@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/cohortSunburst-SL5F36RM.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/cohortSunburst.ts"],
+  "sourcesContent": ["import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from './PlotBase'\nimport { Menu } from '#dom'\nimport { hierarchy, partition } from 'd3-hierarchy'\nimport { arc as d3arc } from 'd3-shape'\nimport { rgb as d3rgb } from 'd3-color'\nimport { interpolate } from 'd3-interpolate'\nimport { select } from 'd3-selection'\nimport 'd3-transition'\nimport { schemeTableau10 } from 'd3-scale-chromatic'\nimport { deriveCatalogRows, catalogRowKey, cohortMatches, type CatalogRow } from './proteome.catalog'\nimport type { ProteomeCohortSunburstConfig, ProteomeSunburstStat } from '#types'\n\n/*\nZoomable cohort sunburst.\n\nRings follow the dataset's `cohortSunburst.levels` (e.g. species \u2192 sample type \u2192 sample\nsource \u2192 disease \u2192 assay), each wedge sized by the number of sample sets (cohorts) beneath it. Two rings are shown around the centre; clicking an inner wedge zooms\nso that wedge becomes the centre and the next two rings appear; the centre offers Back.\nClicking a sample-set wedge (outermost leaf) toggles it in the selection, and \"Select all\"\nadds every sample set under the current centre. The selection panel launches the same\nactions as the Studies catalog: one cohort \u2192 Analytics Tools, several \u2192 cohort compare.\n\nZooming is animated the way d3's zoomable sunburst does it: every node keeps a\n`current` geometry (angles + ring units, see Geom); a click assigns each node a `target`\nrelative to the new centre, and one transition interpolates current \u2192 target while\nre-drawing arcs and label positions each frame. The clicked wedge's target is the full\ncentre disc (y 0..1), so it visibly sweeps round into a circle and fades as its children\nunfold into the rings; Back runs the same interpolation the other way, so the centre disc\nshrinks back into its wedge. The wedges are created once per data load and only their\nattributes change afterwards.\n*/\n\nconst RINGS = 2\nconst R0 = 74 // centre radius\nconst RING_W = 74\nconst RADIUS = R0 + RINGS * RING_W\nconst SIZE = RADIUS * 2 + 12\nconst DURATION = 750 // ms, zoom transition\nconst HOVER_DARKEN = 0.5 // d3-color darker() amount on hover\n/** how far a wedge of another kind than the selection fades towards white */\nconst DIM = 0.65\nconst WARN = '#b45309'\n/** wedges touch, divided by thin white lines, with bold white labels; the chart sits on the\n *  page background like every other plot */\nconst DIVIDER = '#ffffff'\nconst SELECT_STROKE = '#111827'\nconst CENTRE_FILL = '#f8fafc'\nconst CENTRE_STROKE = '#cbd5e1'\nconst TEXT_DARK = '#111827'\nconst TEXT_MUTED = '#4b5563'\nconst LINK = '#2563eb'\nconst CARD_BORDER = '#d1d5db'\nconst PILL_BG = '#e5e7eb'\nconst RULE = '#e5e7eb'\n/** shade of a ring relative to the centre: the inner ring a touch darker than the species colour */\nconst RING_SHADE = [-0.35, 0]\nconst LABEL_FONT = 12 // px, bold\nconst LABEL_LINE_H = LABEL_FONT * 1.15\nconst LABEL_CHAR_W = LABEL_FONT * 0.55 // rough advance of a bold glyph\nconst LABEL_MAX_LINES = 2\n\n/** radius of a ring-unit coordinate: the centre disc spans 0..1, every ring after is RING_W */\nconst radius = (y: number) => (y < 1 ? y * R0 : R0 + (y - 1) * RING_W)\nconst midRadius = (g: Geom) => (radius(g.y0) + radius(g.y1)) / 2\n\n/** small inline stroke icon for the controls above the chart; `paths` is the svg content */\nconst icon = (paths: string) =>\n\t`<svg width=\"13\" height=\"13\" viewBox=\"0 0 24 24\" style=\"vertical-align:-2px;margin-right:6px\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"2.4\" stroke-linecap=\"round\" stroke-linejoin=\"round\">${paths}</svg>`\n\ntype HNode = any // d3 HierarchyRectangularNode<TreeNode>\n/** a card: rounded box with a spaced-capitals title and an optional right-hand slot in its head */\ntype Card = { box: any; title: any; headRight: any; body: any }\n\nconst defaultConfig = { chartType: 'cohortSunburst' }\n\nclass CohortSunburst extends PlotBase implements RxComponent {\n\tstatic type = 'cohortSunburst'\n\ttype: string\n\tdom!: {\n\t\tholder: any\n\t\tbody: any\n\t\t/** path box: species at the start, then the path of clicked wedges */\n\t\tselBox: Card\n\t\t/** the selected sample sets, with the analyze/compare action */\n\t\tsel: Card\n\t\treset: any\n\t\t/** \"select all\" control beside reset, for the sample sets under the centre */\n\t\tselectAll: any\n\t\tsvg: any\n\t\tg: any\n\t\t/** centre disc (drawn beneath the wedges) and the text on it */\n\t\tcentre: any\n\t\tcentreText: any\n\t\t/** one <path> per node, whole tree; hidden ones have fill-opacity 0 */\n\t\tpaths: any\n\t\t/** one <text> per node, matching