@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/chunk-DFHERVYA.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/aggregateMatrix.ts", "../plots/aggregateMatrix/model/AggMatrixModel.ts", "../plots/aggregateMatrix/settings/defaults.ts", "../plots/aggregateMatrix/viewModel/PieViewModel.ts", "../plots/aggregateMatrix/viewModel/AggMatrixViewModel.ts", "../plots/aggregateMatrix/view/LegendRender.ts", "../plots/aggregateMatrix/view/AggMatrixView.ts", "../plots/aggregateMatrix/view/setControls.ts", "../plots/aggregateMatrix/AggregateMatrix.ts"],
+  "sourcesContent": ["import {\n\tCATEGORICAL,\n\tDNA_METHYLATION,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tGENE_VARIANT,\n\tINTEGER,\n\tISOFORM_EXPRESSION,\n\tPSEUDOBULK,\n\tSINGLECELL_CELLTYPE,\n\tSSGSEA\n} from '#types'\nimport { isNonDictionaryType } from './terms.js'\n\n/** Term types that can be rows or columns of the aggregate matrix.\n * Every type here is exercised, as both a row and a column, by\n * server/src/test/aggregateMatrix.request.integration.spec.ts. Add a type here only with a test for it. */\nexport const AGG_MATRIX_TERM_TYPES: string[] = [\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tGENE_VARIANT,\n\tSINGLECELL_CELLTYPE\n]\n\n/** True when a term of this type is one term that expands into a row or column for each of its observed values:\n * dictionary terms (categories, bins) and the cell type of single cell data. The other types are one row or column\n * per term. */\nexport function expandsToValues(type: string): boolean {\n\treturn type == SINGLECELL_CELLTYPE || !isNonDictionaryType(type)\n}\n\n/** The type of every term of an axis, in order. Does not validate: anything that is not a term wrapper has no type. */\nexport function getAxisTermTypes(axis: any): any[] {\n\treturn axis && typeof axis == 'object'\n\t\t? Object.values<any>(axis).flatMap(terms => (Array.isArray(terms) ? terms.map(tw => tw?.term?.type) : []))\n\t\t: []\n}\n\n/** True when every dot of the matrix is a pie: all terms of one axis are gene variant terms, and all terms of the\n * other axis are of another type. There is then nothing to color with a gradient, so no gradient method is needed.\n * A matrix with both kinds of term on one axis has dots that are not pies, so it still needs one.\n * Does not validate: terms that are not term wrappers are ignored. */\nexport function isPieOnly(rows: any, columns: any): boolean {\n\tconst rowTypes = getAxisTermTypes(rows)\n\tconst colTypes = getAxisTermTypes(columns)\n\tconst allVariants = (list: any[]) => list.length > 0 && list.every(type => type == GENE_VARIANT)\n\tconst noVariants = (list: any[]) => list.length > 0 && list.every(type => type && type != GENE_VARIANT)\n\treturn (allVariants(rowTypes) && noVariants(colTypes)) || (allVariants(colTypes) && noVariants(rowTypes))\n}\n\n/** True when the matrix is drawn as pies: a gene variant term on one axis, and a term of another type on the other.\n * The gene variant terms give the slices and the other terms decide which samples are in the pie.\n * Does not validate: terms that are not term wrappers are ignored. */\nexport function hasPieAxes(rows: any, columns: any): boolean {\n\tconst rowTypes = getAxisTermTypes(rows)\n\tconst colTypes = getAxisTermTypes(columns)\n\tconst hasOther = (list: any[]) => list.some(type => type && type != GENE_VARIANT)\n\treturn (\n\t\t(rowTypes.includes(GENE_VARIANT) && hasOther(colTypes)) || (colTypes.includes(GENE_VARIANT) && hasOther(rowTypes))\n\t)\n}\n\n/** Term types accepted for rows. */\nexport const AGG_MATRIX_ROW_TYPES: string[] = AGG_MATRIX_TERM_TYPES\n\n/** Term types accepted for columns. Pseudobulk columns read precomputed values from dataset files, so\n * they must be the only kind of column in the matrix and their rows must be genes (geneExpression terms). */\nexport const AGG_MATRIX_COLUMN_TYPES: string[] = [...AGG_MATRIX_TERM_TYPES, PSEUDOBULK]\n\ntype AxisName = 'rows' | 'columns'\n\n/** Identifier of one non-dictionary term, which is one row or column of the matrix.\n *\n * Uses .gene, .id, or .name. A geneVariant term may have only .genes[], so its identifier is built from\n * the gene (or the name or coordinates of a region) of each entry, joined by a comma.\n * Returns undefined when the term has nothing to identify it. */\nexport function getAggMatrixTermId(term: any): string | undefined {\n\tconst id = term?.gene || term?.id || term?.name\n\tif (id) return String(id)\n\tif (!Array.isArray(term?.genes) || !term.genes.length) return\n\tconst ids = term.genes.map(getGeneEntryId)\n\tif (ids.some((id: string) => !id)) return\n\treturn ids.join(',')\n}\n\n/** Label of one non-dictionary term. A term without a .name is labeled by its identifier. */\nexport function getAggMatrixTermLabel(term: any): string | undefined {\n\treturn term?.name || getAggMatrixTermId(term)\n}\n\nfunction getGeneEntryId(entry: any): string | undefined {\n\tconst id = entry?.gene || entry?.name || entry?.id\n\tif (id) return String(id)\n\tif (entry?.chr && Number.isFinite(entry.start) && Number.isFinite(entry.stop)) {\n\t\treturn `${entry.chr}:${entry.start}-${entry.stop}`\n\t}\n}\n\n/** Validate one axis of the aggregate matrix, that is, a map of section names to term wrappers.\n *\n * - Every section has a name and at least one term wrapper ({ term, q }); bare terms are not accepted.\n * - Every term in a section has the same, supported term type.\n * - A section of a dictionary type (e.g. categorical, float) holds one term, which expands into its categories\n *   or bins. A section of a non-dictionary type (e.g. geneExpression, geneVariant) holds many terms, one\n *   row or column each.\n *\n * Throws an Error that describes the first problem found.\n * @param allowEmpty permit an axis without sections, e.g. when only asking which methods are available */\nexport function validateAggMatrixAxis(axis: any, name: AxisName, allowEmpty = false) {\n\tif (!axis || typeof axis != 'object' || Array.isArray(axis)) throw new Error(`invalid .${name}`)\n\tconst sections = Object.entries<any>(axis)\n\tif (!sections.length && !allowEmpty) throw new Error(`invalid .${name}: no sections`)\n\tconst allowedTypes = name == 'rows' ? AGG_MATRIX_ROW_TYPES : AGG_MATRIX_COLUMN_TYPES\n\tfor (const [section, terms] of sections) {\n\t\tif (!section.trim()) throw new Error(`every .${name} section requires a name`)\n\t\tif (!Array.isArray(terms) || !terms.length) throw new Error(`invalid .