@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/chunk-H3BSKMND.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.xtw.ts", "../plots/matrix/matrix.js"],
+  "sourcesContent": ["import type { ContinuousXTW, DiscreteXTW } from '#tw'\nimport { TwRouter } from '#tw'\nimport type { TermWrapper } from '#types'\nimport { convertUnits } from '#shared/helpers.js'\n\nlet addons\n\nexport function getTermGroups(termgroups, app) {\n\tconst termGroups = structuredClone(termgroups)\n\t// should only set the addons once, it should not vary from one call to the next\n\tif (!addons)\n\t\taddons = {\n\t\t\tQualTWValues: discreteAddons,\n\t\t\tQualTWPredefinedGS: discreteAddons,\n\t\t\tQualTWCustomGS: discreteAddons,\n\t\t\tNumTWRegularBin: discreteAddons,\n\t\t\tNumTWCustomBin: discreteAddons,\n\t\t\tNumTWCont: continuousAddons\n\t\t}\n\n\tconst opts = {\n\t\tvocabApi: app.vocabApi,\n\t\taddons\n\t}\n\n\tfor (const [origIndex, tG] of termGroups.entries()) {\n\t\ttG.origIndex = origIndex\n\t\tif (tG.type == 'hierCluster') continue\n\t\tconst xtwlst: (MatrixTWObj | TermWrapper)[] = []\n\t\tfor (const tw of tG.lst) {\n\t\t\txtwlst.push(tw.type in opts.addons ? TwRouter.init(tw, opts) : tw)\n\t\t}\n\t\ttG.lst = xtwlst\n\t}\n\treturn termGroups\n}\n\nexport type SetCellPropsSignature = {\n\tvalue: (\n\t\t/** a plain object for matrix cell data to be rendered, including sibling cells */\n\t\tcell: any,\n\t\tanno: any,\n\t\tvalue: string | number,\n\t\ts: any,\n\t\tt: any,\n\t\tself: any,\n\t\twidth: number,\n\t\theight: number,\n\t\tdx: number,\n\t\tdy: number,\n\t\ti: number\n\t) => any\n}\n\ninterface MatrixTWObj {\n\tsetCellProps: SetCellPropsSignature\n}\n\nconst discreteAddons: MatrixTWObj = {\n\tsetCellProps: {\n\t\tvalue: function (\n\t\t\tthis: DiscreteXTW,\n\t\t\tcell: any,\n\t\t\tanno: any,\n\t\t\tvalue: string | number,\n\t\t\ts: any,\n\t\t\tt: any,\n\t\t\tself: any,\n\t\t\twidth: number,\n\t\t\theight: number,\n\t\t\tdx: number,\n\t\t\tdy: number,\n\t\t\ti: number\n\t\t) {\n\t\t\tconst tw = this.getTw()\n\t\t\tconst key = anno.key\n\t\t\tconst values = tw.term.values || {}\n\t\t\tcell.label = 'label' in anno ? anno.label : values[key]?.label ? values[key].label : key\n\t\t\tconst tw$id = tw.$id\n\t\t\tcell.fill =\n\t\t\t\tself.config.settings.matrix.twSpecificSettings?.[tw$id!]?.[key]?.color ||\n\t\t\t\tanno.color ||\n\t\t\t\tvalues[anno.key]?.color ||\n\t\t\t\tself.data.refs.byTermId?.[tw$id!]?.bins?.find(b => anno.key == b.name)?.color\n\t\t\t// only for numeric terms for now\n\t\t\t// TODO: should also consider categorical term.values[*].order\n\t\t\tcell.order = t.ref.bins ? t.ref.bins.findIndex(bin => bin.name == key) : 0\n\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y = height * i\n\t\t\tconst group = tw.legend?.group || tw$id\n\t\t\treturn { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } }\n\t\t}\n\t}\n}\n\nconst continuousAddons: MatrixTWObj = {\n\tsetCellProps: {\n\t\tvalue: function (\n\t\t\tthis: ContinuousXTW,\n\t\t\tcell: any,\n\t\t\tanno: any,\n\t\t\tvalue: string | number,\n\t\t\ts: any,\n\t\t\tt: any,\n\t\t\tself: any,\n\t\t\twidth: number,\n\t\t\theight: number,\n\t\t\tdx: number,\n\t\t\tdy: number,\n\t\t\ti: number\n\t\t) {\n\t\t\tconst tw = this.getTw()\n\t\t\tconst key = anno.key\n\t\t\tconst values = tw.term.values || {}\n\t\t\tcell.label = 'label' in anno ? anno.label : values[key]?.label ? values[key].label : key\n\t\t\tcell.fill = anno.color || values[anno.key]?.color\n\t\t\tconst tw$id = tw.