paths */\n\t\tlabels: any\n\t\tstats: any\n\t\ttip: Menu\n\t\theader?: any\n\t}\n\tui?: SunburstUiConfig\n\troot?: HNode\n\tfocus?: HNode\n\t/** stat box elements and the value they currently show, for the count animation */\n\tstatValues: Map<string, { el: any; value: number }> = new Map()\n\t/** selected cohorts by key, in selection order */\n\tselected: Map<string, CatalogRow> = new Map()\n\t/** leaf node of each cohort by key, for its species colour and ring label */\n\tleafNode: Map<string, HNode> = new Map()\n\tbaseColor: Map<string, string> = new Map()\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = CohortSunburst.type\n\t}\n\n\tasync init() {\n\t\t// the plot holder inherits nowrap from the sandbox; the cards need their text to wrap\n\t\tconst holder = this.opts.holder.append('div').style('padding', '10px').style('white-space', 'normal')\n\t\tconst body = holder.append('div')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tbody,\n\t\t\tselBox: undefined as any,\n\t\t\tsel: undefined as any,\n\t\t\treset: undefined,\n\t\t\tselectAll: undefined,\n\t\t\tsvg: undefined,\n\t\t\tg: undefined,\n\t\t\tcentre: undefined,\n\t\t\tcentreText: undefined,\n\t\t\tpaths: undefined,\n\t\t\tlabels: undefined,\n\t\t\tstats: undefined,\n\t\t\ttip: new Menu({ padding: '' }),\n\t\t\theader: this.opts.header\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Explore cohorts')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config: any = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\tasync main() {\n\t\tconst proteome = this.app.vocabApi.termdbConfig?.queries?.proteome\n\t\tconst ui: SunburstUiConfig | undefined = proteome?.cohortSunburst\n\t\tthis.dom.body.selectAll('*').remove()\n\t\tif (!ui?.levels?.length || !proteome?.organisms) {\n\t\t\tthis.dom.body\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.style('color', '#666')\n\t\t\t\t.text('No cohort sunburst is configured.')\n\t\t\treturn\n\t\t}\n\t\tthis.ui = ui\n\t\tconst tree = buildTree(deriveCatalogRows(proteome.organisms), ui)\n\t\tthis.root = hierarchy<TreeNode>(tree)\n\t\t\t.sum(d => (d.cohort ? 1 : 0))\n\t\t\t.sort(() => 0)\n\t\tpartition<TreeNode>().size([2 * Math.PI, this.root.height + 1])(this.root)\n\t\tthis.focus = this.root\n\t\tthis.leafNode = new Map(this.root.leaves().map((l: HNode) => [cohortKey(l.data.cohort), l]))\n\t\t// first-ring colours: dataset colors, else a palette in ring order\n\t\tthis.baseColor.clear()\n\t\tlet pi = 0\n\t\tfor (const c of this.root.children || []) {\n\t\t\tthis.baseColor.set(c.data.name, ui.colors?.[c.data.name] || schemeTableau10[pi++ % schemeTableau10.length])\n\t\t}\n\n\t\tconst layout = this.dom.body\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', '24px')\n\t\t\t.style('align-items', 'flex-start')\n\t\t//  path box to the left of the chart\n\t\tthis.dom.selBox = this.card(layout, 'Selection')\n\t\tthis.dom.selBox.box.style('flex', '0 0 230px')\n\t\tconst left = layout.append('div')\n\t\tconst panel = left.append('div').style('width', `${SIZE}px`)\n\t\t// controls above the chart, in spaced capitals: reset, and select all\n\t\t// sample sets under the centre\n\t\tconst toolbar = panel\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('justify-content', 'center')\n\t\t\t.style('gap', '28px')\n\t\t\t.style('min-height', '20px')\n\t\tconst control = () =>\n\t\t\ttoolbar\n\t\t\t\t.append('div')\n\t\t\t\t.style('letter-spacing', '0.15em')\n\t\t\t\t.style('font-size', '11px')\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('user-select', 'none')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\tthis.dom.reset = control()\n\t\t\t.html(`${icon('<path d=\"M3 12a9 9 0 1 0 3-6.7\"/><polyline points=\"3 3 3 9 9 9\"/>')}RESET`)\n\t\t\t.on('click', () => {\n\t\t\t\tif (this.focus!.depth) this.zoomTo(this.root)\n\t\t\t})\n\t\tthis.dom.selectAll = control().on('click', () => this.toggleSelectAll())\n\t\tthis.dom.svg = panel.append('svg').attr('width', SIZE).attr('height', SIZE).style('display', 'block')\n\t\tthis.dom.g = this.dom.svg.append('g').attr('transform', `translate(${SIZE / 2},${SIZE / 2})`)\n\t\tconst right = layout\n\t\t\t.append('div')\n\t\t\t.style('flex', '0 0 300px')\n\t\t\t.style('min-width', '0')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-direction', 'column')\n\t\t\t.style('gap', '12px')\n\t\t// stat boxes; their numbers follow the centre of the chart and count up/down\n\t\tthis.dom.stats = right\n\t\t\t.append('div')\n\t\t\t.style('display', 'grid')\n\t\t\t.style('grid-template-columns', '1fr 1fr')\n\t\t\t.style('gap', '8px')\n\t\tthis.statValues = new Map()\n\t\tfor (const def of ui.stats || []) {\n\t\t\tconst box = this.card(this.dom.stats, def.label)\n\t\t\tbox.box.style('padding', '8px 12px')\n\t\t\tbox.title.style('margin-bottom', '0')\n\t\t\tconst num = box.body\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '24px')\n\t\t\t\t.style('font-weight', '500')\n\t\t\t\t.style('color', TEXT_DARK)\n\t\t\t\t.style('font-variant-numeric', 'tabular-nums')\n\t\t\t\t.text('0')\n\t\t\tthis.statValues.set(def.label, { el: num, value: 0 })\n\t\t}\n\t\tthis.dom.sel = this.card(right, 'Selected sample sets')\n\t\tthis.buildChart()\n\t\tthis.renderStats()\n\t}\n\n\t/************ shared pieces ************/\n\n\t/** the card every box on the page is built from: rounded border, spaced-capitals title,\n\t *  a right-hand slot in the head for a count or control, and a body */\n\tcard(holder: any, title: string): Card {\n\t\tconst box = holder\n\t\t\t.append('div')\n\t\t\t.style('border', `1px solid ${CARD_BORDER}`)\n\t\t\t.style('border-radius', '10px')\n\t\t\t.style('padding', '10px 12px')\n\t\t\t.style('box-sizing', 'border-box')\n\t\tconst head = box\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('justify-content', 'space-between')\n\t\t\t.style('gap', '8px')\n\t\tconst titleDiv = head\n\t\t\t.append('div')\n\t\t\t.style('font-size', '10px')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('letter-spacing', '0.12em')\n\t\t\t.style('text-transform', 'uppercase')\n\t\t\t.style('color', TEXT_MUTED)\n\t\t\t.style('margin-bottom', '8px')\n\t\t\t.text(title)\n\t\tconst headRight = head.append('div').style('display', 'flex').style('align-items', 'center').style('gap', '8px')\n\t\treturn { box, title: titleDiv, headRight, body: box.append('div') }\n\t}\n\n\t/** colour-coded square with the short code of a name */\n\tbadge(holder: any, name: string, color: string, size = 30) {\n\t\treturn holder\n\t\t\t.append('span')\n\t\t\t.style('flex', '0 0 auto')\n\t\t\t.style('min-width', `${size}px`)\n\t\t\t.style('height', `${size}px`)\n\t\t\t.style('line-height', `${size}px`)\n\t\t\t.style('padding', '0 4px')\n\t\t\t.style('box-sizing', 'border-box')\n\t\t\t.style('border-radius', '6px')\n\t\t\t.style('background', color)\n\t\t\t.style('color', '#fff')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-size', size >= 30 ? '0.8em' : '0.7em')\n\t\t\t.style('text-align', 'center')\n\t\t\t.text(this.badgeCode(name))\n\t}\n\n\t/** rounded pill: the primary action button, or a count */\n\tpill(holder: any, opts: { button?: boolean } = {}) {\n\t\tconst el = holder\n\t\t\t.append(opts.button ? 'button' : 'span')\n\t\t\t.style('border-radius', '999px')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-variant-numeric', 'tabular-nums')\n\t\tif (opts.button)\n\t\t\tel.style('border', 'none')\n\t\t\t\t.style('background', SELECT_STROKE)\n\t\t\t\t.style('color', '#fff')\n\t\t\t\t.style('font-size', '13px')\n\t\t\t\t.style('padding', '8px 16px')\n\t\t\t\t.style('width', '100%')\n\t\t\t\t.style('cursor', 'pointer')\n\t\telse\n\t\t\tel.style('background', PILL_BG).style('color', TEXT_DARK).style('font-size', '11px').style('padding', '1px 8px')\n\t\treturn el\n\t}\n\n\t/************ colours ************/\n\n\t/** the first-ring (species) colour a wedge or cohort belongs to */\n\tspeciesColor(d: HNode): string {\n\t\tlet top = d\n\t\twhile (top.depth > 1) top = top.parent\n\t\treturn this.baseColor.get(top.data.name) || '#9ca3af'\n\t}\n\n\t/** the species colour, shaded by the ring the wedge occupies around the current centre\n\t *  (so a wedge keeps its species hue at every zoom level) */\n\tcolor(d: HNode): string {\n\t\tif (d.depth === 0) return CENTRE_FILL\n\t\tconst base = this.speciesColor(d)\n\t\tconst ring = Math.max(0, Math.min(RING_SHADE.length - 1, d.depth - (this.focus?.depth ?? 0) - 1))\n\t\tconst c = d3rgb(base).brighter(RING_SHADE[ring]).formatHex()\n\t\treturn d.dim ? d3rgb(interpolate(c, '#ffffff')(DIM)).formatHex() : c\n\t}\n\n\thoverColor(d: HNode): string {\n\t\treturn d3rgb(this.color(d)).darker(HOVER_DARKEN).formatHex()\n\t}\n\n\t/************ rendering ************/\n\n\tarc = d3arc()\n\t\t.startAngle((d: any) => d.x0)\n\t\t.endAngle((d: any) => d.x1)\n\t\t.innerRadius((d: any) => radius(d.y0))\n\t\t.outerRadius((d: any) => Math.max(radius(d.y0), radius(d.y1)))\n\n\t/** build every wedge and label once; zoomTo() then only animates their attributes */\n\tbuildChart() {\n\t\tconst g = this.dom.g\n\t\tg.selectAll('*').remove()\n\t\tconst root = this.root!\n\t\troot.each((d: HNode) => (d.current = { x0: d.x0, x1: d.x1, y0: d.y0, y1: d.y1 } as Geom))\n\t\tconst nodes = root.descendants().slice(1)\n\n\t\t// centre sits beneath the wedges so a clicked wedge can sweep over it as it grows;\n\t\t// hidden wedges have pointer-events none, so clicks fall through to the disc\n\t\tthis.dom.centre = g.append('g')\n\t\tthis.dom.centre\n\t\t\t.append('circle')\n\t\t\t.attr('r', R0 - 3)\n\t\t\t.attr('fill', CENTRE_FILL)\n\t\t\t.attr('stroke', CENTRE_STROKE)\n\t\t\t.attr('stroke-width', 1.5)\n\t\t\t.on('click', () => {\n\t\t\t\tif (this.focus!.depth) this.zoomTo(this.focus!.parent)\n\t\t\t})\n\t\tthis.dom.centreText = this.dom.centre.append('g').attr('pointer-events', 'none')\n\n\t\tthis.dom.paths = g\n\t\t\t.append('g')\n\t\t\t.selectAll('path')\n\t\t\t.data(nodes)\n\t\t\t.join('path')\n\t\t\t.attr('class', 'sjpp-sunburst-wedge')\n\t\t\t.attr('fill', (d: HNode) => this.color(d))\n\t\t\t.attr('fill-opacity', (d: HNode) => (arcVisible(d.current, RINGS) ? 