${name}[${section}]`)\n\t\tif (terms.some(tw => !tw?.term || typeof tw.term != 'object')) {\n\t\t\tthrow new Error(`${name} section '${section}' must contain term wrappers, such as { term, q }`)\n\t\t}\n\t\tconst types = new Set(terms.map(tw => tw.term.type))\n\t\tif (types.size != 1 || types.has(undefined)) {\n\t\t\tthrow new Error(`${name} section '${section}' must contain one term type`)\n\t\t}\n\t\tconst termType = terms[0].term.type\n\t\tif (!allowedTypes.includes(termType)) {\n\t\t\tthrow new Error(`${name} section '${section}' has unsupported term type '${termType}'`)\n\t\t}\n\t\tif (termType == SINGLECELL_CELLTYPE) {\n\t\t\tif (terms.length != 1) throw new Error(`${name} cell type section '${section}' must contain one term`)\n\t\t\tif (!getAggMatrixTermId(terms[0].term)) {\n\t\t\t\tthrow new Error(`${name} section '${section}' has a ${termType} term without an identifier`)\n\t\t\t}\n\t\t} else if (!isNonDictionaryType(termType)) {\n\t\t\tif (terms.length != 1) throw new Error(`${name} dictionary section '${section}' must contain one term`)\n\t\t} else if (terms.some(tw => !getAggMatrixTermId(tw.term))) {\n\t\t\tthrow new Error(`${name} section '${section}' has a ${termType} term without an identifier`)\n\t\t}\n\t}\n}\n\n/** Validate the rows and columns of an aggregate matrix, and the combinations of their term types. */\nexport function validateAggMatrixAxes(rows: any, columns: any) {\n\tvalidateAggMatrixAxis(rows, 'rows')\n\tvalidateAggMatrixAxis(columns, 'columns')\n\tconst termTypes = (axis: any) => Object.values<any[]>(axis).flatMap(terms => terms.map(tw => tw.term.type))\n\t/* The terms of cell type are cells. Every other supported term, pseudobulk included, is a value of a sample,\n\tsuch as a patient. A matrix counts one kind of sample, so the two cannot be combined until cells can be\n\tmapped to their samples. */\n\tconst allTypes = new Set<string>([...termTypes(rows), ...termTypes(columns)])\n\tif (allTypes.has(SINGLECELL_CELLTYPE) && allTypes.size > 1) {\n\t\tconst others = [...allTypes].filter(type => type != SINGLECELL_CELLTYPE).join(', ')\n\t\tthrow new Error(\n\t\t\t`${SINGLECELL_CELLTYPE} terms are cells and cannot be combined with sample-level terms (${others}) in an aggregate matrix`\n\t\t)\n\t}\n\tconst columnTypes = new Set(Object.values<any[]>(columns).flatMap(terms => terms.map(tw => tw.term.type)))\n\tif (!columnTypes.has(PSEUDOBULK)) return\n\tif (columnTypes.size > 1) {\n\t\tthrow new Error('pseudobulk columns cannot be combined with other column term types')\n\t}\n\tconst rowTypes = new Set(Object.values<any[]>(rows).flatMap(terms => terms.map(tw => tw.term.type)))\n\tif (rowTypes.size != 1 || !rowTypes.has(GENE_EXPRESSION)) {\n\t\tthrow new Error(`pseudobulk columns require ${GENE_EXPRESSION} rows`)\n\t}\n}\n", "import { type AggregateMatrix, validatePlotConfig } from '../AggregateMatrix.ts'\nimport type { AppApi } from '#rx'\nimport { isPieOnly } from '#shared/aggregateMatrix.js'\n\nexport class AggMatrixModel {\n\tag: AggregateMatrix\n\tapp: AppApi\n\n\tconstructor(ag: AggregateMatrix) {\n\t\tthis.ag = ag\n\t\tthis.app = ag.app\n\t}\n\n\tasync getData() {\n\t\tconst state = this.ag.state\n\t\tconst config = structuredClone(state.config)\n\n\t\tvalidatePlotConfig(config)\n\n\t\tconst settings = config.settings.aggregateMatrix || {}\n\n\t\tconst body = {\n\t\t\trows: config.rows,\n\t\t\tcolumns: config.columns,\n\t\t\t// not needed when every dot is a pie\n\t\t\tgradientMethod: isPieOnly(config.rows, config.columns) ? undefined : settings.gradientMethod,\n\t\t\tsizeMethod: settings.sizeMethod,\n\t\t\tminDotSize: settings.minDotSize,\n\t\t\tmaxDotSize: settings.maxDotSize,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tsignal: this.ag.api?.getAbortSignal()\n\t\t}\n\n\t\treturn await this.app.vocabApi.getAggregateMatrixData(body)\n\t}\n}\n", "import type { AggregateMatrixSettings } from './Settings.ts'\nimport { getAxisTermTypes } from '#shared/aggregateMatrix.js'\n\nconst dotSizeDefaults = {\n\tminDotSize: 5,\n\tmaxDotSize: 20,\n\tdotInputMin: 2,\n\tdotInputMax: 35\n}\n/** Pies need more room than dots, so a pie chart defaults to larger sizes. */\nconst pieSizeDefaults = {\n\tminDotSize: 30,\n\tmaxDotSize: 60,\n\tdotInputMin: dotSizeDefaults.minDotSize,\n\tdotInputMax: 300\n}\n/** The length of a row or column as a multiple of the largest dot: the dot and room around it */\nexport const cellToDotSize = 2.5\n/** What the labels, axis titles, and legend take of the width and the height, so the cells cannot use it.\n * An estimate: the labels depend on the data, and the plot may not fill the window. */\nconst reservedSpace = { width: 400, height: 250 }\n\n/** The default sizes of a pie chart, scaled down so that every row and column fits in the window. This is an estimate\n * of the room the plot has. The count is of the terms of the request, as the categories that a term expands into are\n * not known yet. Sizes are never above the pie defaults or below the dot defaults, and a min or max set by the user\n * is left alone. The viewport is the room that the plot is estimated to have. */\nexport function getPieSizeDefaults(\n\trows: any,\n\tcolumns: any,\n\toverrides: Partial<AggregateMatrixSettings> = {},\n\tviewport = { width: window.innerWidth, height: window.innerHeight }\n) {\n\tif (overrides.minDotSize !== undefined || overrides.maxDotSize !== undefined) return pieSizeDefaults\n\tconst cellSize = Math.min(\n\t\t(viewport.width - reservedSpace.width) / getAxisTermTypes(columns).length,\n\t\t(viewport.height - reservedSpace.height) / getAxisTermTypes(rows).length\n\t)\n\tconst maxDotSize = Math.min(\n\t\tpieSizeDefaults.maxDotSize,\n\t\tMath.max(dotSizeDefaults.maxDotSize, Math.floor(cellSize / cellToDotSize))\n\t)\n\t// the min size keeps its ratio to the max size\n\tconst minDotSize = Math.round((pieSizeDefaults.minDotSize * maxDotSize) / pieSizeDefaults.maxDotSize)\n\treturn { ...pieSizeDefaults, minDotSize, maxDotSize }\n}\n\nexport function getAggregateMatrixSettings(overrides = {}, sizeDefaults = {}): AggregateMatrixSettings {\n\tconst defaults = {\n\t\tstartColor: '#ff9400',\n\t\tstopColor: '#0080ff',\n\t\tgradientMethod: 'mean',\n\t\tsizeMethod: 'percent',\n\t\t...dotSizeDefaults,\n\t\t...sizeDefaults\n\t}\n\n\tconst mergedSettings = Object.assign({}, defaults, overrides)\n\tconst isValidMinMax = validateMinMaxDotSetting(mergedSettings, mergedSettings.minDotSize, mergedSettings.maxDotSize)\n\tif (isValidMinMax !