$id\n\t\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\t\tif (!twSpecificSettings[tw$id!]) twSpecificSettings[tw$id!] = {}\n\t\t\tconst twSettings = twSpecificSettings[tw$id!]\n\t\t\tif (!twSettings.contBarH) twSettings.contBarH = s.barh\n\t\t\tif (!('gap' in twSettings)) twSettings.contBarGap = 4\n\n\t\t\tconst specialValue = tw.term.values?.[cell.key]\n\n\t\t\t// handle uncomputable values\n\t\t\t// TODO: the server response data should not have uncomputable values when mode='continuous'\n\t\t\t// this may be implemented in getData(), but will require lots of testing since it is used\n\t\t\t// by multiple charts\n\t\t\tif (specialValue?.uncomputable) {\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\tcell.y = height * i\n\t\t\t\tcell.height = twSettings.contBarH\n\t\t\t\tcell.fill = 'transparent'\n\t\t\t\tcell.label = specialValue.label\n\t\t\t\tconst group = tw.legend?.group || tw.$id\n\t\t\t\treturn {\n\t\t\t\t\tref: t.ref,\n\t\t\t\t\tgroup,\n\t\t\t\t\tvalue: specialValue.label || specialValue.key,\n\t\t\t\t\tentry: { key, label: cell.label, fill: cell.fill }\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// TODO: may use color scale instead of bars\n\t\t\t// for bars, use a hardcoded color; TODO: allow a user to customize the bar color?\n\t\t\tcell.fill = self.config.settings.matrix.twSpecificSettings?.[tw$id!]?.contBarColor || '#555'\n\t\t\tif (s.transpose) {\n\t\t\t\tcell.height = t.scale(cell.key)\n\t\t\t\tcell.x = twSettings.contBarGap // - cell.width\n\t\t\t} else {\n\t\t\t\tconst vc = cell.term.valueConversion\n\t\t\t\tlet renderV = vc ? cell.key * vc.scaleFactor : cell.key\n\t\t\t\t// todo: convert from a boolean into maybe `q.units or q.transform: 'zscore' | ...`\n\t\t\t\tif (this.q.convert2ZScore) {\n\t\t\t\t\trenderV = (renderV - t.mean) / t.std\n\n\t\t\t\t\t// show positive z-score as soft red and negative z-score as soft blue\n\t\t\t\t\tcell.fill = renderV > 0 ? '#FF6666' : '#6666FF'\n\t\t\t\t\tcell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`\n\t\t\t\t}\n\t\t\t\tcell.label =\n\t\t\t\t\t'label' in anno\n\t\t\t\t\t\t? anno.label\n\t\t\t\t\t\t: values[key]?.label\n\t\t\t\t\t\t? values[key].label\n\t\t\t\t\t\t: this.term.unit\n\t\t\t\t\t\t? `${cell.key.toFixed(2)} ${this.term.unit}`\n\t\t\t\t\t\t: cell.key.toFixed(2)\n\t\t\t\tcell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV)\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\tcell.y =\n\t\t\t\t\trenderV >= 0\n\t\t\t\t\t\t? t.counts.posMaxHt + twSettings.contBarGap - cell.height\n\t\t\t\t\t\t: t.counts.posMaxHt + twSettings.contBarGap\n\t\t\t\tcell.convertedValueLabel = !vc ? '' : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t\t\t}\n\t\t}\n\t}\n}\n", "import { getCompInit, copyMerge, deepEqual } from '#rx'\nimport { setMatrixDom } from './matrix.dom'\nimport { setInteractivity } from './matrix.interactivity'\nimport { setRenderers } from './matrix.renderers'\nimport { MatrixCluster } from './matrix.cluster'\nimport { MatrixControls } from './matrix.controls'\nimport * as matrixData from './matrix.data'\nimport * as matrixLayout from './matrix.layout'\nimport * as matrixSerieses from './matrix.serieses'\nimport * as matrixLegend from './matrix.legend'\nimport * as matrixGroups from './matrix.groups'\nimport { setComputedConfig } from './matrix.config'\nimport { getTermGroups } from './matrix.xtw'\nimport svgLegend from '#dom/svg.legend'\nimport { mclass, dt2label, morigin, dtsnvindel, dtcnv } from '#shared/common.js'\nimport { select } from 'd3-selection'\nimport { sayerror } from '#dom'\nimport { getCombinedTermFilter } from '#filter'\nimport { rebaseGroupFilter } from '../../mass/groups.js'\nimport { PlotBase } from '#plots/PlotBase.js'\n\nexport class Matrix extends PlotBase {\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = 'matrix'\n\t\tthis.holderTitle = 'Sample Matrix'\n\t\tthis.optionalFeatures = JSON.parse(sessionStorage.getItem('optionalFeatures') || `{}`)?.matrix || []\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\t}\n\n\tasync init(appState) {\n\t\tconst opts = this.opts\n\t\tif (opts.reactsTo) this.reactsTo = opts.reactsTo\n\t\tthis.setDom = setMatrixDom\n\t\tthis.setDom(opts)\n\n\t\tthis.config = appState.plots.find(p => p.id === this.id)\n\t\tthis.settings = Object.assign({}, this.config.settings.matrix)\n\t\tthis.computed = {} // will hold settings/configuration/data that are computed or derived from other data\n\t\tif (this.dom.header) this.dom.header.html(this.config.preBuiltPlotTitle || this.holderTitle)\n\n\t\tthis.setControls(appState)\n\t\tthis.clusterRenderer = new MatrixCluster({ holder: this.dom.cluster, app: this.app, parent: this })\n\t\tthis.legendRenderer = svgLegend({\n\t\t\tholder: this.dom.legendG,\n\t\t\trectFillFxn: d => d.color,\n\t\t\ticonStroke: '#aaa',\n\t\t\thandlers: {\n\t\t\t\tlegend: {\n\t\t\t\t\tclick: this.legendClick\n\t\t\t\t}\n\t\t\t},\n\t\t\tsettings: {\n\t\t\t\tisExcludedAttr: 'isExcluded'\n\t\t\t},\n\t\t\tnote: 'CLICK A ROW LABEL OR ITEM TO APPLY FILTERING'\n\t\t})\n\n\t\t// enable embedding of termsetting and tree menu inside self.dom.menu\n\t\tthis.customTipApi = this.dom.tip.getCustomApi({\n\t\t\td: this.dom.menubody,\n\t\t\tclear: event => {\n\t\t\t\tif (event?.target) this.dom.menutop.style('display', 'none')\n\t\t\t\tthis.dom.menubody.selectAll('*').remove()\n\t\t\t\treturn this.customTipApi\n\t\t\t},\n\t\t\tshow: () => {\n\t\t\t\tthis.dom.menubody.style('display', 'block')\n\t\t\t},\n\t\t\thide: () => {\n\t\t\t\t//this.dom.menubody.style('display', 'none')\n\t\t\t}\n\t\t})\n\n\t\tthis.setPill(appState)\n\n\t\t/*\n\t\tLevels of mclass overrides, from more general to more specific. Same logic for dt2label\n\n\t\t1. server-level:\n\t\t  - specified as serverconfig.commonOverrides\n\t\t  - applied to the mclass from #shared/common on server startup\n\t\t  - applies to all datasets and charts\n\t\t  - overrides are applied to the static common.mclass object\n\t\t\n\t\t2. dataset-level: \n\t\t  - specified as termdb.mclass in the dataset's js file\n\t\t  - applied to the termdbConfig.mclass payload as returned from the /termdb?getTermdbConfig=1 route\n\t\t  - applies to all charts rendered for only the dataset/dslabel\n\t\t  - overrides are applied to a copy of common.mclass, not the original \"static\" object\n\n\t\t3. chart-level: \n\t\t  - specified as termdb[chartType].mclass in the dataset's js file\n\t\t  - applied to the termdbConfig[chartType].mclass payload as returned from the /termdb?getTermdbConfig=1 route\n\t\t  - applies to only the specific chart type as rendered for the dataset/dslabel\n\t\t  - overrides are applied to a copy of common.mclass + termdb.mclass\n\n\t\t!!! NOTE: \n\t\t\tBoolean configuration flags for mutually exclusive values may cause conflicting configurations\n\t\t\tin the resulting merged overrides, as outputted by rx.copyMerge()\n\t\t!!!\n\t\t*/\n\t\tconst commonKeys = { mclass, dt2label, morigin }\n\t\tfor (const k in commonKeys) {\n\t\t\tconst v = commonKeys[k]\n\t\t\tthis[k] = copyMerge({}, v, appState.termdbConfig[k] || {}, appState.termdbConfig.matrix?.