\t\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\t\t\treturn plot.chartType == 'hierCluster' ? 'none' : 'table-row'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Group spacing',\n\t\t\t\t\t\t\t\ttitle: 'Set the spacing between column and row groups.',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [\n\t\t\t\t\t\t\t\t\tthis.parent.chartType == 'hierCluster'\n\t\t\t\t\t\t\t\t\t\t? { label: 'N/A' }\n\t\t\t\t\t\t\t\t\t\t: { settingsKey: 'colgspace', min: 0, max: 20, step: 1 },\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'rowgspace', min: 0, max: 20, step: 1 }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\theader: ['Labels', 'Columns', 'Rows'],\n\t\t\t\t\t\trows: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Offset',\n\t\t\t\t\t\t\t\ttitle: 'Set the gap between the label text and matrix edge',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'collabelgap', min: 0, max: 20, step: 1 },\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'rowlabelgap', min: 0, max: 20, step: 1 }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Spacing',\n\t\t\t\t\t\t\t\ttitle: 'Set the gap between labels',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tinputs: [\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'collabelpad', min: 0, max: 20, step: 1 },\n\t\t\t\t\t\t\t\t\t{ settingsKey: 'rowlabelpad', min: 0, max: 20, step: 1 }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Min font size',\n\t\t\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t\t\t'Set the minimum auto-computed font size for labels. Note that labels will be hidden if the auto-computed values falls below this minimum.',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'minLabelFontSize',\n\t\t\t\t\t\t\t\tmin: 0,\n\t\t\t\t\t\t\t\tmax: 24,\n\t\t\t\t\t\t\t\tstep: 0.1\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Max font size',\n\t\t\t\t\t\t\t\ttitle: 'Set the maximum auto-computed font size for labels',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\talign: 'center',\n\t\t\t\t\t\t\t\tcolspan: 2,\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tsettingsKey: 'maxLabelFontSize',\n\t\t\t\t\t\t\t\tmin: 0,\n\t\t\t\t\t\t\t\tmax: 24,\n\t\t\t\t\t\t\t\tstep: 0.1\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: 'Group label<br/>position',\n\t\t\t\t\t\t\t\ttitle: 'Set which side of the matrix to display group labels',\n\t\t\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\t\t\twidth: 50,\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\tlabelDisplay: 'block',\n\t\t\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\t\t\treturn plot.chartType == 'hierCluster' ? 'none' : 'table-row'\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tinputs: [\n\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\tsettingsKey: 'collabelpos',\n\t\t\t\t\t\t\t\t\t\t// switched since settings.collabelpos refers to the individual column label, not group\n\t\t\t\t\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t\t\t\t\t{ label: 'Top', value: 'bottom', title: `Display ${l.sample} group labels at the bottom` },\n\t\t\t\t\t\t\t\t\t\t\t{ label: 'Bottom', value: 'top', title: `Display ${l.sample} group labels on top` }\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\t{\n\t\t\t\t\t\t\t\t\t\tsettingsKey: 'rowlabelpos',\n\t\t\t\t\t\t\t\t\t\t// switched since settings.rowlabelpos refers to the individual column label, not group\n\t\t\t\t\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\t\tlabel: 'Left',\n\t\t\t\t\t\t\t\t\t\t\t\tvalue: 'right',\n\t\t\t\t\t\t\t\t\t\t\t\ttitle: `Display gene or variable group labels on the left side`\n\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\t\tlabel: 'Right',\n\t\t\t\t\t\t\t\t\t\t\t\tvalue: 'left',\n\t\t\t\t\t\t\t\t\t\t\t\ttitle: `Display gene or variable group labels on the right side`\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}\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\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\tsetLegendBtn(s) {\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.datum({\n\t\t\t\tlabel: 'Legend Layout',\n\t\t\t\trows: [\n\t\t\t\t\t//ontop: false,\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Font Size',\n\t\t\t\t\t\ttitle: 'Set the font size for the legend text',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'fontsize'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Line Height',\n\t\t\t\t\t\ttitle: 'Set the line height for a legend group',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'lineh'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Icon Height',\n\t\t\t\t\t\ttitle: 'Set the icon height for a legend item',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'iconh'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Icon Width',\n\t\t\t\t\t\ttitle: 'Set the icon width for a legend item',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'iconw'\n\t\t\t\t\t},\n\t\t\t\t\t/*{\n\t\t\t\t\t\tlabel: 'Bottom margin',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'padbtm'\n\t\t\t\t\t},*/\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Item Left Pad',\n\t\t\t\t\t\ttitle: 'Set a left margin for each legend item',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'padx'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Left Margin',\n\t\t\t\t\t\ttitle: 'Set a left margin for the whole legend',\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'padleft'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Left Indent',\n\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t`Set a left margin for the first legend item in each group, and should be set to the length of the longest group label.` +\n\t\t\t\t\t\t\t` The left indent will align the legend group label text to the right.