== null) {\n\t\tthrow new Error(`Invalid min/max dot size settings: ${isValidMinMax}`)\n\t}\n\n\treturn mergedSettings\n}\n\nexport function validateMinMaxDotSetting(settings: AggregateMatrixSettings, min, max): string | null {\n\tif (min < settings.dotInputMin) {\n\t\treturn `Minimum dot size must be greater than or equal to ${settings.dotInputMin}`\n\t}\n\tif (max > settings.dotInputMax) {\n\t\treturn `Maximum dot size must be less than or equal to ${settings.dotInputMax}`\n\t}\n\tif (min > max) {\n\t\treturn `Minimum dot size must be less than or equal to maximum dot size`\n\t}\n\treturn null\n}\n", "import { arc, pie } from 'd3-shape'\nimport { capitalizeFirstLetter } from '#dom'\nimport type { AggMatrixDot, AggMatrixPie, ValidAggMatrixResponse } from '#types'\nimport { GENE_VARIANT } from '#types'\nimport { mclass } from '#shared/common.js'\nimport type { AggregateMatrixSettings } from '../settings/Settings.ts'\nimport type {\n\tAggMatrixDotPosition,\n\tAggMatrixPiePosition,\n\tAggMatrixViewData,\n\tPieLegendEntry\n} from './ViewModelDataTypes.ts'\n\n/** View model logic of the pies of the aggregate matrix. Pure functions: the server decides which slices a pie\n * has and how large it is relative to the others, and this turns that into what the client draws. */\n\ntype PieSlice = AggMatrixPie['slices'][number]\n\n/** The term type of each section of an axis, by section name. */\nexport type SectionTypes = Map<string, string | undefined>\n\nexport function getSectionTypes(axis: any): SectionTypes {\n\treturn new Map(Object.entries<any[]>(axis || {}).map(([section, terms]) => [section, terms[0]?.term?.type]))\n}\n\n/** True when the dot is where a gene variant term meets a term of another type. Such a dot is a pie or it is no\n * data. A dot of any other two terms is an ordinary dot, also in a matrix that has pies elsewhere. */\nexport function isPieCell(dot: AggMatrixDot, rowTypes: SectionTypes, columnTypes: SectionTypes): boolean {\n\treturn (rowTypes.get(dot.rowSection) == GENE_VARIANT) !== (columnTypes.get(dot.colSection) == GENE_VARIANT)\n}\n\n/** What a dot adds to the view data when it has a pie.\n * - pie: what to draw. Not set when there is nothing to draw: the dot has no pie, or all of its slices are hidden.\n * - tipData: the number of samples and every slice, hidden ones too, for the tooltip.\n * - isNoData: the dot is treated as having no data. A pie dot with nothing to draw is blank and its tooltip\n *   reports that no data is available. */\nexport function getDotPie(\n\tdot: AggMatrixDot,\n\tsettings: AggregateMatrixSettings,\n\tisPie: boolean,\n\tsampleType?: ValidAggMatrixResponse['sampleType']\n) {\n\tconst position = dot.pie ? getPiePosition(dot.pie, settings) : undefined\n\tconst pie = position?.slices.length ? position : undefined\n\treturn {\n\t\tpie,\n\t\ttipData: dot.pie && pie ? getPieTipData(dot.pie, settings, sampleType) : [],\n\t\tisNoData: isPie && !pie\n\t}\n}\n\n/** Whether a slice is not drawn. The server flags the slices that are hidden by default, such as wildtype, until\n * the user chooses which slices to hide in the legend. */\nexport function isSliceHidden(slice: PieSlice, settings: Pick<AggregateMatrixSettings, 'hiddenSliceKeys'>): boolean {\n\treturn settings.hiddenSliceKeys ? settings.hiddenSliceKeys.includes(slice.key) : !!slice.hidden\n}\n\n/** The server sends default labels and colors for variant classes. The mclass of the client has the\n * mclassOverride of the launch arguments applied, so a variant class is described by it instead. */\nexport function describeSlice(slice: PieSlice, termType?: string) {\n\tif (termType == GENE_VARIANT && Object.prototype.hasOwnProperty.call(mclass, slice.key)) {\n\t\tconst { label, color } = mclass[slice.key]\n\t\treturn { label, color }\n\t}\n\treturn { label: slice.label, color: slice.color }\n}\n\n/** Pie area is proportional to the number of samples. A pie is never smaller than the smallest dot.\n * Slices that are hidden, such as wildtype, are not drawn, so the pie shows the rest of the samples. */\nexport function getPiePosition(data: AggMatrixPie, settings: AggregateMatrixSettings): AggMatrixPiePosition {\n\tconst radius = Math.max(settings.minDotSize, data.radius * settings.maxDotSize)\n\tconst arcs = pie<PieSlice>()\n\t\t.sort(null)\n\t\t.value(slice => slice.count)(data.slices.filter(slice => !isSliceHidden(slice, settings)))\n\tconst makePath = arc<any>().innerRadius(0).outerRadius(radius)\n\treturn {\n\t\tradius,\n\t\tn: data.n,\n\t\tslices: arcs.map(a => ({\n\t\t\tkey: a.data.key,\n\t\t\tcount: a.data.count,\n\t\t\t...describeSlice(a.data, data.termType),\n\t\t\tpath: makePath(a) || ''\n\t\t}))\n\t}\n}\n\n/** The tooltip reports only the slices that are drawn, so a slice that is hidden is not listed and is not in the total.\n * - gene variant: the samples with a variant, which does not follow the hidden slices, and the variants of the drawn slices\n * - other terms: the samples of the drawn slices */\nexport function getPieTipData(\n\tdata: AggMatrixPie,\n\tsettings: Pick<AggregateMatrixSettings, 'hiddenSliceKeys'>,\n\tsampleType?: ValidAggMatrixResponse['sampleType']\n) {\n\tconst drawn = data.slices.filter(slice => !isSliceHidden(slice, settings))\n\tconst total = drawn.reduce((sum, slice) => sum + slice.count, 0)\n\tconst samples = capitalizeFirstLetter(sampleType?.plural_name || 'samples')\n\tconst entries: AggMatrixDotPosition['tipData'] = []\n\tif (data.termType == GENE_VARIANT && data.variantSamples !== undefined) {\n\t\tentries.push({ label: `${samples} with a variant`, value: data.variantSamples })\n\t\tentries.push({ label: 'Variants', value: total })\n\t} else {\n\t\tentries.push({ label: samples, value: total })\n\t}\n\tfor (const slice of drawn) {\n\t\tconst { label, color } = describeSlice(slice, data.termType)\n\t\tentries.push({ label, value: slice.count, color })\n\t}\n\treturn entries\n}\n\n/** One entry for every slice that can be drawn, hidden or not, in order of first appearance.\n * Slices that are not computable are never sent by the server, so they are not here. */\nexport function getPieLegend(\n\tdata: AggMatrixDot[][],\n\tsettings: Pick<AggregateMatrixSettings, 'hiddenSliceKeys'> = {}\n): AggMatrixViewData['pieLegend'] {\n\tconst entries = new Map<string, PieLegendEntry>()\n\tlet termType: string | undefined\n\tfor (const row of data) {\n\t\tfor (const dot of row) {\n\t\t\tif (!dot.pie) continue\n\t\t\ttermType ??= dot.pie.termType\n\t\t\tfor (const slice of dot.pie.slices) {\n\t\t\t\tif (!entries.has(slice.key)) {\n\t\t\t\t\tentries.set(slice.key, {\n\t\t\t\t\t\tkey: slice.key,\n\t\t\t\t\t\t...describeSlice(slice, dot.pie.termType),\n\t\t\t\t\t\thidden: isSliceHidden(slice, settings)\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\treturn { title: termType == GENE_VARIANT ? 