1 : 0))\n\t\t\t.attr('stroke-opacity', (d: HNode) => (arcVisible(d.current, RINGS) ? 1 : 0))\n\t\t\t.attr('pointer-events', (d: HNode) => (arcVisible(d.current, RINGS) ? 'auto' : 'none'))\n\t\t\t.attr('d', (d: HNode) => this.arc(d.current))\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.on('mouseenter', (event: any, d: HNode) => {\n\t\t\t\tselect(event.currentTarget).attr('fill', this.hoverColor(d))\n\t\t\t\tthis.showTip(event, d)\n\t\t\t})\n\t\t\t.on('mouseleave', (event: any, d: HNode) => {\n\t\t\t\tselect(event.currentTarget).attr('fill', this.color(d))\n\t\t\t\tthis.dom.tip.hide()\n\t\t\t})\n\t\t\t.on('click', (_: any, d: HNode) => this.onWedgeClick(d))\n\n\t\tthis.dom.labels = g\n\t\t\t.append('g')\n\t\t\t.attr('pointer-events', 'none')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.style('user-select', 'none')\n\t\t\t.selectAll('text')\n\t\t\t.data(nodes)\n\t\t\t.join('text')\n\t\t\t.attr('font-size', `${LABEL_FONT}px`)\n\t\t\t.attr('font-weight', 'bold')\n\t\t\t.attr('fill', '#fff')\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.attr('fill-opacity', (d: HNode) => (this.labelVisible(d.current) ? 1 : 0))\n\t\t\t.attr('transform', (d: HNode) => this.labelTransform(d.current))\n\t\t\t.each((d: HNode, i: number, els: any[]) => this.setLabelText(select(els[i]), d, d.current))\n\n\t\tthis.refreshSelection()\n\t\tthis.renderCentre()\n\t\tthis.renderSelBox()\n\t}\n\n\t/** a label shows only where its wedge is visible and at least one line fits along the arc */\n\tlabelVisible(g: Geom): boolean {\n\t\treturn arcVisible(g, RINGS) && (g.x1 - g.x0) * midRadius(g) >= LABEL_LINE_H + 2\n\t}\n\n\t/** along the wedge's mid radius, reading outward; flipped in the left half so it is upright */\n\tlabelTransform(g: Geom): string {\n\t\tconst a = ((g.x0 + g.x1) / 2) * (180 / Math.PI)\n\t\treturn `rotate(${a - 90}) translate(${midRadius(g)},0) rotate(${a < 180 ? 0 : 180})`\n\t}\n\n\t/** wrap the node name into as many lines as the wedge's arc length allows (max 2), each\n\t *  no longer than the ring is thick */\n\tsetLabelText(text: any, d: HNode, g: Geom) {\n\t\tconst arcLen = (g.x1 - g.x0) * midRadius(g)\n\t\tconst nLines = Math.max(1, Math.min(LABEL_MAX_LINES, Math.floor(arcLen / LABEL_LINE_H)))\n\t\tconst maxChars = Math.floor((RING_W - 8) / LABEL_CHAR_W)\n\t\tconst lines = splitLabel(d.data.name, maxChars, nLines)\n\t\ttext.selectAll('tspan').remove()\n\t\tlines.forEach((l: string, i: number) => {\n\t\t\ttext\n\t\t\t\t.append('tspan')\n\t\t\t\t.attr('x', 0)\n\t\t\t\t.attr('dy', i === 0 ? `${(-(lines.length - 1) * LABEL_LINE_H) / 2}px` : `${LABEL_LINE_H}px`)\n\t\t\t\t.text(l)\n\t\t})\n\t}\n\n\t/** name, sample-set count and Back on the centre disc */\n\trenderCentre() {\n\t\tconst focus = this.focus!\n\t\tconst t = this.dom.centreText\n\t\tt.selectAll('*').remove()\n\t\tthis.dom.centre.select('circle').style('cursor', focus.depth ? 'pointer' : 'default')\n\t\tconst name = focus.depth ? focus.data.name : 'All sample sets'\n\t\tconst nameLines = splitLabel(name, Math.floor((2 * (R0 - 16)) / (15 * 0.6)), 2)\n\t\tconst n = countLeaves(focus.data)\n\t\tconst rows: { text: string; size: number; weight?: string; color: string; h: number }[] = [\n\t\t\t...nameLines.map(l => ({ text: l, size: 15, weight: 'bold', color: TEXT_DARK, h: 18 })),\n\t\t\t{ text: `${n} sample set${n === 1 ? '' : 's'}`, size: 12, color: TEXT_MUTED, h: 16 }\n\t\t]\n\t\tif (focus.depth) rows.push({ text: '\u2039  BACK', size: 12, weight: 'bold', color: LINK, h: 22 })\n\t\tconst total = rows.reduce((s, r) => s + r.h, 0)\n\t\tlet y = -total / 2\n\t\tfor (const r of rows) {\n\t\t\tt.append('text')\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t.attr('y', y + r.h / 2)\n\t\t\t\t.attr('font-size', `${r.size}px`)\n\t\t\t\t.attr('font-weight', r.weight || 'normal')\n\t\t\t\t.attr('fill', r.color)\n\t\t\t\t.attr('letter-spacing', r.text.endsWith('BACK') ? '0.12em' : null)\n\t\t\t\t.text(r.text)\n\t\t\ty += r.h\n\t\t}\n\t}\n\n\t/** selection strokes on the wedges plus the selection panel; no geometry changes */\n\trefreshSelection() {\n\t\t// a wedge is dimmed when nothing beneath it can join the current selection\n\t\tconst kind = this.selectedKind()\n\t\tthis.root!.each((d: HNode) => {\n\t\t\td.dim = kind !== undefined && !leavesOf(d.data).some(l => this.compatible(l.cohort!))