[k] || {})\n\t\t}\n\t}\n\n\tsetControls(appState) {\n\t\t//if (this.opts.controls) return\n\t\tthis.controlsRenderer = new MatrixControls(\n\t\t\t{\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tparent: this,\n\t\t\t\tholder: this.dom.controls,\n\t\t\t\tgetSvg: () => this.dom.svg.node()\n\t\t\t},\n\t\t\tappState\n\t\t)\n\t}\n\n\t// reactsTo(action) {\n\t// \t// note: a parent app or 'plot' component is expected to already have\n\t// \t// a comprehensive reactsTo() call to filter the actions for this component,\n\t// \t// so only farther selective action filters should be applied here as needed\n\t// \treturn true\n\t// }\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tconst filter0 = appState.termfilter.filter0\n\t\tthis.prevFilter0 = this.state?.filter0 // will be used to detect cohort change\n\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\tisVisible: true,\n\t\t\tconfig,\n\t\t\tfilter: termfilter.filter,\n\t\t\tfilter0, // read-only, invisible filter currently only used for gdc dataset\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),\n\t\t\ttokenVerificationMessage: this.app.vocabApi.tokenVerificationMessage,\n\t\t\tvocab: appState.vocab,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tclusterMethod: config.settings.hierCluster?.clusterMethod,\n\t\t\tdistanceMethod: config.settings.hierCluster?.distanceMethod,\n\t\t\tclusterSamples: config.settings.hierCluster?.clusterSamples,\n\t\t\tclusterRows: config.settings.hierCluster?.clusterRows,\n\t\t\tzScoreTransformation: config.settings.hierCluster?.zScoreTransformation,\n\t\t\tnav: appState.nav,\n\t\t\tgroups: rebaseGroupFilter(appState)\n\t\t}\n\t}\n\n\tasync main() {\n\t\ttry {\n\t\t\tthis.config = await this.getMutableConfig()\n\t\t\tif (this.mayRequireToken()) return\n\t\t\t// do not assign this.termgroups until the data request is complete, to avoid stale value in a race condition;\n\t\t\t// this termGroups value is directly associated with the submitted data request, and the response will match\n\t\t\t// the tw.$id's in these term groups\n\t\t\tconst termGroups = getTermGroups(this.config.termgroups, this.app)\n\n\t\t\tconst prevTranspose = this.settings.transpose\n\t\t\t// controlsRenderer.getSettings() supplies settings that are not tracked in the global app and plot state\n\t\t\t// use structuredClone to avoid overwriting of original settings.matrix\n\t\t\tObject.assign(this.settings, structuredClone(this.config.settings), this.controlsRenderer.getSettings())\n\n\t\t\tthis.dom.loadingDiv.selectAll('*').remove()\n\t\t\tthis.dom.loadingDiv.html('').style('display', '').style('position', 'relative').style('left', '45%')\n\t\t\tthis.dom.svg.style('opacity', 0.1).style('pointer-events', 'none')\n\n\t\t\t// reset highlighted top/left dendrogram children to black when data request is triggered\n\t\t\tdelete this.clickedClusterIds\n\t\t\tdelete this.clickedLeftClusterIds\n\n\t\t\ttry {\n\t\t\t\tsetComputedConfig(this.config)\n\t\t\t\tconst promises = []\n\t\t\t\t// get the data\n\t\t\t\tif (this.setHierClusterData) promises.push(this.setHierClusterData())\n\t\t\t\tpromises.push(this.setData())\n\t\t\t\tthis.dom.loadingDiv.html('Processing data ...')