'Variant class' : 'Category', entries: [...entries.values()] }\n}\n", "import type { AggregateMatrix } from '../AggregateMatrix.ts'\nimport { getMaxLabelWidth, capitalizeFirstLetter } from '#dom'\nimport { scaleLinear } from 'd3-scale'\nimport type { AggMatrixDot, AxisLayoutColumns, AxisLayoutRows, ValidAggMatrixResponse } from '#types'\nimport type { AggregateMatrixSettings } from '../settings/Settings.ts'\nimport { roundValue } from '#shared/roundValue.js'\nimport type { AggMatrixViewData, AggMatrixDotPosition } from './ViewModelDataTypes.ts'\nimport { getDotPie, getPieLegend, getSectionTypes, isPieCell } from './PieViewModel.ts'\nimport { cellToDotSize } from '../settings/defaults.ts'\n\nexport class AggMatrixViewModel {\n\tag: AggregateMatrix\n\tviewData!: AggMatrixViewData\n\tmaxRowLabelLgth!: number\n\tmaxColLabelLgth!: number\n\trowTermLabelLgth!: number\n\tcolTermLabelLgth!: number\n\tmaxRowSectionLabelWdth!: number\n\tmaxColSectionLabelHght!: number\n\ttotalRowHght!: number\n\ttotalColWdth!: number\n\tlastX!: number\n\tlastY!: number\n\trowSectionRotateFlags: boolean[] = []\n\tcolSectionRotateFlags: boolean[] = []\n\tsizeScale!: (value: number) => number\n\n\treadonly topPad = 20\n\treadonly hoziPad = 20\n\treadonly bottomPad = 20\n\treadonly sectionGap = 8\n\treadonly colSectionGap = 4\n\treadonly minColSectionLineInset = 2\n\treadonly colSectionLabelLineGap = 3\n\treadonly colSectionLabelGap = 8\n\treadonly labelFontPx = 12\n\n\tconstructor(ag: AggregateMatrix) {\n\t\tthis.ag = ag\n\t\tthis.sizeScale = (value: number) => value\n\t}\n\n\tprocessData(data: ValidAggMatrixResponse) {\n\t\tthis.viewData = this.getDefaultViewData()\n\n\t\tconst settings = this.ag.state.config.settings.aggregateMatrix\n\t\tconst cellSize = settings.maxDotSize * cellToDotSize\n\t\tconst measureSvg = this.ag.dom.mainDiv.append('svg') as any\n\n\t\t/** Must determine the maximum amount of space needed for the rows.\n\t\t * If there isn't enough space to show the row section label above the\n\t\t * relevant terms, the section label is shown horizontally. This extra\n\t\t * space is taken into account here. */\n\t\tconst rowData = data.axesLayout.rows\n\t\tthis.rowTermLabelLgth = getMaxLabelWidth(measureSvg, [rowData.longestLabel])\n\t\tconst rowSectionLayout = this.getSectionLabelLayout(rowData.sections, cellSize, measureSvg, true)\n\t\tthis.rowSectionRotateFlags = rowSectionLayout.rotateFlags\n\t\tthis.maxRowSectionLabelWdth = rowSectionLayout.maxCrossAxisSpace\n\t\tthis.maxRowLabelLgth =\n\t\t\tthis.rowTermLabelLgth + (this.maxRowSectionLabelWdth ? this.sectionGap + this.maxRowSectionLabelWdth : 0)\n\t\tthis.totalRowHght = cellSize * rowData.rowCount\n\n\t\t/** Same as the rows above. Takes into account the extra space needed if >=1 col\n\t\t * labels is rotated to be shown. */\n\t\tconst colData = data.axesLayout.columns\n\t\tthis.colTermLabelLgth = getMaxLabelWidth(measureSvg, [colData.longestLabel])\n\t\tconst colSectionLayout = this.getSectionLabelLayout(colData.sections, cellSize, measureSvg, false)\n\t\tthis.colSectionRotateFlags = colSectionLayout.rotateFlags\n\t\tthis.maxColSectionLabelHght = colSectionLayout.maxCrossAxisSpace\n\t\tthis.maxColLabelLgth =\n\t\t\tthis.colTermLabelLgth + (this.maxColSectionLabelHght ? this.colSectionGap + this.maxColSectionLabelHght : 0)\n\t\tthis.totalColWdth = cellSize * colData.colCount\n\t\tmeasureSvg.remove()\n\n\t\tthis.getPlotDimensions()\n\t\tthis.getAxisLabelPositions(rowData, colData, cellSize)\n\t\tthis.viewData.hasColorScale = !!data.colorScale\n\t\tif (data.colorScale) this.setColorScale(settings, data.colorScale)\n\t\tthis.sizeScale = scaleLinear()\n\t\t\t.domain([data.sizeScale.min, data.sizeScale.max])\n\t\t\t.range([settings.minDotSize, settings.maxDotSize])\n\t\t\t.clamp(true)\n\t\tthis.getDotPositions(data.data, cellSize, settings, data.sampleType)\n\t\tthis.viewData.pieLegend = getPieLegend(data.data, settings)\n\t}\n\n\tgetSectionLabelLayout(sections: AxisLayoutRows['sections'], cellSize: number, measureSvg, isYaxis: boolean) {\n\t\tconst rotateFlags: boolean[] = []\n\t\tconst widthCache = new Map<string, number>()\n\t\tlet maxCrossAxisSpace = 0\n\n\t\tfor (const section of sections) {\n\t\t\tconst label = section.id || ''\n\t\t\tlet labelWidth = 0\n\t\t\tif (label) {\n\t\t\t\tif (!widthCache.has(label)) widthCache.set(label, getMaxLabelWidth(measureSvg, [label]))\n\t\t\t\tlabelWidth = widthCache.get(label) || 0\n\t\t\t}\n\t\t\tconst sectionSpan = section.terms.length * cellSize\n\n\t\t\t// If a section label cannot fit in the term span on its preferred orientation,\n\t\t\t// flip orientation per axis: Y-axis becomes horizontal, X-axis becomes vertical.\n\t\t\tconst rotate = isYaxis ? labelWidth <= sectionSpan : labelWidth > sectionSpan\n\t\t\trotateFlags.push(rotate)\n\n\t\t\tconst crossAxisSpace = rotate\n\t\t\t\t? isYaxis\n\t\t\t\t\t? this.labelFontPx\n\t\t\t\t\t: labelWidth\n\t\t\t\t: isYaxis\n\t\t\t\t? labelWidth\n\t\t\t\t: this.labelFontPx\n\t\t\tmaxCrossAxisSpace = Math.max(maxCrossAxisSpace, crossAxisSpace)\n\t\t}\n\n\t\treturn { rotateFlags, maxCrossAxisSpace }\n\t}\n\n\tgetPlotDimensions() {\n\t\tconst plotDim = {\n\t\t\tsvg: {\n\t\t\t\twidth: this.hoziPad + this.maxRowLabelLgth + this.totalColWdth + this.hoziPad,\n\t\t\t\theight: this.topPad + this.totalRowHght + this.maxColLabelLgth + this.bottomPad\n\t\t\t},\n\t\t\trowLabels: {\n\t\t\t\tx: this.hoziPad + this.maxRowLabelLgth,\n\t\t\t\ty: this.topPad\n\t\t\t},\n\t\t\tcolLabels: {\n\t\t\t\tx: 0,\n\t\t\t\ty: this.topPad + this.totalRowHght\n\t\t\t}\n\t\t}\n\t\tthis.viewData.plotDim = plotDim\n\t}\n\n\tgetDefaultViewData(): AggMatrixViewData {\n\t\treturn {\n\t\t\tplotDim: {\n\t\t\t\tsvg: { width: 0, height: 0 },\n\t\t\t\trowLabels: { x: 0, y: 0 },\n\t\t\t\tcolLabels: { x: 0, y: 0 }\n\t\t\t},\n\t\t\trowLabels: [],\n\t\t\tcolLabels: [],\n\t\t\trowSectionLabels: [],\n\t\t\tcolSectionLabels: [],\n\t\t\trowSectionLines: [],\n\t\t\tcolSectionLines: [],\n\t\t\tdotPositions: [],\n\t\t\tpieLegend: { title: '', entries: [] },\n\t\t\thasColorScale: true,\n\t\t\tcolorScale: {\n\t\t\t\t//TODO: If the user cannot set the min and max for color values,\n\t\t\t\t// revert to colorScale = scale\n\t\t\t\tscale: () => '',\n\t\t\t\tabsMin: 0,\n\t\t\t\tabsMax: 0\n\t\t\t}\n\t\t}\n\t}\n\n\tgetAxisLabelPositions(rowData: AxisLayoutRows, colData: AxisLayoutColumns, cellSize: number) {\n\t\tconst rowSectionLineX = -(this.rowTermLabelLgth + this.sectionGap / 2)\n\t\tconst rowSectionLabelGap = this.sectionGap / 2\n\t\tconst rowSectionRotateExtraGap = this.labelFontPx / 2 + 1\n\t\t// Rotated term labels are end-anchored so their last letter sits on one reference line.