`,\n\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'hangleft'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Item Layout',\n\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t'Option to separate each legend item into a new line, instead of a horizontal layout in the same line.',\n\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\tchartType: 'legend',\n\t\t\t\t\t\tsettingsKey: 'linesep',\n\t\t\t\t\t\tboxLabel: 'Line separated'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t})\n\t\t\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\t// Mutation button for selecting mutations to display on the matrix\n\tsetMutationBtn() {\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.datum({\n\t\t\t\tlabel: 'Mutation',\n\t\t\t\tupdateBtn: btn => {\n\t\t\t\t\tconst s = this.parent.config.settings.matrix\n\t\t\t\t\tbtn\n\t\t\t\t\t\t.style('text-decoration', s.allMatrixMutationHidden ? 'line-through' : '')\n\t\t\t\t\t\t.style('text-decoration-thickness', s.allMatrixMutationHidden ? '2px' : '')\n\t\t\t\t},\n\t\t\t\trows: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttitle: `Show mutation options`,\n\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'showMatrixMutation',\n\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t{ label: 'Show all mutations', value: 'all' },\n\t\t\t\t\t\t\t{ label: `Show only truncating mutations`, value: 'onlyTruncating' },\n\t\t\t\t\t\t\t{ label: `Show only protein-changing mutations`, value: 'onlyPC' },\n\t\t\t\t\t\t\t{ label: `Do not show mutations`, value: 'none' },\n\t\t\t\t\t\t\t{ label: `Show selected mutation`, value: 'bySelection' }\n\t\t\t\t\t\t],\n\t\t\t\t\t\tlabelDisplay: 'block',\n\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\treturn plot.chartType == 'hierCluster' ? 'none' : 'table-row'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tcallback: this.parent.mutationControlCallback\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\tcustomInputs: this.generateMutationItems\n\t\t\t})\n\t\t\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\t// CNV button for selecting the CNVs to display on the matrix\n\tsetCNVBtn() {\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.datum({\n\t\t\t\tlabel: 'CNV',\n\t\t\t\tupdateBtn: btn => {\n\t\t\t\t\tconst s = this.parent.config.settings.matrix\n\t\t\t\t\tconst notRendered = s.allMatrixCNVHidden\n\t\t\t\t\tbtn\n\t\t\t\t\t\t.style('text-decoration', notRendered ? 'line-through' : '')\n\t\t\t\t\t\t.style('text-decoration-thickness', notRendered ? '2px' : '')\n\t\t\t\t},\n\t\t\t\trows: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttitle: `Show CNV options`,\n\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\tsettingsKey: 'showMatrixCNV',\n\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t{ label: 'Show all CNV', value: 'all' },\n\t\t\t\t\t\t\t{ label: `Do not show CNV`, value: 'none' },\n\t\t\t\t\t\t\t{ label: `Show selected CNV`, value: 'bySelection' }\n\t\t\t\t\t\t],\n\t\t\t\t\t\tlabelDisplay: 'block',\n\t\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\t\treturn plot.chartType == 'hierCluster' ? 'none' : 'table-row'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tcallback: this.parent.CNVControlCallback\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\tcustomInputs: this.generateCNVItems\n\t\t\t})\n\t\t\t.html(d => d.label)\n\t\t\t.style('margin', '2px 0')\n\t\t\t.on('click', (event, d) => this.callback(event, d))\n\t}\n\n\tsetDownloadBtn(s) {\n\t\tthis.opts.holder\n\t\t\t.append('button')\n\t\t\t.style('margin', '2px 0')\n\t\t\t//.property('disabled', d => d.disabled)\n\t\t\t.text('Download')\n\t\t\t.on('focus', () => this.parent.app.tip.hide())\n\t\t\t.on('click.sjpp-matrix-download', event => {\n\t\t\t\tconst p = this.parent\n\t\t\t\tif (!p.dom.downloadMenu) p.dom.downloadMenu = new Menu({ padding: '' })\n\t\t\t\tconst downloadMenu = p.dom.downloadMenu.clear()\n\t\t\t\tconst div = downloadMenu.d.append('div')\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(`SVG image`)\n\t\t\t\t\t.on('click.sjpp-matrix-download', () => {\n\t\t\t\t\t\tto_svg(this.opts.getSvg(), 'matrix', { apply_dom_styles: true })\n\t\t\t\t\t\tp.dom.downloadMenu.destroy()\n\t\t\t\t\t})\n\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(`TSV data`)\n\t\t\t\t\t.on('click.sjpp-matrix-download', () => {\n\t\t\t\t\t\tconst lst = p.data.lst\n\t\t\t\t\t\tconst allTerms = p.termOrder.map(t => t.tw)\n\t\t\t\t\t\tconst assayAvailability = p.state.termdbConfig.assayAvailability\n\t\t\t\t\t\tconst controlLabels = p.settings.matrix.controlLabels\n\t\t\t\t\t\tif (p.config.divideBy?.id && !allTerms.find(a => a.id == p.config.divideBy.id)) {\n\t\t\t\t\t\t\t// when divideBy term is not in the matrix terms\n\t\t\t\t\t\t\tallTerms.push(p.config.divideBy)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tconst activeSamples = []\n\t\t\t\t\t\tfor (const d of lst) {\n\t\t\t\t\t\t\tfor (const tw of allTerms) {\n\t\t\t\t\t\t\t\tif (tw.$id in d) {\n\t\t\t\t\t\t\t\t\tactiveSamples.push(d)\n\t\t\t\t\t\t\t\t\tbreak\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\tconst header = [controlLabels.Sample]\n\t\t\t\t\t\tfor (const tw of allTerms) header.push(tw.term.name)\n\n\t\t\t\t\t\tconst rows = [header]\n\t\t\t\t\t\tfor (const s of activeSamples) {\n\t\t\t\t\t\t\tconst row = [s._ref_.label]\n\t\t\t\t\t\t\tfor (const tw of allTerms) {\n\t\t\t\t\t\t\t\tif (!s[tw.$id]) {\n\t\t\t\t\t\t\t\t\trow.push('')\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\tif (tw.term.type == 'geneVariant') {\n\t\t\t\t\t\t\t\t\t\tconst allVariant = []\n\t\t\t\t\t\t\t\t\t\tfor (const v of s[tw.$id].renderedValues) {\n\t\t\t\t\t\t\t\t\t\t\t// when assayAvailability presents, has WT and Blank\n\t\t\t\t\t\t\t\t\t\t\tconst hasAssayAvailability = assayAvailability?.byDt?.