\n\t\t})\n\t\tthis.dom.paths\n\t\t\t.attr('fill', (d: HNode) => this.color(d))\n\t\t\t.attr('stroke', (d: HNode) => (this.isSelected(d) ? SELECT_STROKE : DIVIDER))\n\t\t\t.attr('stroke-width', (d: HNode) => (this.isSelected(d) ? 3 : 1))\n\t\t\t.attr('stroke-linejoin', 'round')\n\t\t\t.style('cursor', (d: HNode) => (d.dim && this.terminalLeaf(d) ? 'not-allowed' : 'pointer'))\n\t\tthis.dom.labels.attr('fill', (d: HNode) => (d.dim ? TEXT_MUTED : '#fff'))\n\t\tthis.renderToolbar()\n\t\tthis.renderSidebar()\n\t}\n\n\t/************ selection kind ************/\n\n\tkindKeys(): string[] {\n\t\treturn this.ui?.selectionKind?.keys || []\n\t}\n\n\t/** the kind of the current selection; undefined when nothing is selected */\n\tselectedKind(): string | undefined {\n\t\tconst first = this.selected.values().next()\n\t\treturn first.done ? undefined : kindOf(first.value, this.kindKeys())\n\t}\n\n\t/** whether a cohort could be added to the current selection */\n\tcompatible(r: CatalogRow): boolean {\n\t\tconst kind = this.selectedKind()\n\t\treturn kind === undefined || kindOf(r, this.kindKeys()) === kind\n\t}\n\n\t/** short code for a badge: short upper-case names as they are (AD, CSF), initials of\n\t *  multi-word names (Frontal Cortex \u2192 FC), else the first two letters (Human \u2192 HU) */\n\tbadgeCode(name: string): string {\n\t\tif (name.length <= 4 && name === name.toUpperCase()) return name\n\t\tconst words = name.split(/[\\s()]+/).filter(Boolean)\n\t\tif (words.length > 1)\n\t\t\treturn words\n\t\t\t\t.map(w => w[0])\n\t\t\t\t.join('')\n\t\t\t\t.toUpperCase()\n\t\t\t\t.slice(0, 3)\n\t\treturn name.slice(0, 2).toUpperCase()\n\t}\n\n\t/** the selection box: at the root it lists the first ring (species) to click into; once\n\t *  zoomed it shows the path of clicked wedges, each with a colour-coded badge, and clicking\n\t *  a line zooms back to it */\n\trenderSelBox() {\n\t\tconst box = this.dom.selBox.body\n\t\tbox.selectAll('*').remove()\n\t\tconst focus = this.focus!\n\t\tconst atRoot = !focus.depth\n\t\tthis.dom.selBox.title.text(atRoot ? `${this.ui!.levels[0]?.name || ''} selection`.trim() : 'Selection')\n\t\tconst nodes: HNode[] = atRoot ? this.root!.children || [] : focus.ancestors().reverse().slice(1)\n\t\tconst STEP = 7 // px indent per ring, so the path reads as parent \u2192 child\n\t\tnodes.forEach((d: HNode, i: number) => {\n\t\t\tconst isFocus = d === focus\n\t\t\tconst indent = atRoot ? 0 : i * STEP\n\t\t\tconst row = box.append('div').style('position', 'relative').style('margin-left', `${indent}px`)\n\t\t\tif (indent) {\n\t\t\t\t// elbow connector from the parent's badge column down into this line\n\t\t\t\trow\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t.style('left', `${-STEP + 2}px`)\n\t\t\t\t\t.style('top', '-6px')\n\t\t\t\t\t.style('width', `${STEP - 4}px`)\n\t\t\t\t\t.style('height', '22px')\n\t\t\t\t\t.style('border-left', '1px solid #cbd5e1')\n\t\t\t\t\t.style('border-bottom', '1px solid #cbd5e1')\n\t\t\t\t\t.style('border-bottom-left-radius', '4px')\n\t\t\t}\n\t\t\tconst line = row\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '8px')\n\t\t\t\t.style('padding', '4px 6px')\n\t\t\t\t.style('margin', '2px 0')\n\t\t\t\t.style('border-radius', '6px')\n\t\t\t\t.style('background', isFocus ? '#eef2ff' : 'transparent')\n\t\t\t\t.style('cursor', isFocus ? 'default' : 'pointer')\n\t\t\t\t.attr('title', isFocus ? d.data.name : `Go to ${d.data.name}`)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (!isFocus) this.zoomTo(d)\n\t\t\t\t})\n\t\t\t\t.on('mouseenter', (event: any) => {\n\t\t\t\t\tif (!isFocus) select(event.currentTarget).style('background', '#f3f4f6')\n\t\t\t\t})\n\t\t\t\t.on('mouseleave', (event: any) => {\n\t\t\t\t\tif (!isFocus) select(event.currentTarget).style('background', 'transparent')\n\t\t\t\t})\n\t\t\tthis.badge(line, d.data.name, this.color(d))\n\t\t\tconst text = line.append('div').style('min-width', '0').style('line-height', '1.2')\n\t\t\ttext\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.9em')\n\t\t\t\t.style('font-weight', isFocus ? 'bold' : 'normal')\n\t\t\t\t.style('color', '#111827')\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('text-overflow', 'ellipsis')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.text(d.data.name)\n\t\t\tconst n = countLeaves(d.data)\n\t\t\ttext\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.7em')\n\t\t\t\t.style('color', '#6b7280')\n\t\t\t\t.text(`${d.data.level} \u00B7 ${n} sample set${n === 1 ? '' : 's'}`)\n\t\t})\n\t}\n\n\t/** stat boxes for the sample sets under the centre; numbers roll from the previous value */\n\trenderStats() {\n\t\tconst leaves = leavesOf(this.focus!.data)\n\t\tfor (const def of this.ui!.stats || []) {\n\t\t\tconst box = this.statValues.get(def.label)\n\t\t\tif (!box) continue\n\t\t\tconst