\n\t\tconst colTermY = this.labelFontPx\n\t\tconst colTermBandDepth = colTermY + this.colTermLabelLgth\n\t\tconst colSectionBandStart = colTermBandDepth + (this.maxColSectionLabelHght ? this.colSectionGap : 0)\n\t\tconst colSectionLineY = Math.max(0, colSectionBandStart - this.colSectionLabelLineGap)\n\t\tconst colSectionLineInset = Math.max(this.minColSectionLineInset, cellSize * 0.06)\n\n\t\tthis.lastY = 0\n\t\tthis.lastX = this.hoziPad + this.maxRowLabelLgth\n\n\t\tthis.viewData.rowLabels = []\n\t\tthis.viewData.colLabels = []\n\t\tthis.viewData.rowSectionLabels = []\n\t\tthis.viewData.colSectionLabels = []\n\t\tthis.viewData.rowSectionLines = []\n\t\tthis.viewData.colSectionLines = []\n\n\t\tfor (const [rowSectionIndex, section] of rowData.sections.entries()) {\n\t\t\tconst sectionStartY = this.lastY\n\t\t\tfor (const term of section.terms) {\n\t\t\t\tconst row = {\n\t\t\t\t\tx: 0,\n\t\t\t\t\ty: this.lastY + cellSize / 2,\n\t\t\t\t\tlabel: term.label || term.id\n\t\t\t\t}\n\t\t\t\tthis.viewData.rowLabels.push(row)\n\t\t\t\tthis.lastY += cellSize\n\t\t\t}\n\n\t\t\tconst sectionCenterY = sectionStartY + (section.terms.length * cellSize) / 2\n\t\t\tconst sectionEndY = sectionStartY + section.terms.length * cellSize\n\t\t\tconst rotate = this.rowSectionRotateFlags[rowSectionIndex]\n\t\t\tthis.viewData.rowSectionLabels.push({\n\t\t\t\tx: rowSectionLineX - rowSectionLabelGap - (rotate ? rowSectionRotateExtraGap : 0),\n\t\t\t\ty: sectionCenterY,\n\t\t\t\tlabel: section.id,\n\t\t\t\trotate\n\t\t\t})\n\t\t\tthis.viewData.rowSectionLines.push({\n\t\t\t\tx: rowSectionLineX,\n\t\t\t\ty1: sectionStartY + cellSize / 2,\n\t\t\t\ty2: sectionEndY - cellSize / 2\n\t\t\t})\n\t\t}\n\n\t\tfor (const [colSectionIndex, section] of colData.sections.entries()) {\n\t\t\tconst sectionStartX = this.lastX\n\t\t\tfor (const term of section.terms) {\n\t\t\t\tconst col = {\n\t\t\t\t\tx: this.lastX + cellSize / 2,\n\t\t\t\t\ty: colTermY,\n\t\t\t\t\tlabel: term.label || term.id\n\t\t\t\t}\n\t\t\t\tthis.viewData.colLabels.push(col)\n\t\t\t\tthis.lastX += cellSize\n\t\t\t}\n\n\t\t\tconst sectionCenterX = sectionStartX + (section.terms.length * cellSize) / 2\n\t\t\tconst rotate = this.colSectionRotateFlags[colSectionIndex]\n\t\t\tconst colSectionLabelY = colSectionLineY + this.colSectionLabelGap + (rotate ? 0 : this.labelFontPx / 2)\n\t\t\tthis.viewData.colSectionLabels.push({\n\t\t\t\tx: sectionCenterX,\n\t\t\t\ty: colSectionLabelY,\n\t\t\t\tlabel: section.id,\n\t\t\t\trotate\n\t\t\t})\n\t\t\tthis.viewData.colSectionLines.push({\n\t\t\t\ty: colSectionLineY,\n\t\t\t\tx1: sectionStartX + colSectionLineInset,\n\t\t\t\tx2: this.lastX - colSectionLineInset\n\t\t\t})\n\t\t}\n\t}\n\n\tsetColorScale(settings: AggregateMatrixSettings, colorScaleData: NonNullable<ValidAggMatrixResponse['colorScale']>) {\n\t\tconst domain =\n\t\t\tcolorScaleData.min === colorScaleData.max\n\t\t\t\t? /** Instances, like count, may return identical min and max values.\n\t\t\t\t   * Slightly adjust the domain to avoid having identical min and max values.\n\t\t\t\t   * Circumvents ColorScale requirement for unique values.\n\t\t\t\t   * If reverted, reinstate check in agg matrix route. */\n\t\t\t\t  [\n\t\t\t\t\t\tcolorScaleData.min - Math.max(Math.abs(colorScaleData.min) * 0.01, 1e-12),\n\t\t\t\t\t\tcolorScaleData.max + Math.max(Math.abs(colorScaleData.max) * 0.01, 1e-12)\n\t\t\t\t  ]\n\t\t\t\t: [colorScaleData.min, colorScaleData.max]\n\t\tconst scale = scaleLinear()\n\t\t\t.domain(domain)\n\t\t\t.range([settings.startColor as any, settings.stopColor as any])\n\t\tthis.viewData.colorScale = {\n\t\t\tscale,\n\t\t\tabsMin: colorScaleData.min,\n\t\t\tabsMax: colorScaleData.max\n\t\t}\n\t}\n\n\tgetDotPositions(\n\t\tdata: AggMatrixDot[][],\n\t\tcellSize: number,\n\t\tsettings: AggregateMatrixSettings,\n\t\tsampleType?: ValidAggMatrixResponse['sampleType']\n\t) {\n\t\tconst startX = this.hoziPad + this.maxRowLabelLgth\n\t\tconst startY = this.topPad\n\n\t\tthis.lastY = startY\n\t\tthis.lastX = startX\n\n\t\tconst { rows, columns } = this.ag.state.config\n\t\tconst rowTypes = getSectionTypes(rows)\n\t\tconst columnTypes = getSectionTypes(columns)\n\n\t\tfor (const [i, row] of data.entries()) {\n\t\t\tfor (const dot of row) {\n\t\t\t\tconst {\n\t\t\t\t\tpie,\n\t\t\t\t\ttipData: pieTipData,\n\t\t\t\t\tisNoData\n\t\t\t\t} = getDotPie(dot, settings, isPieCell(dot, rowTypes, columnTypes), sampleType)\n\t\t\t\tconst hasColorScale = this.viewData.hasColorScale\n\t\t\t\tconst noData = (hasColorScale && dot.colorValue === null) || dot.sizeValue === null || isNoData\n\t\t\t\tconst hasData = !noData\n\t\t\t\tconst dotPos = {\n\t\t\t\t\tx: this.lastX + cellSize / 2,\n\t\t\t\t\ty: this.lastY + cellSize / 2,\n\t\t\t\t\t/** Regardless if the size and color value are available, the dot will render.\n\t\t\t\t\t * This will allow the tooltip to appear, displaying the data or lack thereof\n\t\t\t\t\t * to the user. */\n\t\t\t\t\tsize: hasData ? this.sizeScale(dot.sizeValue!) : settings.maxDotSize,\n\t\t\t\t\tcolor: hasData && hasColorScale ? this.viewData.colorScale.scale(dot.colorValue!) : 'transparent',\n\t\t\t\t\thasData,\n\t\t\t\t\trow: dot.row,\n\t\t\t\t\trowSection: dot.rowSection,\n\t\t\t\t\tcolumn: dot.column,\n\t\t\t\t\tcolSection: dot.colSection,\n\t\t\t\t\tpie,\n\t\t\t\t\ttipData: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: dot.rowSection,\n\t\t\t\t\t\t\tvalue: dot.row\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: dot.colSection,\n\t\t\t\t\t\t\tvalue: dot.column\n\t\t\t\t\t\t},\n\t\t\t\t\t\t// The color value, unless there is no color scale\n\t\t\t\t\t\t...(hasColorScale\n\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: capitalizeFirstLetter(settings.gradientMethod),\n\t\t\t\t\t\t\t\t\t\tvalue: noData ? 'No available data' : roundValue(dot.colorValue!, 2)\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t  ]\n\t\t\t\t\t\t\t: []),\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\t// Show the size value\n\t\t\t\t\t\t\tlabel: capitalizeFirstLetter(settings.sizeMethod),\n\t\t\t\t\t\t\tvalue: noData ? 'No available data' : roundValue(dot.sizeValue!, 2)\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t} satisfies AggMatrixDotPosition\n\t\t\t\tdotPos.tipData.push(...pieTipData)\n\t\t\t\tthis.viewData.dotPositions.push(dotPos)\n\t\t\t\tthis.lastX += cellSize\n\t\t\t}\n\t\t\tthis.lastX = startX\n\t\t\tthis.lastY = startY + (i + 1) * cellSize\n\t\t}\n\t}\n}\n", "import type { AggregateMatrix } from '../AggregateMatrix.ts'\nimport type { AggMatrixViewData } from '../viewModel/ViewModelDataTypes.ts'\nimport { ColorScale, DotSizeScale, LegendItemMenu, capitalizeFirstLetter } from '#dom'\nimport { rgb } from 'd3-color'\nimport { validateMinMaxDotSetting } from '../settings/defaults.ts'\n\nexport class LegendRender {\n\tag: AggregateMatrix\n\treadonly xStart = 15\n\tpieLegendMenu: LegendItemMenu\n\n\tconstructor(ag: AggregateMatrix) {\n\t\tthis.ag = ag\n\t\tthis.pieLegendMenu = new LegendItemMenu({\n\t\t\tcallback: hiddenSliceKeys => {\n\t\t\t\tthis.ag.