\n\t\t\t\tawait Promise.all(promises)\n\t\t\t\tthis.applyLegendValueFilter() // need to applyLegendValueFiter before combineData to avoid error for hierCluster\n\t\t\t\tif (this.combineData) this.combineData()\n\t\t\t\t// tws in the config may be filled-in based on applicable server response data;\n\t\t\t\t// these filled-in config, such as tw.term.values|category2samplecount, will need to replace\n\t\t\t\t// the corresponding tracked state values in the app store, without causing unnecessary\n\t\t\t\t// dispatch notifications, so use app.save()\n\t\t\t\tthis.app.save({ type: 'plot_edit', id: this.id, config: this.config })\n\t\t\t} catch (e) {\n\t\t\t\tif (e == 'no data') {\n\t\t\t\t\tthis.showNoMatchingDataMessage()\n\t\t\t\t\treturn\n\t\t\t\t} else if (this.app.isAbortError(e)) {\n\t\t\t\t\t// ignore this error, but skip this update since a subsequent action is being processed\n\t\t\t\t\treturn\n\t\t\t\t} else {\n\t\t\t\t\tthis.dom.svg.style('display', 'none')\n\t\t\t\t\tthrow e\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tthis.termGroups = termGroups // onl assign this as instance value after the data request, to prevent incorrect reference in a race condition\n\t\t\tthis.dom.loadingDiv.html('Updating ...').style('display', '')\n\t\t\tthis.termOrder = this.getTermOrder(this.data)\n\t\t\tthis.sampleGroups = this.getSampleGroups(this.hierClusterSamples || this.data)\n\t\t\tthis.sampleOrder = this.getSampleOrder(this.data)\n\t\t\t// even though there may not be sampleOrder (matrix columns) to render,\n\t\t\t// should still compute empty series data, legendData, etc to not break\n\t\t\t// controls/interactions handlers that use those data\n\t\t\tthis.setLayout()\n\t\t\tif (this.setHierColorScale) this.setHierColorScale(this.hierClusterData.clustering)\n\t\t\tif (!this.sampleOrder?.length) {\n\t\t\t\tthis.showNoMatchingDataMessage()\n\t\t\t\t// do not return early yet\n\t\t\t}\n\t\t\t// make sure computed dimensions are available from preceding steps, to use as control input values\n\t\t\tthis.controlsRenderer.main() // to update button count or cross out button labels\n\n\t\t\tthis.serieses = this.getSerieses(this.data)\n\t\t\t// TODO: may re-enable below if showing no-data message/suggestions is preferred over rendering empty matrix\n\t\t\t// can now return early before rendering computed data\n\t\t\t// if (!this.sampleOrder?.length) return\n\n\t\t\t// render the data\n\t\t\tthis.dom.loadingDiv.html('Rendering ...')\n\t\t\tif (this.plotDendrogramHclust) this.plotDendrogramHclust()\n\t\t\tthis.render()\n\t\t\tthis.mayDisplayCohortMessage()\n\t\t\tthis.dom.svg.style('display', '').style('opacity', 1).style('pointer-events', '')\n\n\t\t\tconst [xGrps, yGrps] = !this.settings.matrix.transpose ? ['sampleGrps', 'termGrps'] : ['termGrps', 'sampleGrps']\n\t\t\tconst d = this.dimensions\n\t\t\tthis.clusterRenderer.main({\n\t\t\t\tsettings: this.settings.matrix,\n\t\t\t\txGrps: this[xGrps],\n\t\t\t\tyGrps: this[yGrps],\n\t\t\t\tdimensions: d\n\t\t\t})\n\n\t\t\tthis.legendRenderer(this.legendData, {\n\t\t\t\tsettings: Object.assign({}, this.settings.legend, {\n\t\t\t\t\tsvgw: Math.max(400, d.mainw + d.xOffset - this.settings.matrix.margin.right),\n\t\t\t\t\tsvgh: d.mainh + d.yOffset,\n\t\t\t\t\tdimensions: d,\n\t\t\t\t\tpadleft: this.settings.legend.padleft //+ d.xOffset\n\t\t\t\t})\n\t\t\t})\n\t\t\tawait this.adjustSvgDimensions(prevTranspose)\n\t\t\tthis.controlsRenderer.main()\n\t\t\tif (this.data.removedHierClusterTerms) {\n\t\t\t\tfor (const r of this.data.removedHierClusterTerms) {\n\t\t\t\t\tsayerror(this.dom.errorDiv, r.text + ': ' + r.lst.join(', '))\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e) {\n\t\t\t// a new