v = computeStat(leaves, def)\n\t\t\tif (v === null) {\n\t\t\t\tbox.el.text('\u2014').attr('title', `No ${def.key || ''} counts in the dataset yet`)\n\t\t\t\tbox.value = 0\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tbox.el.attr('title', null)\n\t\t\tconst from = box.value\n\t\t\tbox.value = v\n\t\t\tconst i = interpolate(from, v)\n\t\t\tbox.el\n\t\t\t\t.transition()\n\t\t\t\t.duration(DURATION)\n\t\t\t\t.tween('text', () => (t: number) => box.el.text(Math.round(i(t)).toLocaleString()))\n\t\t}\n\t}\n\n\t/** the sample sets Select all would take under the centre: those of the selected kind,\n\t *  or, with nothing selected, of the largest kind there; and whether all are selected */\n\tunderFocus(): { under: TreeNode[]; allIn: boolean; kind: string } {\n\t\tconst leaves = leavesOf(this.focus!.data)\n\t\tconst keys = this.kindKeys()\n\t\tconst kind = this.selectedKind() ?? largestKind(leaves, keys)\n\t\tconst under = leaves.filter(l => kindOf(l.cohort!, keys) === kind)\n\t\tconst allIn = under.length > 0 && under.every(l => this.selected.has(cohortKey(l.cohort!)))\n\t\treturn { under, allIn, kind }\n\t}\n\n\ttoggleSelectAll() {\n\t\tconst { under, allIn } = this.underFocus()\n\t\tif (!under.length) return\n\t\tfor (const l of under) {\n\t\t\tif (allIn) this.selected.delete(cohortKey(l.cohort!))\n\t\t\telse this.selected.set(cohortKey(l.cohort!), l.cohort!)\n\t\t}\n\t\tthis.refreshSelection()\n\t}\n\n\t/** reset is only active when zoomed in; select all follows the centre and flips to\n\t *  deselect once everything under it is selected */\n\trenderToolbar() {\n\t\tconst zoomed = !!this.focus!.depth\n\t\tthis.dom.reset.style('opacity', zoomed ? 1 : 0.35).style('cursor', zoomed ? 'pointer' : 'default')\n\t\tconst { under, allIn, kind } = this.underFocus()\n\t\tconst what = kind ? `${kind} sample sets` : 'sample sets'\n\t\tconst none = !under.length\n\t\tthis.dom.selectAll\n\t\t\t.style('opacity', none ? 0.35 : 1)\n\t\t\t.style('cursor', none ? 'default' : 'pointer')\n\t\t\t.attr(\n\t\t\t\t'title',\n\t\t\t\tnone\n\t\t\t\t\t? `No ${what} under the centre; clear the selection to pick other kinds`\n\t\t\t\t\t: allIn\n\t\t\t\t\t? `Deselect every ${what.replace(/s$/, '')} under the centre`\n\t\t\t\t\t: `Select every ${what.replace(/s$/, '')} under the centre`\n\t\t\t)\n\t\t\t.html(\n\t\t\t\tallIn\n\t\t\t\t\t? `${icon('<circle cx=\"12\" cy=\"12\" r=\"9\"/><path d=\"M8 12h8\"/>')}DESELECT ALL`\n\t\t\t\t\t: `${icon('<circle cx=\"12\" cy=\"12\" r=\"9\"/><path d=\"M12 8v8M8 12h8\"/>')}SELECT ALL ${under.length}${\n\t\t\t\t\t\t\tkind ? ` \u00B7 ${kind.toUpperCase()}` : ''\n\t\t\t\t\t  }`\n\t\t\t)\n\t}\n\n\t/** the selected-sample-sets card: count in the head, one line per set with its species\n\t *  badge, and the analyze/compare action as the footer */\n\trenderSidebar() {\n\t\tconst { title, headRight, body } = this.dom.sel\n\t\theadRight.selectAll('*').remove()\n\t\tbody.selectAll('*').remove()\n\t\theadRight.style('margin-bottom', '8px')\n\t\tconst n = this.selected.size\n\t\ttitle.text(n ? 'Selected sample sets' : 'No sample sets selected')\n\t\tif (n) {\n\t\t\tthis.pill(headRight).text(n)\n\t\t\theadRight\n\t\t\t\t.append('span')\n\t\t\t\t.style('font-size', '11px')\n\t\t\t\t.style('color', LINK)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text('Clear')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.selected.clear()\n\t\t\t\t\tthis.refreshSelection()\n\t\t\t\t})\n\t\t}\n\n\t\tconst kind = this.selectedKind()\n\t\tif (kind) {\n\t\t\tbody\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.75em')\n\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t.style('margin-bottom', '4px')\n\t\t\t\t.text(`${kind} only \u00B7 clear the selection to pick another kind`)\n\t\t}\n\t\tconst list = body\n\t\t\t.append('div')\n\t\t\t.style('max-height', `${SIZE - 200}px`)\n\t\t\t.style('overflow-y', 'auto')\n\t\tif (!n) {\n\t\t\tlist\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t.style('padding', '4px 0')\n\t\t\t\t.text('Click a sample-set wedge, or Select all above the chart.')\n\t\t}\n\t\tfor (const [k, r] of this.selected) {\n\t\t\tconst leaf = this.leafNode.get(k)\n\t\t\tconst line = list\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '8px')\n\t\t\t\t.style('padding', '3px 6px')\n\t\t\t\t.style('margin', '2px 0')\n\t\t\t\t.style('border-radius', '6px')\n\t\t\t\t.on('mouseenter', (event: any) => {\n\t\t\t\t\tselect(event.currentTarget).style('background', '#f3f4f6').select('.sjpp-sunburst-remove').style('opacity', 1)\n\t\t\t\t})\n\t\t\t\t.on('mouseleave', (event: any) => {\n\t\t\t\t\tselect(event.currentTarget)\n\t\t\t\t\t\t.style('background', 'transparent')\n\t\t\t\t\t\t.select('.sjpp-sunburst-remove')\n\t\t\t\t\t\t.style('opacity', 0)\n\t\t\t\t})\n\t\t\tthis.badge(line, leaf?.data.name || r.cohort, leaf ? this.speciesColor(leaf) : '#9ca3af', 24)\n\t\t\tconst text = line.append('div').style('flex', '1 1 auto').style('min-width', '0').style('line-height', '1.2')\n\t\t\ttext\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.9em')\n\t\t\t\t.style('color', TEXT_DARK)\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('text-overflow', 'ellipsis')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.text(this.selectionLabel(r))\n\t\t\ttext\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.7em')\n\t\t\t\t.style('color', '#6b7280')\n\t\t\t\t.text(r.proteome + (r.placeholder ? ' \u00B7 placeholder data' : ''))\n\t\t\tline\n\t\t\t\t.append('span')\n\t\t\t\t.attr('class', 'sjpp-sunburst-remove')\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('color', '#9ca3af')\n\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t.attr('title', 'Remove')\n\t\t\t\t.text('\u2715')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.selected.delete(k)\n\t\t\t\t\tthis.refreshSelection()\n\t\t\t\t})\n\t\t}\n\n\t\t// PTM (site-level) and protein-level z are not comparable\n\t\tconst types = new Set([...this.selected.values()].map(r => r.dataType))\n\t\tif (types.size > 1) {\n\t\t\tbody\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.style('color', WARN)\n\t\t\t\t.style('margin-top', '6px')\n\t\t\t\t.text('Selection mixes PTM (site-level) and protein-level assays; their log2FC-z are not directly comparable.')\n\t\t}\n\n\t\tconst footer = body\n\t\t\t.append('div')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('padding-top', '10px')\n\t\t\t.style('border-top', `1px solid ${RULE}`)\n\t\tthis.pill(footer, { button: true })\n\t\t\t.property('disabled', n === 0)\n\t\t\t.style('opacity', n ? 1 : 0.3)\n\t\t\t.style('cursor', n ? 'pointer' : 'default')\n\t\t\t.text(n >= 2 ? `Compare ${n} cohorts` : 'Analyze cohort')\n\t\t\t.on('click', () => this.onAction())\n\t}\n\n\t/************ interaction ************/\n\n\t/** the single sample set a wedge stands for: the leaf itself, or the only leaf beneath an\n\t *  inner wedge (e.g. a human assay wedge with one cohort), so it can be selected without\n\t *  zooming down to a lone full-circle wedge */\n\tterminalLeaf(d: HNode): CatalogRow | undefined {\n\t\tif (d.data.cohort) return d.data.cohort\n\t\tif (countLeaves(d.data) !== 1) return undefined\n\t\treturn leavesOf(d.data)[0].cohort\n\t}\n\n\tisSelected(d: HNode): boolean {\n\t\tconst r = this.terminalLeaf(d)\n\t\treturn !!r && this.selected.has(cohortKey(r))\n\t}\n\n\t/** animate every wedge from its current geometry to where it sits with `p` at the centre */\n\tzoomTo(p: HNode) {\n\t\tthis.focus = p\n\t\tthis.dom.tip.hide()\n\t\tconst root = this.root!\n\t\troot.each((d: HNode) => (d.target = zoomTarget(d, p)))\n\t\tconst t = this.dom.g.transition().duration(DURATION)\n\n\t\t// no hover or clicks on wedges while they move (a wedge sweeping under the cursor would\n\t\t// otherwise darken and pop a tooltip); the visible ones take pointer events again at the end.\n\t\t// A zoom that interrupts this one re-runs the same steps, so nothing is left disabled.\n\t\tthis.dom.paths.attr('pointer-events', 'none')\n\t\t// judged by the target, not d.current: the group's end event fires a tick before the\n\t\t// wedge tweens write their final frame, so current would still be a hair short of it\n\t\tt.on('end', () =>\n\t\t\tthis.dom.paths.attr('pointer-events', (d: HNode) => (arcVisible(d.target, RINGS) ? 'auto' : 'none'))\n\t\t)\n\t\tthis.dom.paths\n\t\t\t.transition(t)\n\t\t\t// every node's current geometry moves, even hidden ones, so a later zoom starts right\n\t\t\t.tween('data', (d: HNode) => {\n\t\t\t\tconst i = interpolate(d.current, d.target)\n\t\t\t\treturn (k: number) => (d.current = i(k))\n\t\t\t})\n\t\t\t.filter(function (this: any, d: HNode) {\n\t\t\t\treturn +this.getAttribute('fill-opacity') || arcVisible(d.target, RINGS)\n\t\t\t})\n\t\t\t.attr('fill-opacity', (d: HNode) => (arcVisible(d.target, RINGS) ? 1 : 0))\n\t\t\t.attr('stroke-opacity', (d: HNode) => (arcVisible(d.target, RINGS) ? 1 : 0))\n\t\t\t.attr('fill', (d: HNode) => this.color(d))\n\t\t\t.attrTween('d', (d: HNode) => () => this.arc(d.current))\n\n\t\tthis.dom.labels\n\t\t\t.filter((d: HNode, i: number, els: any[]) => +els[i].getAttribute('fill-opacity') || this.labelVisible(d.target))\n\t\t\t.each((d: HNode, i: number, els: any[]) => this.setLabelText(select(els[i]), d, d.target))\n\t\t\t.transition(t)\n\t\t\t.attr('fill-opacity', (d: HNode) => (this.labelVisible(d.target) ? 