[parseInt(v.dt)]\n\t\t\t\t\t\t\t\t\t\t\tif (v.dt == dtsnvindel) {\n\t\t\t\t\t\t\t\t\t\t\t\tallVariant.push(\n\t\t\t\t\t\t\t\t\t\t\t\t\t(v.origin ? `${v.origin} ` : '') +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t(hasAssayAvailability ? `${dt2label[v.dt]}:` : '') +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t`${mclass[v.class]?.label}` +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t(v.mname ? `,${v.mname}` : '')\n\t\t\t\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\t\t\t} else if (v.dt == dtcnv) {\n\t\t\t\t\t\t\t\t\t\t\t\tconst cnvValue = v.value\n\t\t\t\t\t\t\t\t\t\t\t\t\t? `${hasAssayAvailability ? '' : 'CNV:'}${v.value}` //show v.value for numerical CNV, otherwise show CNV gain/loss\n\t\t\t\t\t\t\t\t\t\t\t\t\t: v.class == 'CNV_amp'\n\t\t\t\t\t\t\t\t\t\t\t\t\t? 'CNV gain'\n\t\t\t\t\t\t\t\t\t\t\t\t\t: v.class == 'CNV_loss'\n\t\t\t\t\t\t\t\t\t\t\t\t\t? 'CNV loss'\n\t\t\t\t\t\t\t\t\t\t\t\t\t: v.class == 'CNV_homozygous_deletion'\n\t\t\t\t\t\t\t\t\t\t\t\t\t? 'CNV homozygous deletion'\n\t\t\t\t\t\t\t\t\t\t\t\t\t: v.class == 'CNV_amplification'\n\t\t\t\t\t\t\t\t\t\t\t\t\t? 'CNV amplification'\n\t\t\t\t\t\t\t\t\t\t\t\t\t: v.class == 'CNV_loh'\n\t\t\t\t\t\t\t\t\t\t\t\t\t? 'CNV loss of heterozygosity'\n\t\t\t\t\t\t\t\t\t\t\t\t\t: mclass[v.class]?.label\n\n\t\t\t\t\t\t\t\t\t\t\t\tallVariant.push(\n\t\t\t\t\t\t\t\t\t\t\t\t\t(v.origin ? `${v.origin} ` : '') +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t(hasAssayAvailability ? `${dt2label[v.dt]}:` : '') +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tcnvValue\n\t\t\t\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\t\t\t} else if (v.dt == dtfusionrna || v.dt == dtsv) {\n\t\t\t\t\t\t\t\t\t\t\t\tallVariant.push(\n\t\t\t\t\t\t\t\t\t\t\t\t\t(v.origin ? `${v.origin} ` : '') +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t(hasAssayAvailability ? `${dt2label[v.dt]}:` : '') +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t`${mclass[v.class]?.label}` +\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t(v.gene && v.mname ? `(${v.gene}::${v.mname})` : '')\n\t\t\t\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\t\t\tallVariant.push(`DO NOT SUPPORT dt='${v.dt}'`)\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\trow.push(allVariant.join('|'))\n\t\t\t\t\t\t\t\t\t} else if (\n\t\t\t\t\t\t\t\t\t\ttw.term.type == TermTypes.GENE_EXPRESSION ||\n\t\t\t\t\t\t\t\t\t\ttw.term.type == TermTypes.METABOLITE_INTENSITY ||\n\t\t\t\t\t\t\t\t\t\ttw.term.type == TermTypes.PROTEOME_ABUNDANCE\n\t\t\t\t\t\t\t\t\t) {\n\t\t\t\t\t\t\t\t\t\trow.push(s[tw.$id]?.renderedValues?.[0]?.value || '')\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\trow.push(s[tw.$id]?.renderedValues?.[0] || s[tw.$id]?.value || '')\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\trows.push(row)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tconst matrix = rows.map(row => row.join('\\t')).join('\\n')\n\t\t\t\t\t\tconst a = document.createElement('a')\n\t\t\t\t\t\tdocument.body.appendChild(a)\n\t\t\t\t\t\ta.addEventListener(\n\t\t\t\t\t\t\t'click',\n\t\t\t\t\t\t\tfunction () {\n\t\t\t\t\t\t\t\tconst currentDate = new Date().toISOString().split('T')[0]\n\t\t\t\t\t\t\t\ta.download = p.config.settings?.hierCluster?.termGroupName?.startsWith('Gene Expression')\n\t\t\t\t\t\t\t\t\t? `GeneExpression.${currentDate}.tsv`\n\t\t\t\t\t\t\t\t\t: p.chartType == 'hierCluster'\n\t\t\t\t\t\t\t\t\t? `HierCluster.${currentDate}.tsv`\n\t\t\t\t\t\t\t\t\t: `${p.app.vocabApi.termdbConfig.matrix?.appName || 'Matrix'}.${currentDate}.tsv`\n\t\t\t\t\t\t\t\ta.href = URL.createObjectURL(new Blob([matrix], { type: 'text/tab-separated-values' }))\n\t\t\t\t\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tfalse\n\t\t\t\t\t\t)\n\t\t\t\t\t\ta.click()\n\t\t\t\t\t\tp.dom.downloadMenu.destroy()\n\t\t\t\t\t})\n\t\t\t\tdownloadMenu.showunder(event.target)\n\t\t\t})\n\t}\n\n\tmain(overrides = {}) {\n\t\tthis.overrides = overrides\n\t\tthis.parent.app.tip.hide()\n\n\t\tthis.btns\n\t\t\t.text(d =>\n\t\t\t\t!d.getCount || d.showCount == 'hide'\n\t\t\t\t\t? d.label\n\t\t\t\t\t: d.showCount == 'append'\n\t\t\t\t\t? `${d.label} (n=${d.getCount()})`\n\t\t\t\t\t: `${d.getCount()} ${d.label}`\n\t\t\t)\n\t\t\t.each(function (d) {\n\t\t\t\tif (d.updateBtn) d.updateBtn(select(this))\n\t\t\t})\n\n\t\tconst s = this.parent.settings.matrix || this.parent.config.settings.matrix\n\t\tconst min = s.colwMin / s.colw\n\t\tconst max = s.colwMax / s.colw\n\t\tconst increment = Math.max(0.01, Number((min / max).toFixed(2)))\n\n\t\tconst d = this.parent.dimensions\n\t\tif (this.zoomApi)\n\t\t\tthis.zoomApi.update({\n\t\t\t\tvalue: s.zoomLevel.toFixed(2),\n\t\t\t\tmin,\n\t\t\t\tmax,\n\t\t\t\tincrement,\n\t\t\t\tstep: s.zoomStep || 1\n\t\t\t})\n\n\t\tif (this.svgScrollApi && d) {\n\t\t\tthis.svgScrollApi.update({\n\t\t\t\tx: d.xOffset,\n\t\t\t\ty: d.yOffset - s.scrollHeight,\n\t\t\t\ttotalWidth: d.zoomedMainW,\n\t\t\t\tvisibleWidth: d.mainw,\n\t\t\t\tzoomCenter: s.zoomCenterPct * d.mainw - d.seriesXoffset\n\t\t\t})\n\t\t}\n\n\t\tif (this.dragToggleApi) {\n\t\t\tthis.dragToggleApi.update(s.mouseMode ? { mouseMode: s.mouseMode } : {})\n\t\t}\n\t}\n\n\tgetSettings() {\n\t\t// return control settings that are not tracked in the global app state or plot state\n\t\treturn {\n\t\t\tmouseMode: this.dragToggleApi.getSettings().mouseMode\n\t\t}\n\t}\n\n\tasync callback(event, d) {\n\t\tconst { clientX, clientY } = event\n\t\tconst app = this.opts.app\n\t\tconst parent = this.opts.parent\n\t\tconst tables = d.tables || [d]\n\n\t\tevent.target.focus()\n\t\tapp.tip.clear()\n\n\t\tconst table = app.tip.d.append('table').attr('class', 'sjpp-controls-table')\n\t\tfor (const t of tables) {\n\t\t\t//if (d.customHeaderRows) d.customHeaderRows(parent, table)\n\t\t\tif (t.header) {\n\t\t\t\ttable\n\t\t\t\t\t.append('tr')\n\t\t\t\t\t.selectAll('th')\n\t\t\t\t\t.data(t.header)\n\t\t\t\t\t.enter()\n\t\t\t\t\t.append('th')\n\t\t\t\t\t.html(d => d)\n\t\t\t}\n\n\t\t\tfor (const inputConfig of t.rows) {\n\t\t\t\tconst holder = table.append('tr')\n\t\t\t\tconst input = await initByInput[inputConfig.type](\n\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t{},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tholder,\n\t\t\t\t\t\t\tapp,\n\t\t\t\t\t\t\tdispatch: action => app.dispatch(action),\n\t\t\t\t\t\t\tid: parent.id,\n\t\t\t\t\t\t\tdebug: this.opts.debug,\n\t\t\t\t\t\t\tparent\n\t\t\t\t\t\t},\n\t\t\t\t\t\tinputConfig\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t\tinput.main(parent.config)\n\t\t\t}\n\n\t\t\tif (t.customInputs) t.customInputs(this, app, parent, table)\n\t\t\ttable.selectAll('select, input, button').attr('tabindex', 0).on('keydown', self.keyboardNavHandler)\n\t\t}\n\n\t\tapp.tip.showunder(event.target)\n\t}\n\n\tprependInfo(table, header, value) {\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').text(header).attr('class', 'sja-termdb-config-row-label')\n\t\ttr.append('td').text(value)\n\t}\n\n\tasync addGeneInputs(self, app, parent, table) {\n\t\tif (parent.chartType == 'hierCluster' && parent.config.dataType == TermTypes.GENE_EXPRESSION) {\n\t\t\tself.appendGeneInputs(self, app, parent, table, 'hierCluster')\n\t\t}\n\t\tif (\n\t\t\tparent.state?.termdbConfig?.allowedTermTypes?.includes(TermTypes.GENE_VARIANT) ||\n\t\t\tparent.state.termdbConfig.queries.snvindel\n\t\t)\n\t\t\tself.appendGeneInputs(self, app, parent, table)\n\t}\n\tasync appendGeneInputs(self, app, parent, table, geneInputType) {\n\t\ttip.clear()\n\t\tif (!parent.selectedGroup) parent.selectedGroup = 0\n\n\t\tif (parent.opts.customInputs?.genes) {\n\t\t\t// these are embedder portal specific controls\n\t\t\tfor (const inputConfig of parent.opts.customInputs.genes) {\n\t\t\t\tinputConfig.chartType = 'matrix'\n\t\t\t\tconst holder = table.append('tr')\n\t\t\t\tif (inputConfig.title) holder.attr('aria-label', inputConfig.title)\n\t\t\t\tconst input = await initByInput[inputConfig.type](\n\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t{},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tholder,\n\t\t\t\t\t\t\tapp,\n\t\t\t\t\t\t\tid: parent.id,\n\t\t\t\t\t\t\tdebug: self.opts.debug,\n\t\t\t\t\t\t\tparent\n\t\t\t\t\t\t},\n\t\t\t\t\t\tinputConfig\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t\tinput.main(parent.config)\n\t\t\t}\n\t\t}\n\t\tlet geneInputTr\n\t\tif (geneInputType == 'hierCluster' || parent.chartType !== 'hierCluster') {\n\t\t\t// Insert the gene set edit UI at the top\n\t\t\tgeneInputTr = table.insert('tr', () => table.select('tr').node())\n\t\t} else {\n\t\t\t// Insert after first gene set edit UI\n\t\t\tconst secondTr = table.selectAll('tr').nodes()[1] || null\n\t\t\t// Add visual separator: <hr> row\n\t\t\tconst hrTr = table.insert('tr', () => secondTr)\n\t\t\thrTr.append('td').attr('colspan', 2).append('hr').style('border', '1px solid #ccc')\n\t\t\tgeneInputTr = table.insert('tr', () => secondTr)\n\t\t}\n\t\tself.addGenesetInput(app, parent, geneInputTr, geneInputType)\n\t}\n\n\taddGenesetInput(app, parent, tr, geneInputType) {\n\t\tconst controlPanelBtn = this.btns.filter(d => d.label.endsWith('Genes'))?.node()\n\t\tconst tip = app.tip //new Menu({ padding: '5px' })\n\t\tconst tg = parent.config.termgroups\n\n\t\tlet selectedGroup\n\t\tconst triggerGenesetEdit = holder => {\n\t\t\tholder.selectAll('*').remove()\n\t\t\tconst geneList = selectedGroup.lst.map(item => {\n\t\t\t\treturn { gene: item.name }\n\t\t\t}) //To do, selectedGroup.lst may replace name with gene as well\n\t\t\tnew GeneSetEditUI({\n\t\t\t\tholder,\n\t\t\t\tgenome: app.opts.genome,\n\t\t\t\tgeneList,\n\t\t\t\t// Remove the GFF Loads Gene Sets option from unclustered genes panel.\n\t\t\t\tcustomInputs:\n\t\t\t\t\tparent.chartType !== 'hierCluster' || geneInputType == 'hierCluster'\n\t\t\t\t\t\t? this.parent.opts.customInputs?.geneset\n\t\t\t\t\t\t: undefined,\n\t\t\t\t/* running hier clustering and the editing group is the group used for clustering\n\t\t\t\tpass this mode value to inform ui to support the optional button \"top variably exp gene\"\n\t\t\t\tthis is hardcoded for the purpose of gene expression and should be improved\n\t\t\t\t*/\n\n\t\t\t\tmode: selectedGroup.mode,\n\t\t\t\tminNumGenes: selectedGroup.mode == 'geneExpression' ? 3 : 1,\n\t\t\t\tvocabApi: this.opts.app.vocabApi,\n\t\t\t\tcallback: async ({ geneList, groupName }) => {\n\t\t\t\t\tif (!selectedGroup) throw `missing selectedGroup`\n\t\t\t\t\ttip.hide()\n\t\t\t\t\tconst group = selectedGroup.status == 'new' ? { name: groupName, lst: [] } : tg[selectedGroup.index]\n\t\t\t\t\tif (selectedGroup.status == 'new') tg.push(group)\n\t\t\t\t\tconst targetTermType = selectedGroup.mode == 'geneExpression' ? 'geneExpression' : 'geneVariant'\n\t\t\t\t\t// remove gene terms to be replaced by the new lst, keep all other term types in the group\n\t\t\t\t\tconst lst = group.lst.filter(tw => tw.term.type != targetTermType)\n\t\t\t\t\tconst tws = await Promise.all(\n\t\t\t\t\t\tgeneList.map(async d => {\n\t\t\t\t\t\t\tlet term\n\t\t\t\t\t\t\tif (targetTermType == 'geneExpression') {\n\t\t\t\t\t\t\t\tconst gene = d.symbol || d.gene\n\t\t\t\t\t\t\t\tconst unit = app.vocabApi.termdbConfig.queries.geneExpression?.unit || 'Gene Expression'\n\t\t\t\t\t\t\t\tconst name = `${gene} ${unit}`\n\t\t\t\t\t\t\t\tterm = { gene, name, type: 'geneExpression' }\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tterm = {\n\t\t\t\t\t\t\t\t\tgene: d.symbol || d.gene,\n\t\t\t\t\t\t\t\t\tname: d.symbol || d.gene,\n\t\t\t\t\t\t\t\t\ttype: 'geneVariant'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t//if it was present use the previous term, genomic range terms require chr, start and stop fields, found in the original term\n\t\t\t\t\t\t\tlet tw = group.lst.find(t => {\n\t\t\t\t\t\t\t\tconst geneName = t.term.gene || t.term.name\n\t\t\t\t\t\t\t\tconst match = d.symbol ? geneName === d.symbol : d.gene ? geneName === d.gene : false\n\t\t\t\t\t\t\t\treturn match && t.term.type == targetTermType\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tif (!tw) {\n\t\t\t\t\t\t\t\ttw = { term }\n\t\t\t\t\t\t\t\tawait fillTermWrapper(tw, this.opts.app.vocabApi)\n\t\t\t\t\t\t\t} else if (!tw.$id) {\n\t\t\t\t\t\t\t\ttw.