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.ag.id,\n\t\t\t\t\tconfig: { settings: { aggregateMatrix: { hiddenSliceKeys } } }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\trender(viewData: AggMatrixViewData, div: any) {\n\t\tconst settings = this.ag.state.config.settings.aggregateMatrix\n\t\tif (viewData.hasColorScale) {\n\t\t\tconst colorScaleSvg = div.append('svg').style('display', 'block').attr('height', 100)\n\t\t\tthis.renderColorScale(viewData.colorScale, settings, colorScaleSvg)\n\t\t}\n\t\t//The size is set in renderDotScaleRef, from the bounding box of the rendered scale\n\t\tconst dotScaleSvg = div.append('svg').style('display', 'block')\n\t\tthis.renderDotScaleRef(dotScaleSvg, settings)\n\t\tif (viewData.pieLegend.entries.length) this.renderPieLegend(viewData.pieLegend, div)\n\t}\n\n\t/** One shared legend of the slice colors, as every pie uses the same colors and order. It has every slice,\n\t * hidden or not. Hidden slices are crossed out, and clicking an entry opens a menu to show or hide slices. */\n\trenderPieLegend(legend: AggMatrixViewData['pieLegend'], div: any) {\n\t\tconst rowHeight = 18\n\t\tconst svg = div\n\t\t\t.append('svg')\n\t\t\t.attr('class', 'sjpp-ag-matrix-pie-legend')\n\t\t\t.attr('data-testid', 'sjpp-ag-matrix-pie-legend')\n\t\t\t.style('display', 'block')\n\t\t\t.attr('width', 260)\n\t\t\t.attr('height', 30 + legend.entries.length * rowHeight)\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.attr('x', this.xStart)\n\t\t\t.attr('y', 20)\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-size', '0.8em')\n\t\t\t.text(legend.title)\n\t\tconst keys = legend.entries.map(entry => entry.key)\n\t\tconst hiddenKeys = legend.entries.filter(entry => entry.hidden).map(entry => entry.key)\n\t\tlegend.entries.forEach((entry, i) => {\n\t\t\tconst y = 30 + i * rowHeight\n\t\t\tconst g = svg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('class', 'sjpp-ag-matrix-pie-legend-item')\n\t\t\t\t.attr('data-testid', 'sjpp-ag-matrix-pie-legend-item')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tthis.pieLegendMenu.show({ target: event.currentTarget, key: entry.key, keys, hiddenKeys })\n\t\t\t\t})\n\t\t\tg.append('rect')\n\t\t\t\t.attr('x', this.xStart)\n\t\t\t\t.attr('y', y)\n\t\t\t\t.attr('width', 12)\n\t\t\t\t.attr('height', 12)\n\t\t\t\t.attr('fill', entry.color)\n\t\t\t\t.attr('fill-opacity', entry.hidden ? 0.3 : 1)\n\t\t\t\t.attr('stroke', '#999')\n\t\t\t\t.attr('stroke-width', 0.5)\n\t\t\tg.append('text')\n\t\t\t\t.attr('x', this.xStart + 18)\n\t\t\t\t.attr('y', y + 10)\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.style('text-decoration', entry.hidden ? 'line-through' : 'none')\n\t\t\t\t.style('opacity', entry.hidden ? 0.6 : 1)\n\t\t\t\t.text(entry.label)\n\t\t})\n\t}\n\n\trenderColorScale(colorScale, settings, svg) {\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.attr('x', this.xStart)\n\t\t\t.attr('y', 20)\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-size', '0.8em')\n\t\t\t.text(capitalizeFirstLetter(settings.gradientMethod))\n\n\t\tnew ColorScale({\n\t\t\tholder: svg,\n\t\t\tdomain: colorScale.scale.domain(),\n\t\t\tcolors: [settings.startColor, settings.stopColor],\n\t\t\tbarheight: 20,\n\t\t\tbarwidth: 200,\n\t\t\tposition: `${this.xStart + 10}, 35`,\n\t\t\tsetColorsCallback: (val, idx) => {\n\t\t\t\tconst hexColor = rgb(val).formatHex()\n\t\t\t\tconst colorKey = idx == 0 ? 'startColor' : 'stopColor'\n\t\t\t\tthis.ag.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.ag.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\taggregateMatrix: {\n\t\t\t\t\t\t\t\t[colorKey]: hexColor\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\trenderDotScaleRef(svg, settings) {\n\t\tnew DotSizeScale({\n\t\t\tg: svg.append('g').attr('transform', `translate(${this.xStart}, 15)`),\n\t\t\tinputMax: settings.dotInputMax,\n\t\t\tinputMin: settings.dotInputMin,\n\t\t\tmaxRadius: settings.maxDotSize,\n\t\t\tminRadius: settings.minDotSize,\n\t\t\tisAscending: true,\n\t\t\ttitle: `${capitalizeFirstLetter(settings.sizeMethod)} size (in pixels)`,\n\t\t\tmenu: {\n\t\t\t\tminMaxLabel: 'pixels',\n\t\t\t\tcallback: async (obj: { min: number; max: number }) => {\n\t\t\t\t\tconst { min, max } = obj\n\t\t\t\t\tconst isValid = validateMinMaxDotSetting(settings, min, max)\n\t\t\t\t\tif (isValid !== null) {\n\t\t\t\t\t\talert(isValid)\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tthis.ag.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.ag.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\taggregateMatrix: {\n\t\t\t\t\t\t\t\t\tminDotSize: min,\n\t\t\t\t\t\t\t\t\tmaxDotSize: max\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\n\t\t//Fit the svg to what was rendered, including the group's translation, title and labels\n\t\tconst box = svg.node().getBBox()\n\t\tsvg.attr('width', Math.ceil(box.x + box.width + this.xStart)).attr('height', Math.ceil(box.y + box.height + 15))\n\t}\n}\n", "import { table2col } from '#dom'\nimport type { AggregateMatrix } from '../AggregateMatrix.ts'\nimport type { AggMatrixDotPosition, AggMatrixViewData } from '../viewModel/ViewModelDataTypes.ts'\nimport { LegendRender } from './LegendRender.ts'\nimport { PSEUDOBULK } from '#types'\n\nexport class AggMatrixView {\n\tag: AggregateMatrix\n\tlegendRender: LegendRender\n\tdom!: any\n\n\tconstructor(ag: AggregateMatrix) {\n\t\tthis.ag = ag\n\t\tthis.legendRender = new LegendRender(ag)\n\t}\n\n\trender(viewData: AggMatrixViewData) {\n\t\tthis.initDom(viewData.plotDim)\n\t\tthis.renderAxesLabels(\n\t\t\tviewData.colLabels,\n\t\t\tviewData.rowLabels,\n\t\t\tviewData.colSectionLabels,\n\t\t\tviewData.rowSectionLabels,\n\t\t\tviewData.colSectionLines,\n\t\t\tviewData.rowSectionLines\n\t\t)\n\t\tthis.renderDots(viewData.dotPositions)\n\t\tthis.legendRender.render(viewData, this.dom.legendDiv)\n\t}\n\n\tinitDom(plotDim: AggMatrixViewData['plotDim']) {\n\t\tconst mainDiv = this.ag.dom.mainDiv as any\n\t\tmainDiv.selectAll('*').remove()\n\n\t\tconst svg = mainDiv\n\t\t\t.append('svg')\n\t\t\t.attr('width', plotDim.svg.width)\n\t\t\t.attr('height', plotDim.svg.height)\n\t\t\t.attr('data-testid', 'sjpp-ag-matrix-svg')\n\n\t\tconst rowLabels = svg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-ag-matrix-row-labels')\n\t\t\t.attr('transform', `translate(${plotDim.rowLabels.x}, ${plotDim.rowLabels.y}) `)\n\n\t\tconst colLabels = svg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-ag-matrix-col-labels')\n\t\t\t.attr('transform', `translate(${plotDim.colLabels.x}, ${plotDim.colLabels.y})`)\n\n\t\tconst legendDiv = mainDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-ag-matrix-legend')\n\t\t\t.attr('data-testid', 'sjpp-ag-matrix-legend')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', `${this.ag.viewModel.topPad}px ${this.ag.viewModel.hoziPad}px`)\n\n\t\tthis.dom = {\n\t\t\tsvg,\n\t\t\trowLabels,\n\t\t\tcolLabels,\n\t\t\tlegendDiv\n\t\t}\n\t}\n\n\trenderAxesLabels(\n\t\tcolLabels: AggMatrixViewData['colLabels'],\n\t\trowLabels: AggMatrixViewData['rowLabels'],\n\t\tcolSectionLabels: AggMatrixViewData['colSectionLabels'],\n\t\trowSectionLabels: AggMatrixViewData['rowSectionLabels'],\n\t\tcolSectionLines: AggMatrixViewData['colSectionLines'],\n\t\trowSectionLines: AggMatrixViewData['rowSectionLines']\n\t) {\n\t\tconst { rowLabels: rowLabelsGroup, colLabels: colLabelsGroup } = this.dom\n\n\t\trowLabelsGroup\n\t\t\t.selectAll('text')\n\t\t\t.data(rowLabels)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-ag-matrix-row-label')\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.attr('fill', '#3f3f46')\n\t\t\t.attr('font-size', 12)\n\t\t\t.attr('font-weight', 400)\n\t\t\t.attr('transform', d => `translate(${d.x}, ${d.y})`)\n\t\t\t.text(d => d.label)\n\n\t\trowLabelsGroup\n\t\t\t.selectAll('.sjpp-ag-matrix-row-section-label')\n\t\t\t.data(rowSectionLabels)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-ag-matrix-row-section-label')\n\t\t\t.attr('text-anchor', d => (d.rotate ? 