token message error may have been triggered by the data request here,\n\t\t\t// even if the initial state did not have a token message at the start of a dispatch\n\t\t\tconst message = this.app.vocabApi.tokenVerificationMessage\n\t\t\tthis.mayRequireToken(message)\n\t\t\tif (!message) {\n\t\t\t\tthis.app.tip.hide()\n\t\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\t\tthrow e\n\t\t\t}\n\t\t}\n\n\t\tthis.resetInteractions()\n\t}\n\n\tshowNoMatchingDataMessage() {\n\t\tthis.forcedSampleCount = 0\n\t\tthis.dom.svg.style('opacity', 0.001).style('display', 'none')\n\t\t// an error on initial load/data request will cause computed data/settings to be empty,\n\t\t// which would cause input values to be empty for controls and likely thrown errors\n\t\tif (this.termOrder && this.dimensions) this.controlsRenderer.main({ sampleCount: 0 })\n\t\tthis.dom.loadingDiv.html('')\n\t\tconst div = this.dom.loadingDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('left', '-150px')\n\t\tdiv.append('div').style('margin', '5px 10px').html('No matching cohort sample data for the current gene list.')\n\n\t\tif (this.settings.matrix.showHints?.includes('genesetEdit')) {\n\t\t\tconst div1 = div.append('div').style('margin', '5px 10px')\n\t\t\tdiv1.append('span').html('You may change the selected cohort,')\n\n\t\t\tif (this.config.legendGrpFilter?.lst.length || this.config.legendValueFilter?.lst.length) {\n\t\t\t\tconst cnvBtn = this.controlsRenderer.btns.filter(d => d.label == 'CNV')?.node()\n\t\t\t\tif (cnvBtn) {\n\t\t\t\t\tdiv1.append('br')\n\t\t\t\t\tdiv1.append('span').html('show hidden ')\n\t\t\t\t\tdiv1\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.html('CNV')\n\t\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tcnvBtn.click()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tconst mutationBtn = this.controlsRenderer.btns.filter(d => d.label == 'Mutation')?.node()\n\n\t\t\t\tif (cnvBtn && mutationBtn) div1.append('span').html(' or ')\n\t\t\t\tif (mutationBtn) {\n\t\t\t\t\tdiv1\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t\t\t.html('Mutation')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tmutationBtn.click()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tif (cnvBtn || mutationBtn) div1.append('span').html(' data,')\n\t\t\t}\n\n\t\t\tdiv1.append('br')\n\t\t\tdiv1.append('span').html('or edit the gene list from the ')\n\t\t\tdiv1\n\t\t\t\t.append('span')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t.html('Gene Set Edit Group menu.')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst GenesBtn = this.controlsRenderer.btns\n\t\t\t\t\t\t.filter(d => d.label == 'Genes')\n\t\t\t\t\t\t?.node()\n\t\t\t\t\t\t.click()\n\t\t\t\t\tconst i = setInterval(() => {\n\t\t\t\t\t\tconst editBtn = this.app.tip.d\n\t\t\t\t\t\t\t.selectAll('button')\n\t\t\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\t\t\treturn this.innerHTML == 'Edit Group'\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.node()\n\t\t\t\t\t\tif (editBtn) {\n\t\t\t\t\t\t\teditBtn.click()\n\t\t\t\t\t\t\tclearInterval(i)\n\t\t\t\t\t\t}\n\t\t\t\t\t}, 100)\n\t\t\t\t})\n\t\t}\n\t\tthis.dom.svg.style('display', 'none')\n\t}\n\n\tmayDisplayCohortMessage() {\n\t\tconst msg =\n\t\t\t!this.prevFilter0 || deepEqual(this.state.filter0, this.prevFilter0)\n\t\t\t\t? ''\n\t\t\t\t: 'The gene list is persisted across cohorts.'