$id = await get$id(this.opts.app.vocabApi.getTwMinCopy({ term }))\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\treturn tw\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t\tgroup.lst = [...lst, ...tws]\n\t\t\t\t\tif (!group.lst.length) tg.splice(selectedGroup.index, 1)\n\t\t\t\t\tapp.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.parent.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\ttermgroups: tg\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t},\n\t\t\t\tbackBtn: {\n\t\t\t\t\ttarget: 'Genes Menu',\n\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\tcontrolPanelBtn.click()\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\ttermsAsListed:\n\t\t\t\t\t(geneInputType == 'hierCluster' && !this.parent.config.settings.hierCluster.clusterRows) ||\n\t\t\t\t\t(geneInputType != 'hierCluster' && this.parent.config.settings.matrix.sortTermsBy == 'asListed')\n\t\t\t})\n\t\t}\n\n\t\t//the number of groups in the current matrix that is editable: hiercluster group should not be edited from \"Genes\" control panel.\n\t\tconst numOfEditableGrps = tg.filter(g => g.type != 'hierCluster').length\n\n\t\ttr.append('td')\n\t\t\t.attr('class', 'sja-termdb-config-row-label')\n\t\t\t.html(geneInputType == 'hierCluster' ? 'Hierarchical Clustering Gene Set' : 'Genomic Alteration Gene Set')\n\n\t\tif (numOfEditableGrps > 0 || geneInputType == 'hierCluster') {\n\t\t\tconst td1 = tr.append('td').style('display', 'block').style('padding', '5px 0px')\n\t\t\tconst editGrpDiv = td1.append('div').append('label')\n\n\t\t\tconst editBtn = editGrpDiv\n\t\t\t\t.append('button')\n\t\t\t\t.html(\n\t\t\t\t\tnumOfEditableGrps > 1 && geneInputType !== 'hierCluster'\n\t\t\t\t\t\t? 'Edit Selected Group'\n\t\t\t\t\t\t: geneInputType == 'hierCluster'\n\t\t\t\t\t\t? 'Edit Gene Set'\n\t\t\t\t\t\t: 'Edit Current Group'\n\t\t\t\t)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.clear()\n\t\t\t\t\tthis.setMenuBackBtn(tip.d.append('div').style('padding', '5px'), () => controlPanelBtn.click(), `Back`)\n\t\t\t\t\tconst genesetEdiUiHolder = tip.d.append('div')\n\t\t\t\t\ttriggerGenesetEdit(genesetEdiUiHolder)\n\t\t\t\t})\n\n\t\t\tif (numOfEditableGrps > 1 && geneInputType !== 'hierCluster') {\n\t\t\t\tconst { nonHierClusterGroups, groupSelect } = this.setTermGroupSelector(editGrpDiv, tg)\n\t\t\t\tselectedGroup = nonHierClusterGroups.find(g => g.selected)\n\t\t\t\tgroupSelect.on('change', () => {\n\t\t\t\t\tselectedGroup = nonHierClusterGroups[groupSelect.property('value')]\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\tconst s = parent.config.settings.hierCluster\n\t\t\t\tconst g =\n\t\t\t\t\tgeneInputType == 'hierCluster' ? tg.find(g => g.type == 'hierCluster') : tg.find(g => g.type != 'hierCluster')\n\n\t\t\t\tselectedGroup = {\n\t\t\t\t\tindex:\n\t\t\t\t\t\tgeneInputType == 'hierCluster' ? tg.findIndex(g => g.type == 'hierCluster') : tg[0].type == g.type ? 0 : 1,\n\t\t\t\t\tname: g.name,\n\t\t\t\t\ttype: g.type,\n\t\t\t\t\tlst:\n\t\t\t\t\t\tg.type == 'hierCluster'\n\t\t\t\t\t\t\t? g.lst.map(tw => ({ name: tw.term.gene || tw.term.name }))\n\t\t\t\t\t\t\t: g.lst.filter(tw => tw.term.type == TermTypes.GENE_VARIANT).map(tw => ({ name: tw.term.name })),\n\t\t\t\t\tmode:\n\t\t\t\t\t\tg.type == 'hierCluster'\n\t\t\t\t\t\t\t? s.dataType // is clustering group, pass dataType\n\t\t\t\t\t\t\t: // !!subject to change!! when group is not clustering, and ds has mutation, defaults to MUTATION_CNV_FUSION\n\t\t\t\t\t\t\tthis.parent.state.termdbConfig.queries?.snvindel\n\t\t\t\t\t\t\t? TermTypes.GENE_VARIANT\n\t\t\t\t\t\t\t: '',\n\t\t\t\t\tselected: true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (geneInputType == 'hierCluster') {\n\t\t\t// Gene set edit UI under \"Clustering\" control panel doen't need \"create New Group\"\n\t\t\treturn\n\t\t}\n\t\tconst td2 = tr.append('td').style('display', 'block').style('padding', '5px 0px')\n\t\tconst createNewGrpDiv = td2.append('div').append('label')\n\n\t\tconst createBtn = createNewGrpDiv\n\t\t\t.append('button')\n\t\t\t.html('Create New Group')\n\t\t\t.property('disabled', true)\n\t\t\t.on('click', () => {\n\t\t\t\ttip.clear()\n\t\t\t\tthis.setMenuBackBtn(tip.d.append('div'), () => controlPanelBtn.click(), 'Back')\n\t\t\t\tconst name = nameInput.property('value')\n\t\t\t\tconst s = parent.config.settings.hierCluster\n\t\t\t\tselectedGroup = {\n\t\t\t\t\tindex: tg.length,\n\t\t\t\t\tname,\n\t\t\t\t\tlabel: name,\n\t\t\t\t\tlst: [],\n\t\t\t\t\tstatus: 'new',\n\t\t\t\t\tmode: parent.state.termdbConfig.queries?.snvindel ? TermTypes.GENE_VARIANT : ''\n\t\t\t\t}\n\t\t\t\ttriggerGenesetEdit(tip.d.append('div'))\n\t\t\t})\n\n\t\tconst nameInput = createNewGrpDiv\n\t\t\t.append('input')\n\t\t\t.style('margin', '2px 5px')\n\t\t\t.style('width', '210px')\n\t\t\t.attr('placeholder', 'Group Name')\n\t\t\t.on('input', () => {\n\t\t\t\tcreateBtn.property('disabled', !nameInput.property('value'))\n\t\t\t})\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.key == 'Enter' && !createBtn.property('disabled')) {\n\t\t\t\t\tcreateBtn.node().click()\n\t\t\t\t}\n\t\t\t})\n\n\t\t// if (parent.opts.customInputs?.geneset) {\n\t\t// \tfor (const btn of parent.opts.customInputs.geneset) {\n\t\t// \t\ttd.append('button')\n\t\t// \t\t\t.html(btn.label)\n\t\t// \t\t\t.on('click', () => {\n\t\t// \t\t\t\ttip.hide()\n\t\t// \t\t\t\tbtn.showInput({\n\t\t// \t\t\t\t\tcallback: genesArr => {\n\t\t// \t\t\t\t\t\tconst geneLst = genesArr.map(gene => ({ gene }))\n\t\t// \t\t\t\t\t\t// TODO: this may not be the first term group\n\t\t// \t\t\t\t\t\tlet group = tg.find(g => g.lst.find(tw => tw.term?.type == 'geneVariant'))\n\t\t// \t\t\t\t\t\tif (!group) group = tg[0]\n\t\t// \t\t\t\t\t\tconst lst = group.lst.filter(tw => tw.term.type != 'geneVariant')\n\t\t// \t\t\t\t\t\tconst tws = geneLst.map(d => {\n\t\t// \t\t\t\t\t\t\t//if it was present use the previous term, genomic range terms require chr, start and stop fields, found in the original term\n\t\t// \t\t\t\t\t\t\tlet