'middle' : 'end'))\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.attr('fill', '#111827')\n\t\t\t.attr('font-size', 12)\n\t\t\t.attr('letter-spacing', '0.02em')\n\t\t\t.attr('transform', d => (d.rotate ? `translate(${d.x}, ${d.y}) rotate(-90)` : `translate(${d.x}, ${d.y})`))\n\t\t\t.text(d => d.label)\n\n\t\trowLabelsGroup\n\t\t\t.selectAll('.sjpp-ag-matrix-row-section-line')\n\t\t\t.data(rowSectionLines)\n\t\t\t.enter()\n\t\t\t.append('line')\n\t\t\t.attr('class', 'sjpp-ag-matrix-row-section-line')\n\t\t\t.attr('stroke', '#6b7280')\n\t\t\t.attr('stroke-width', 1)\n\t\t\t.attr('opacity', 0.9)\n\t\t\t.attr('x1', d => d.x)\n\t\t\t.attr('x2', d => d.x)\n\t\t\t.attr('y1', d => d.y1)\n\t\t\t.attr('y2', d => d.y2)\n\n\t\tcolLabelsGroup\n\t\t\t.selectAll('text')\n\t\t\t.data(colLabels)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-ag-matrix-col-label')\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.attr('fill', '#3f3f46')\n\t\t\t.attr('font-size', 12)\n\t\t\t.attr('font-weight', 400)\n\t\t\t.attr('transform', d => `translate(${d.x}, ${d.y}) rotate(-90)`)\n\t\t\t.text(d => d.label)\n\n\t\tcolLabelsGroup\n\t\t\t.selectAll('.sjpp-ag-matrix-col-section-label')\n\t\t\t.data(colSectionLabels)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-ag-matrix-col-section-label')\n\t\t\t.attr('text-anchor', d => (d.rotate ? 'end' : 'middle'))\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.attr('fill', '#111827')\n\t\t\t.attr('font-size', 12)\n\t\t\t.attr('letter-spacing', '0.02em')\n\t\t\t.attr('transform', d => (d.rotate ? `translate(${d.x}, ${d.y}) rotate(-90)` : `translate(${d.x}, ${d.y})`))\n\t\t\t.text(d => d.label)\n\n\t\tcolLabelsGroup\n\t\t\t.selectAll('.sjpp-ag-matrix-col-section-line')\n\t\t\t.data(colSectionLines)\n\t\t\t.enter()\n\t\t\t.append('line')\n\t\t\t.attr('class', 'sjpp-ag-matrix-col-section-line')\n\t\t\t.attr('stroke', '#6b7280')\n\t\t\t.attr('stroke-width', 1)\n\t\t\t.attr('opacity', 0.9)\n\t\t\t.attr('x1', d => d.x1)\n\t\t\t.attr('x2', d => d.x2)\n\t\t\t.attr('y1', d => d.y)\n\t\t\t.attr('y2', d => d.y)\n\t}\n\n\trenderDots(dotPositions: AggMatrixDotPosition[]) {\n\t\tfor (const dot of dotPositions) {\n\t\t\tconst circle = this.renderDotShape(dot)\n\t\t\t\t.on('mouseover', (event: MouseEvent) => {\n\t\t\t\t\tthis.ag.dom.tip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\tconst table = table2col({ holder: this.ag.dom.tip.d })\n\t\t\t\t\tfor (const v of dot.tipData) {\n\t\t\t\t\t\taddTableRow(table, v.label, v.value, v.color)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\tthis.ag.dom.tip.clear().hide()\n\t\t\t\t})\n\t\t\tif (dot.hasData) {\n\t\t\t\tcircle.on('click', () => {\n\t\t\t\t\tconst config = this.ag.state.config\n\t\t\t\t\tconst colTerms = config.columns?.[dot.colSection] || []\n\t\t\t\t\tconst colTerm = colTerms.find(term => term.id === dot.column)\n\t\t\t\t\tif (!colTerm) return\n\t\t\t\t\tif (colTerm.type !== PSEUDOBULK) return\n\t\t\t\t\tconst tmp = structuredClone(colTerm)\n\n\t\t\t\t\t//TODO: Move this to interactions\n\t\t\t\t\tconst idName = `geneExpression ${dot.row} ${dot.column}`\n\t\t\t\t\ttmp.gene = dot.row\n\t\t\t\t\ttmp.category = dot.column\n\t\t\t\t\ttmp.id = idName\n\t\t\t\t\ttmp.name = idName\n\t\t\t\t\tthis.ag.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\tterm: tmp,\n\t\t\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\t/** A circle, or a pie of slices when the server returned a composition for the dot.\n\t * Both keep the dot class and test id, so a pie counts as a dot. */\n\trenderDotShape(dot: AggMatrixDotPosition) {\n\t\tif (!dot.pie) {\n\t\t\treturn this.dom.svg\n\t\t\t\t.append('circle')\n\t\t\t\t.attr('class', 'sjpp-ag-matrix-dot')\n\t\t\t\t.attr('data-testid', `sjpp-ag-matrix-dot-${dot.row}-${dot.column}`)\n\t\t\t\t.attr('cx', dot.x)\n\t\t\t\t.attr('cy', dot.y)\n\t\t\t\t.attr('r', dot.size)\n\t\t\t\t.attr('fill', dot.color)\n\t\t}\n\t\tconst g = this.dom.svg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-ag-matrix-dot sjpp-ag-matrix-pie')\n\t\t\t.attr('data-testid', `sjpp-ag-matrix-dot-${dot.row}-${dot.column}`)\n\t\t\t.attr('transform', `translate(${dot.x}, ${dot.y})`)\n\t\tfor (const slice of dot.pie.slices) {\n\t\t\tg.append('path')\n\t\t\t\t.attr('class', 'sjpp-ag-matrix-pie-slice')\n\t\t\t\t.attr('data-testid', `sjpp-ag-matrix-pie-slice-${slice.key}`)\n\t\t\t\t.attr('d', slice.path)\n\t\t\t\t.attr('fill', slice.color)\n\t\t\t\t.attr('stroke', '#fff')\n\t\t\t\t.attr('stroke-width', 0.5)\n\t\t}\n\t\treturn g\n\t}\n}\n\nfunction addTableRow(table: any, label: string, value: any, color?: string) {\n\tconst [td1, td2] = table.addRow()\n\tif (color) {\n\t\ttd1\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sjpp-ag-matrix-tip-swatch')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('width', '10px')\n\t\t\t.style('height', '10px')\n\t\t\t.style('margin-right', '6px')\n\t\t\t.style('background-color', color)\n\t\t\t.style('border', '1px solid #999')\n\t}\n\ttd1.append('span').text(label)\n\ttd2.text(value)\n}\n", "import type { AggregateMatrix } from '../AggregateMatrix'\nimport { controlsInit } from '#plots/controls.js'\nimport { validateMinMaxDotSetting } from '../settings/defaults.ts'\nimport { capitalizeFirstLetter, DownloadMenu } from '#dom'\nimport { isPieOnly } from '#shared/aggregateMatrix.js'\n\nexport async function setControls(controlsDiv, ag: AggregateMatrix, initConfig: any) {\n\tconst settings = initConfig.settings.aggregateMatrix\n\tconst chartType = initConfig.chartType\n\tconst gradientLabel = capitalizeFirstLetter(settings.gradientMethod)\n\n\t// a gradient is never applied to a pie, so a chart of only pies has no colors to set\n\tconst colorInputs = isPieOnly(initConfig.rows, initConfig.columns)\n\t\t? []\n\t\t: [\n\t\t\t\t{\n\t\t\t\t\tlabel: `${gradientLabel} start color`,\n\t\t\t\t\ttype: 'color',\n\t\t\t\t\tchartType,\n\t\t\t\t\tsettingsKey: 'startColor'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `${gradientLabel} stop color`,\n\t\t\t\t\ttype: 'color',\n\t\t\t\t\tchartType,\n\t\t\t\t\tsettingsKey: 'stopColor'\n\t\t\t\t}\n\t\t  ]\n\n\tconst inputs: any = [\n\t\t...colorInputs,\n\t\t{\n\t\t\tlabel: 'Min dot size',\n\t\t\ttitle: 'Set the minimum dot size. Number must be between 2 and 35',\n\t\t\ttype: 'number',\n\t\t\tchartType,\n\t\t\tsettingsKey: 'minDotSize',\n\t\t\tstep: 1,\n\t\t\tmax: settings.dotInputMax,\n\t\t\tmin: settings.dotInputMin,\n\t\t\twidth: 55,\n\t\t\tdebounceInterval: 300,\n\t\t\tprocessInput: (val: number) => {\n\t\t\t\tconst currentSettings = ag.state.config.settings.aggregateMatrix\n\t\t\t\tconst isValid = validateMinMaxDotSetting(currentSettings, val, currentSettings.maxDotSize)\n\t\t\t\tif (isValid !