\n\t\tif (msg) {\n\t\t\tthis.dom.loadingDiv.html('')\n\t\t\tconst div = this.dom.loadingDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('left', '-150px')\n\t\t\tdiv.append('div').html(msg)\n\n\t\t\tif (this.settings.matrix.showHints?.includes('genesetEdit')) {\n\t\t\t\tconst div1 = div.append('div')\n\t\t\t\tdiv1.append('span').html(' You may edit the gene list from the ')\n\t\t\t\tdiv1\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t\t.html('Gene Set Edit Group menu.')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tconst GenesBtn = this.controlsRenderer.btns\n\t\t\t\t\t\t\t.filter(d => d.label == 'Genes')\n\t\t\t\t\t\t\t?.node()\n\t\t\t\t\t\t\t.click()\n\t\t\t\t\t\tconst i = setInterval(() => {\n\t\t\t\t\t\t\tconst editBtn = this.app.tip.d\n\t\t\t\t\t\t\t\t.selectAll('button')\n\t\t\t\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\t\t\t\treturn this.innerHTML == 'Edit Group'\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t.node()\n\t\t\t\t\t\t\tif (editBtn) {\n\t\t\t\t\t\t\t\teditBtn.click()\n\t\t\t\t\t\t\t\tclearInterval(i)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}, 100)\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tthis.dom.loadingDiv.style('display', msg ? '' : 'none')\n\t}\n\n\tsampleKey(s) {\n\t\treturn s.row.sample\n\t}\n\n\tsampleLabel(s) {\n\t\treturn s.label || s.row._ref_.label || ''\n\t}\n\n\tsampleGrpKey(s) {\n\t\treturn s.grp.name\n\t}\n\n\tsampleGrpLabel(s) {\n\t\treturn s.grp.label || s.grp.name || ''\n\t}\n\n\ttermKey(t) {\n\t\treturn t.tw.$id\n\t}\n\n\ttermLabel(t) {\n\t\treturn t.label\n\t}\n\n\ttermGrpKey(t) {\n\t\treturn t.grp.name\n\t}\n\n\ttermGrpLabel(t) {\n\t\treturn t.grp.label || t.grp.name || [{ text: '\u22EE', dx: 3, cls: 'sjpp-exclude-svg-download' }]\n\t}\n\tdestroy() {\n\t\tselect(window).on(`resize.sjpp-${self.id}`, null)\n\t}\n}\n\n// assign class prototype methods and props that are exported from other matrix.* code files\nfor (const m of [matrixData, matrixGroups, matrixLayout, matrixSerieses, matrixLegend]) {\n\tfor (const methodName in m) {\n\t\tMatrix.prototype[methodName] = m[methodName]\n\t}\n}\n\nexport const matrixInit = getCompInit(Matrix)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = matrixInit\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\n\tchartsInstance.dom.tip.clear()\n\tconst menuDiv = holder.append('div')\n\tif (chartsInstance.state.termdbConfig.matrixplots) {\n\t\tfor (const plot of chartsInstance.state.termdbConfig.matrixplots) {\n\t\t\t/* plot: \n\t\t\t{\n\t\t\t\tname=str\n\t\t\t}\n\t\t\t*/\n\t\t\tmenuDiv\n\t\t\t\t.append('button')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('padding', '10px 15px')\n\t\t\t\t.style('border-radius', '20px')\n\t\t\t\t.style('border-color', '#ededed')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.text(plot.name)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t\t\tconst config = await chartsInstance.app.vocabApi.getMatrixByName(plot.name)\n\t\t\t\t\t//add pre-built plot name to config to be shown in the sandbox header\n\t\t\t\t\tconfig.preBuiltPlotTitle = plot.name\n\t\t\t\t\tchartsInstance.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\t}\n\n\tconst chart = {\n\t\tclickTo: chartsInstance.showTree_selectlst,\n\t\tchartType: 'matrix',\n\t\tusecase: { target: 'matrix', detail: 'termgroups' },\n\t\tprocessSelection: lst => {\n\t\t\treturn [\n\t\t\t\t{\n\t\t\t\t\tname: '',\n\t\t\t\t\tlst: lst.map(term => {\n\t\t\t\t\t\treturn { term }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n\tchartsInstance.showTree_selectlst(chart)\n}\n"],
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+}