tw = group.lst.find(tw => tw.term.name == d.symbol || tw.term.name == d.gene)\n\t\t// \t\t\t\t\t\t\tif (!tw)\n\t\t// \t\t\t\t\t\t\t\ttw = {\n\t\t// \t\t\t\t\t\t\t\t\t$id: get$id(),\n\t\t// \t\t\t\t\t\t\t\t\tterm: {\n\t\t// \t\t\t\t\t\t\t\t\t\tname: d.symbol || d.gene,\n\t\t// \t\t\t\t\t\t\t\t\t\ttype: 'geneVariant'\n\t\t// \t\t\t\t\t\t\t\t\t},\n\t\t// \t\t\t\t\t\t\t\t\tq: {}\n\t\t// \t\t\t\t\t\t\t\t}\n\t\t// \t\t\t\t\t\t\treturn tw\n\t\t// \t\t\t\t\t\t})\n\t\t// \t\t\t\t\t\tgroup.lst = [...lst, ...tws]\n\t\t// \t\t\t\t\t\tif (!group.lst.length) tg.splice(selectedGroup.index, 1)\n\t\t// \t\t\t\t\t\tapp.dispatch({\n\t\t// \t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t// \t\t\t\t\t\t\tid: this.parent.id,\n\t\t// \t\t\t\t\t\t\tconfig: {\n\t\t// \t\t\t\t\t\t\t\ttermgroups: tg\n\t\t// \t\t\t\t\t\t\t}\n\t\t// \t\t\t\t\t\t})\n\t\t// \t\t\t\t\t}\n\t\t// \t\t\t\t})\n\t\t// \t\t\t})\n\t\t// \t}\n\t\t// }\n\t}\n\n\tsetMenuBackBtn(holder, callback, label) {\n\t\tholder\n\t\t\t.attr('tabindex', 0)\n\t\t\t.style('padding', '5px')\n\t\t\t.style('text-decoration', 'underline')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.style('margin-bottom', '12px')\n\t\t\t.html(`&#171; ${label}`)\n\t\t\t.on('click', callback)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.key == 'Enter') event.target.click()\n\t\t\t})\n\t}\n\n\tsetTermGroupSelector(holder, tg) {\n\t\t//const label = grpDiv.append('label')\n\t\t//label.append('span').html('')\n\t\tconst firstGrpWithGeneTw = tg.find(g =>\n\t\t\tg.lst.find(tw => tw.term.type == TermTypes.GENE_VARIANT && g.type !== 'hierCluster')\n\t\t)\n\t\tconst groups = tg.map((g, index) => {\n\t\t\treturn {\n\t\t\t\tindex,\n\t\t\t\tname: g.name,\n\t\t\t\ttype: g.type,\n\t\t\t\tlst: g.lst.filter(tw => tw.term.type == TermTypes.GENE_VARIANT).map(tw => ({ name: tw.term.name })),\n\t\t\t\tmode: this.parent.state.termdbConfig.queries?.snvindel ? TermTypes.GENE_VARIANT : '',\n\t\t\t\tselected: g === firstGrpWithGeneTw\n\t\t\t}\n\t\t})\n\t\tconst nonHierClusterGroups = groups.filter(g => g.type != 'hierCluster')\n\n\t\tconst groupSelect = holder.append('select').style('width', '218px').style('margin', '2px 5px')\n\t\tfor (const [i, group] of nonHierClusterGroups.entries()) {\n\t\t\tif (group.label) continue\n\t\t\tif (group.name) group.label = group.name\n\t\t\telse group.label = `Unlabeled group #${i + 1}` // cannot assume \"gene\" group\n\t\t}\n\n\t\tgroupSelect\n\t\t\t.selectAll('option')\n\t\t\t.data(nonHierClusterGroups)\n\t\t\t.enter()\n\t\t\t.append('option')\n\t\t\t.property('selected', grp => grp.selected)\n\t\t\t.attr('value', (d, i) => i)\n\t\t\t.html(grp => grp.label)\n\n\t\treturn { nonHierClusterGroups, groupSelect }\n\t}\n\n\tappendDictInputs(self, app, parent, table) {\n\t\ttip.clear()\n\t\tif (!parent.selectedGroup) parent.selectedGroup = self.chartType == 'hierCluster' ? 1 : 0\n\t\tapp.tip.d.append('hr')\n\t\tself.addDictMenu(app, parent, app.tip.d.append('div'))\n\t}\n\n\tgenerateCNVItems(self, app, parent, table) {\n\t\ttable.attr('class', null) // remove the hoverover background for CNV button\n\t\tconst m = parent.config.settings.matrix\n\t\tconst mutationLegendGrp = parent.legendData.find(l => l.dt?.includes(dtsnvindel))\n\t\tif (\n\t\t\tm.showMatrixCNV !== 'none' &&\n\t\t\t(m.allMatrixMutationHidden ||\n\t\t\t\t!mutationLegendGrp ||\n\t\t\t\tmutationLegendGrp.crossedOut ||\n\t\t\t\t!mutationLegendGrp.items.find(i => !i.greyedOut && !i.crossedOut))\n\t\t) {\n\t\t\t// when all mutation items in the current matrix are hidden or there is no mutation data\n\t\t\ttable.select(\"input[type='radio'][value='none']\").property('disabled', true)\n\n\t\t\ttable.select(\"input[type='radio'][value='none'] + span\").style('opacity', '0.5').on('mouseup', null)\n\t\t}\n\t\tif (m.addMutationCNVButtons && parent.chartType !== 'hierCluster' && m.showMatrixCNV == 'bySelection')\n\t\t\tparent.CNVControlCallback('bySelection')\n\t}\n\n\tgenerateMutationItems(self, app, parent, table) {\n\t\ttable.attr('class', null) // remove the hoverover background for CNV button\n\t\tconst m = parent.config.settings.matrix\n\t\tconst cnvLegendGrp = parent.legendData.find(l => l.dt?.includes(dtcnv))\n\t\tif (\n\t\t\tm.showMatrixMutation !== 'none' &&\n\t\t\t(m.allMatrixCNVHidden ||\n\t\t\t\t!cnvLegendGrp ||\n\t\t\t\tcnvLegendGrp.crossedOut ||\n\t\t\t\t!cnvLegendGrp.items.find(i => !i.greyedOut && !i.crossedOut))\n\t\t) {\n\t\t\t// when all CNV items in the current matrix are hidden or there is no CNV data\n\t\t\ttable.select(\"input[type='radio'][value='none']\").property('disabled', true)\n\n\t\t\ttable.select(\"input[type='radio'][value='none'] + span\").style('opacity', '0.5').on('mouseup', null)\n\t\t}\n\t\tif (m.addMutationCNVButtons && parent.chartType !== 'hierCluster' && m.showMatrixMutation == 'bySelection')\n\t\t\tparent.mutationControlCallback('bySelection')\n\t}\n\tupdateSamplesControls(self, app, parent, table) {\n\t\tif (parent.chartType == 'hierCluster' && parent.config.settings.hierCluster.clusterSamples) {\n\t\t\tconst l = parent.config.settings.matrix.controlLabels\n\t\t\tconst sortingControl = select(\n\t\t\t\ttable\n\t\t\t\t\t.selectAll('td')\n\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\treturn select(this).text() == `Sort ${l.Sample} Priority`\n\t\t\t\t\t})\n\t\t\t\t\t.node()\n\t\t\t\t\t.closest('tr')\n\t\t\t)\n\t\t\tsortingControl.style('display', 'none')\n\t\t}\n\t}\n\n\tasync addDictMenu(app, parent, holder = undefined) {\n\t\t//app.tip.clear()\n\n\t\tconst termdb = await import('#termdb/app')\n\t\ttermdb.appInit({\n\t\t\tholder: holder || app.tip.d,\n\t\t\tvocabApi: this.parent.app.vocabApi,\n\t\t\tfocus: 'off',\n\t\t\tstate: {\n\t\t\t\tvocab: this.parent.state.vocab,\n\t\t\t\tactiveCohort: this.parent.