== null) {\n\t\t\t\t\talert(isValid)\n\t\t\t\t\treturn currentSettings.minDotSize\n\t\t\t\t}\n\t\t\t\treturn val\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Max dot size',\n\t\t\ttitle: 'Set the maximum dot size. Number must be between 2 and 35',\n\t\t\ttype: 'number',\n\t\t\tchartType,\n\t\t\tsettingsKey: 'maxDotSize',\n\t\t\tstep: 1,\n\t\t\tmax: settings.dotInputMax,\n\t\t\tmin: settings.dotInputMin,\n\t\t\twidth: 55,\n\t\t\tdebounceInterval: 300,\n\t\t\tprocessInput: (val: number) => {\n\t\t\t\tconst currentSettings = ag.state.config.settings.aggregateMatrix\n\t\t\t\tconst isValid = validateMinMaxDotSetting(currentSettings, currentSettings.minDotSize, val)\n\t\t\t\tif (isValid !== null) {\n\t\t\t\t\talert(isValid)\n\t\t\t\t\treturn currentSettings.maxDotSize\n\t\t\t\t}\n\t\t\t\treturn val\n\t\t\t}\n\t\t}\n\t]\n\n\tag.components.controls = await controlsInit({\n\t\tapp: ag.app,\n\t\tid: ag.id,\n\t\tholder: controlsDiv,\n\t\tinputs: inputs\n\t})\n\n\tag.components.controls.on('downloadClick.aggregateMatrix', async event => {\n\t\tconst name = ag.state.config.name || 'Aggregate matrix'\n\t\tconst svg = ag.dom.mainDiv.select('svg')\n\t\tconst chartImages = [{ name, svg }]\n\t\tnew DownloadMenu(chartImages, name).show(event.clientX, event.clientY)\n\t})\n}\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { getCombinedTermFilter } from '#filter'\nimport { AggMatrixModel } from './model/AggMatrixModel'\nimport { getAggregateMatrixSettings, getPieSizeDefaults } from './settings/defaults.ts'\nimport { AggMatrixViewModel } from './viewModel/AggMatrixViewModel.ts'\nimport { AggMatrixView } from './view/AggMatrixView.ts'\nimport { setControls } from './view/setControls.ts'\nimport { Menu, formatHeaderText } from '#dom'\nimport { hasPieAxes, isPieOnly, validateAggMatrixAxes } from '#shared/aggregateMatrix.js'\n\n/**** Plot in development ***\n * The aggregate matrix displays two aggregate values for two terms in a matrix format\n * by size and color gradient.*/\nexport class AggregateMatrix extends PlotBase implements RxComponent {\n\tstatic type = 'aggregateMatrix'\n\n\ttype: string\n\tcomponents: { controls: ComponentApi }\n\tdom: { [index: string]: any }\n\tmodel!: AggMatrixModel\n\tviewModel!: AggMatrixViewModel\n\tview!: AggMatrixView\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = AggregateMatrix.type\n\t\tthis.components = { controls: {} as ComponentApi }\n\n\t\tconst dom = super.getStandardDomLayout(opts.holder)\n\t\tthis.dom = {\n\t\t\tholder: opts.holder,\n\t\t\tcontrols: dom.controls.attr('data-testid', 'sjpp-ag-matrix-controls'),\n\t\t\terrorDiv: dom.errdiv.attr('data-testid', 'sjpp-ag-matrix-error'),\n\t\t\tloadingDiv: dom.loadingDiv.attr('data-testid', 'sjpp-ag-matrix-loading'),\n\t\t\tmainDiv: dom.charts.attr('data-testid', 'sjpp-ag-matrix-main').style('padding', '10px'),\n\t\t\ttip: new Menu({ padding: '3px' })\n\t\t}\n\n\t\tif (opts.header)\n\t\t\tformatHeaderText({\n\t\t\t\theader: opts.header,\n\t\t\t\tchartType: 'AGGREGATE MATRIX'\n\t\t\t})\n\t}\n\n\tgetState(appState: any) {\n\t\tconst config = appState.plots.find((p: any) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermfilter,\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tthis.model = new AggMatrixModel(this)\n\t\tthis.viewModel = new AggMatrixViewModel(this)\n\t\tthis.view = new AggMatrixView(this)\n\n\t\tconst config = this.getState(appState).config\n\t\tawait setControls(this.dom.controls, this, config)\n\t}\n\n\tasync main() {\n\t\tif (!this.model) throw new Error(`Model not initialized`)\n\t\tif (!this.viewModel) throw new Error(`ViewModel not initialized`)\n\t\tif (!this.view) throw new Error(`View not initialized`)\n\n\t\tsuper.toggleLoadingDiv()\n\n\t\ttry {\n\t\t\tconst data = await this.model.getData()\n\t\t\tif (!data || data.error) {\n\t\t\t\tsuper.toggleLoadingDiv('none')\n\t\t\t\tsuper.printError(data?.error || 'No data returned from server')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.viewModel.processData(data)\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(`${e.message || e} [AggregateMatrix main()]`)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tsuper.toggleLoadingDiv('none')\n\t\t\tsuper.printError(e.message || e)\n\t\t\treturn\n\t\t}\n\t\tthis.view.render(this.viewModel.viewData)\n\t\tsuper.toggleLoadingDiv('none')\n\t}\n}\n\nexport const aggMatrixInit = getCompInit(AggregateMatrix)\nexport const componentInit = aggMatrixInit\n\nexport function getPlotConfig(opts: any) {\n\tconst overrides = opts?.settings?.aggregateMatrix\n\tconst sizeDefaults = hasPieAxes(opts?.rows, opts?.columns)\n\t\t? getPieSizeDefaults(opts.rows, opts.columns, overrides)\n\t\t: {}\n\tconst config = {\n\t\thidePlotFilter: true,\n\t\tsettings: { aggregateMatrix: getAggregateMatrixSettings(overrides, sizeDefaults) }\n\t}\n\n\tconst returnConfig = copyMerge(config, opts)\n\tvalidatePlotConfig(returnConfig)\n\n\treturn returnConfig\n}\n\nexport function validatePlotConfig(config: any) {\n\tif (!config || typeof config !== 'object') throw new Error(`Invalid config provided for aggregate matrix plot`)\n\t// Same checks as the termdb/aggregateMatrix route, so unsupported term types fail before a request is made\n\tvalidateAggMatrixAxes(config.rows, config.columns)\n\n\tconst settings = config.settings?.aggregateMatrix || {}\n\tif (typeof settings.sizeMethod != 'string' || !settings.sizeMethod) {\n\t\tthrow new Error(`Invalid aggregate method for dot size`)\n\t}\n\t// a gradient is never applied to a pie, so only a chart with a dot that is not a pie needs a method for it\n\tif (isPieOnly(config.rows, config.columns)) return\n\tif (typeof settings.gradientMethod != 'string' || !settings.gradientMethod) {\n\t\tthrow new Error(`Invalid aggregate method for color gradient`)\n\t}\n\tif (settings.gradientMethod == settings.sizeMethod)\n\t\tthrow new Error(\n\t\t\t'Aggregate method for the color gradient cannot be the same as the aggregate method for the dot size.'\n\t\t)\n}\n"],
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+}