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: { target: 'matrix', detail: 'termgroups' }\n\t\t\t\t}\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tsubmit_lst: termlst => {\n\t\t\t\t\tthis.submit_lst(termlst)\n\t\t\t\t\tapp.tip.hide()\n\t\t\t\t}\n\t\t\t},\n\t\t\tsearch: {\n\t\t\t\tfocus: 'off'\n\t\t\t}\n\t\t})\n\t}\n\n\tasync 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, this.opts.app.vocabApi)\n\t\t\t\treturn tw\n\t\t\t})\n\t\t)\n\n\t\tconst termgroups = structuredClone(this.parent.config.termgroups)\n\n\t\tconst i = termgroups.findIndex(g => g.name == 'Variables')\n\t\tif (i !== -1) {\n\t\t\tconst grp = termgroups[i]\n\t\t\tgrp.lst.push(...newterms)\n\t\t\tthis.parent.app.dispatch({\n\t\t\t\ttype: 'plot_nestedEdits',\n\t\t\t\tid: this.parent.id,\n\t\t\t\tedits: [\n\t\t\t\t\t{\n\t\t\t\t\t\tnestedKeys: ['termgroups', i, '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 grp = { name: 'Variables', lst: newterms }\n\t\t\ttermgroups.push(grp)\n\t\t\tthis.parent.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.parent.id,\n\t\t\t\tconfig: { termgroups }\n\t\t\t})\n\t\t}\n\t}\n\n\tsetZoomInput() {\n\t\tconst holder = this.opts.holder.append('div').style('display', 'inline-block').style('margin-left', '50px')\n\t\tconst s = this.parent.settings.matrix || this.parent.config.settings.matrix\n\t\tthis.zoomApi = zoom({\n\t\t\tholder,\n\t\t\ttitle:\n\t\t\t\t'Zoom factor relative to the ideal column width, as computed for the number of columns versus available screen width',\n\t\t\tunit: '',\n\t\t\twidth: '80px',\n\t\t\tsettings: {\n\t\t\t\tvalue: 1,\n\t\t\t\tmin: 0.1, // will be determined once the auto-computed width is determined\n\t\t\t\tmax: 10, // will be determined once the auto-computed width is determined\n\t\t\t\tincrement: s.zoomIncrement,\n\t\t\t\tstep: s.zoomStep || 5\n\t\t\t},\n\t\t\tcallback: zoomLevel => {\n\t\t\t\tconst p = this.parent\n\t\t\t\tconst d = p.dimensions\n\t\t\t\tconst s = p.settings.matrix\n\t\t\t\tconst c = p.getVisibleCenterCell(0)\n\t\t\t\tp.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: p.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t\tzoomLevel,\n\t\t\t\t\t\t\t\tzoomCenterPct: 0.5,\n\t\t\t\t\t\t\t\tzoomIndex: c.totalIndex,\n\t\t\t\t\t\t\t\tzoomGrpIndex: c.grpIndex\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t},\n\t\t\treset: () => {\n\t\t\t\tconst s = this.parent.settings.matrix\n\t\t\t\tconst d = this.parent.dimensions\n\t\t\t\tthis.parent.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.parent.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t\tzoomLevel: 1,\n\t\t\t\t\t\t\t\tzoomCenterPct: 0\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tsetDragToggle(opts = {}) {\n\t\tconst defaults = {\n\t\t\tmouseMode: 'select',\n\t\t\tactiveBgColor: 'rgb(255, 255, 255)'\n\t\t}\n\n\t\t// hardcode to always be in select mode on first render\n\t\topts.target.style('cursor', 'default')\n\n\t\tconst instance = {\n\t\t\topts: Object.assign({}, defaults, opts),\n\t\t\t//holder: opts.holder.append('div').style('display', 'inline-block')\n\t\t\tdom: {\n\t\t\t\tselectBtn: opts.holder\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.attr('aria-label', 'Click the matrix to select data')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('width', '25px')\n\t\t\t\t\t.style('height', '24.5px')\n\t\t\t\t\t.style('background-color', defaults.activeBgColor)\n\t\t\t\t\t.on('click', () => setMode('select')),\n\n\t\t\t\tgrabBtn: opts.holder\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.attr('aria-label', 'Click the matrix to drag and move')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('width', '25px')\n\t\t\t\t\t.style('height', '24.5px')\n\t\t\t\t\t.on('click', () => setMode('pan'))\n\t\t\t}\n\t\t}\n\n\t\t//icons.crosshair(instance.dom.selectBtn, { width: 18, height: 18, transform: 'translate(50,50)' })\n\t\ticons.arrowPointer(instance.dom.selectBtn, { width: 14, height: 14, transform: 'translate(50,50)' })\n\t\ticons.grab(instance.dom.grabBtn, { width: 14, height: 14, transform: 'translate(30,50)' })\n\n\t\tconst self = this\n\t\tfunction setMode(m) {\n\t\t\tinstance.opts.mouseMode = m\n\t\t\tself.parent.settings.matrix.mouseMode = m\n\t\t\topts.target.style('cursor', m == 'select' ? 'default' : 'grab')\n\t\t\tinstance.dom.selectBtn.style('background-color', m == 'select' ? instance.opts.activeBgColor : '')\n\t\t\tinstance.dom.grabBtn.style('background-color', m == 'pan' ? instance.opts.activeBgColor : '')\n\t\t}\n\n\t\t// NOTE:\n\t\tthis.dragToggleApi = {\n\t\t\tupdate(s = {}) {\n\t\t\t\tObject.assign(instance.opts, s)\n\t\t\t\tsetMode(instance.opts.mouseMode)\n\t\t\t},\n\t\t\tgetSettings() {\n\t\t\t\treturn {\n\t\t\t\t\tmouseMode: instance.opts.mouseMode\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tsetSvgScroll(state) {\n\t\tthis.svgScrollApi = svgScroll({\n\t\t\tholder: this.parent.dom.scroll,\n\t\t\theight: state.config.settings.matrix.scrollHeight,\n\t\t\tcallback: (dx, eventType) => {\n\t\t\t\tconst p = this.parent\n\t\t\t\tconst s = p.settings.matrix\n\t\t\t\tconst d = p.dimensions\n\t\t\t\tif (eventType == 'move') {\n\t\t\t\t\tp.dom.seriesesG.attr('transform', `translate(${d.xOffset + d.seriesXoffset - dx},${d.yOffset})`)\n\t\t\t\t\tp.clusterRenderer.translateElems(-dx, s, d)\n\t\t\t\t\tp.layout.top.attr.adjustBoxTransform(-dx)\n\t\t\t\t\tp.layout.btm.attr.adjustBoxTransform(-dx)\n\t\t\t\t\tif (p.dom.topDendrogram) {\n\t\t\t\t\t\tp.dom.topDendrogram.attr('transform', `translate(${p.topDendroX - dx},0)`)\n\t\t\t\t\t}\n\t\t\t\t} else if (eventType == 'up') {\n\t\t\t\t\tconst c = p.getVisibleCenterCell(-dx)\n\t\t\t\t\tp.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: p.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t\t\tzoomCenterPct: 0.5,\n\t\t\t\t\t\t\t\t\tzoomIndex: c.totalIndex,\n\t\t\t\t\t\t\t\t\tzoomGrpIndex: c.grpIndex\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n}\n"],
+  "mappings": 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CF;AAAA,MACD;AAAA,IACD,CAAC;AAAA,EACF;AACD;",
+  "names": ["s", "a", "d", "self", "tip", "geneList", "g"]
+}

package/dist/chunk-Y3TDC7NU.js

@@ -0,0 +1,170 @@
+import {
+  getEmptyCell,
+  maySetEmptyCell,
+  setCellProps
+} from "./chunk-GPOECA3V.js";
+import {
+  TermTypeGroups
+} from "./chunk-IGEQI6MR.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.serieses.js
+var matrix_serieses_exports = {};
+__export(matrix_serieses_exports, {
+  getSerieses: () => getSerieses
+});
+function getSerieses(data) {
+  const s = this.settings.matrix;
+  const serieses = [];
+  const { colw, dx, dy, xMin, xMax } = this.dimensions;
+  const dvt = this.config.divideBy || {};
+  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
+  const legendGroups = {};
+  this.colorScaleByTermId = {};
+  for (const t of this.termOrder) {
+    const $id = t.tw.$id;
+    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
+    const isDivideByTerm = termid === divideByTermId;
+    const emptyGridCells = [];
+    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
+    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
+    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
+    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
+    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
+    const series = {
+      t,
+      tw: t.tw,
+      cells: [],
+      y,
+      hoverY0,
+      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
+    };
+    for (const so of this.unfilteredSampleOrder) {
+      const { totalIndex, grpIndex, row } = so;
+      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
+      const anno = row[$id];
+      const cellTemplate = {
+        s: so,
+        sample: row.sample,
+        tw: t.tw,
+        term: t.tw.term,
+        termid,
+        $id,
+        totalIndex,
+        grpIndex,
+        row,
+        t,
+        seriesY: y
+      };
+      if (!anno) {
+        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
+          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
+          series.cells.push(cell);
+        }
+        continue;
+      }
+      const key = anno.key;
+      const values = anno.filteredValues || anno.values || [anno.value];
+      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
+      const height = !s.transpose ? s.rowh / numRects : colw;
+      const width = !s.transpose ? colw : colw / values.length;
+      const siblingCells = [];
+      if (!anno || !anno.renderedValues?.length) {
+        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
+          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
+          series.cells.push(cell);
+        }
+        continue;
+      }
+      for (const [i, value] of values.entries()) {
+        const cell = Object.assign({ key, siblingCells }, cellTemplate);
+        cell.valueIndex = i;
+        let legend;
+        if (typeof t.tw.setCellProps == "function") {
+          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
+        } else {
+          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
+          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
+        }
+        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
+        if (legend) {
+          for (const l of [legendGroups, so.grp.legendGroups]) {
+            if (!l) continue;
+            if (!l[legend.group]) {
+              l[legend.group] = {
+                ref: legend.ref,
+                values: {},
+                order: legend.order,
+                $id,
+                origin: legend.entry.origin
+              };
+              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
+            }
+            const lg = l[legend.group];
+            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
+            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
+            if (!lg.values[legendK]) {
+              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
+              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
+            }
+            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
+            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
+              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
+            } else lg.values[legendK].samples.add(row.sample);
+            if (isDivideByTerm) {
+              lg.values[legend.value].isExcluded = so.grp.isExcluded;
+            }
+          }
+        }
+        if (!so.grp.isExcluded) {
+          if (anno.renderedValues.includes(value)) series.cells.push(cell);
+          siblingCells.push(cell);
+        }
+      }
+      if (s.showGrid == "rect" && !so.grp.isExcluded) {
+        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions);
+        if (cell) emptyGridCells.push(cell);
+      }
+    }
+    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
+    if (series.cells.length) serieses.push(series);
+  }
+  addAllHiddenLegendGroups(legendGroups, this);
+  this.legendData = this.getLegendData(legendGroups, data.refs, this);
+  for (const grp of this.sampleGroups) {
+    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
+  }
+  return serieses;
+}
+function addAllHiddenLegendGroups(legendGroups, self) {
+  for (const valueFilter of self.config.legendValueFilter.lst) {
+    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
+      legendGroups[valueFilter.tvs.term.$id] = {
+        ref: {},
+        values: {},
+        $id: valueFilter.tvs.term.$id
+      };
+    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
+      legendGroups[valueFilter.legendGrpName] = {
+        ref: {},
+        values: {},
+        dt: [valueFilter.tvs.values[0].dt],
+        origin: valueFilter.tvs.values[0].origin
+      };
+    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
+      legendGroups[valueFilter.tvs.term.$id] = {
+        ref: {},
+        values: {},
+        $id: valueFilter.tvs.term.$id
+      };
+    }
+  }
+}
+
+export {
+  getSerieses,
+  matrix_serieses_exports
+};
+//# sourceMappingURL=chunk-Y3TDC7NU.js.map