1 : 0))\n\t\t\t.attrTween('transform', (d: HNode) => () => this.labelTransform(d.current))\n\n\t\t// the new centre text fades in beneath the wedge sweeping over the disc\n\t\tthis.renderCentre()\n\t\tthis.dom.centreText.attr('opacity', 0).transition(t).attr('opacity', 1)\n\t\tthis.renderStats()\n\t\tthis.renderToolbar()\n\t\tthis.renderSelBox()\n\t\tthis.renderSidebar()\n\t}\n\n\tonWedgeClick(d: HNode) {\n\t\tconst r = this.terminalLeaf(d)\n\t\tif (r) {\n\t\t\tif (!this.compatible(r)) return // the tooltip says why\n\t\t\tconst k = cohortKey(r)\n\t\t\tif (this.selected.has(k)) this.selected.delete(k)\n\t\t\telse this.selected.set(k, r)\n\t\t\tthis.refreshSelection()\n\t\t} else this.zoomTo(d)\n\t}\n\n\tshowTip(event: any, d: HNode) {\n\t\tthis.dom.tip.clear().show(event.clientX, event.clientY)\n\t\tconst box = this.dom.tip.d\n\t\t\t.append('div')\n\t\t\t.style('padding', '10px 14px')\n\t\t\t.style('min-width', '170px')\n\t\t\t.style('font-size', '13px')\n\t\t\t.style('line-height', '1.45')\n\t\tbox.append('div').style('font-weight', 'bold').style('font-size', '14px').text(d.data.name)\n\t\tconst r = this.terminalLeaf(d)\n\t\tconst stat = (label: string, value: string | number) => {\n\t\t\tconst line = box.append('div').style('color', '#374151')\n\t\t\tline.append('span').text(`${label}: `)\n\t\t\tline.append('b').text(String(value))\n\t\t}\n\t\tconst note = (text: string, color: string) =>\n\t\t\tbox.append('div').style('margin-top', '4px').style('color', color).text(text)\n\t\tconst kind = this.selectedKind()\n\t\tif (r) {\n\t\t\tbox.append('div').style('color', '#6b7280').text(`${r.species} \u00B7 ${r.proteome} \u00B7 ${r.cohort}`)\n\t\t\tif (r.placeholder) box.append('div').style('color', WARN).text('placeholder data')\n\t\t\tif (!this.compatible(r))\n\t\t\t\tnote(`Clear the ${kind} selection to select a ${kindOf(r, this.kindKeys())} sample set`, WARN)\n\t\t\telse note(this.selected.has(cohortKey(r)) ? 'click to deselect' : 'click to select', LINK)\n\t\t} else {\n\t\t\tbox.append('div').style('color', '#6b7280').text(d.data.level)\n\t\t\tstat('Sample sets', countLeaves(d.data))\n\t\t\tif (d.dim) note(`No ${kind} sample sets here; clear the selection to pick from these`, WARN)\n\t\t\tnote('click to zoom in', LINK)\n\t\t}\n\t}\n\n\t/** label for the selection list / compare plot; adds the assay when several are selected */\n\tselectionLabel(r: CatalogRow): string {\n\t\tconst species = r.species\n\t\tconst leaf = this.leafNode.get(cohortKey(r))\n\t\tconst base = `${species} ${leaf?.data.name || r.cohort}`\n\t\tconst assays = new Set([...this.selected.values()].map(x => x.proteome))\n\t\treturn assays.size > 1 ? `${base} (${r.proteome})` : base\n\t}\n\n\tonAction() {\n\t\tconst sel = [...this.selected.values()]\n\t\tif (sel.length === 1) {\n\t\t\tconst c = sel[0]\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'ProteomeInput',\n\t\t\t\t\tproteomeDetails: { organism: c.organism, assay: c.assay, cohort: c.cohort },\n\t\t\t\t\thidePlotFilter: true\n\t\t\t\t}\n\t\t\t})\n\t\t} else if (sel.length >= 2) {\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'proteomeCohortCompare',\n\t\t\t\t\tcohorts: sel.map(c => ({\n\t\t\t\t\t\torganism: c.organism,\n\t\t\t\t\t\tassay: c.assay,\n\t\t\t\t\t\tcohort: c.cohort,\n\t\t\t\t\t\tlabel: this.selectionLabel(c)\n\t\t\t\t\t}))\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n}\n\n/*********** tree building and zoom geometry (DOM-free) ***********/\n\ntype SunburstUiConfig = ProteomeCohortSunburstConfig\ntype Level = SunburstUiConfig['levels'][number]\n\ntype TreeNode = {\n\tname: string\n\t/** ring name (Level.name); undefined for the root and the leaves */\n\tlevel?: string\n\tchildren?: TreeNode[]\n\t/** leaves only */\n\tcohort?: CatalogRow\n}\n\n/** the value of one ring for a cohort, '' if the ring does not apply to it */\nfunction levelValue(row: CatalogRow, level: Level): string {\n\tfor (const v of level.values) {\n\t\tif (v.when && !cohortMatches(v.when, row.organism, row.assay, row)) continue\n\t\tif (v.const) return v.const\n\t\tif (v.key && row[v.key]) return String(row[v.key])\n\t}\n\treturn ''\n}\n\nfunction leafLabel(row: CatalogRow, cfg: SunburstUiConfig['leafLabel']): string {\n\tconst pick = (keys: string[]) =>\n\t\tkeys\n\t\t\t.map(k => row[k])\n\t\t\t.filter(Boolean)\n\t\t\t.map(String)\n\tconst a = pick(cfg.keys)\n\tif (a.length) return a.join(' ')\n\tconst b = pick(cfg.fallbackKeys || [])\n\treturn b.length ? b.join(' ') : row.cohort\n}\n\n/** nest cohorts by their ring values, in first-seen order. A ring without a value for a\n *  cohort is skipped for that cohort, so branches may differ in depth. */\nfunction buildTree(rows: CatalogRow[], ui: SunburstUiConfig, rootName = 'All sample sets'): TreeNode {\n\tconst root: TreeNode = { name: rootName, children: [] }\n\tfor (const r of rows) {\n\t\tlet node = root\n\t\tfor (const level of ui.levels) {\n\t\t\tconst v = levelValue(r, level)\n\t\t\tif (!v) continue\n\t\t\tif (!node.children) node.children = []\n\t\t\tlet child = node.children.find(c => c.name === v && c.level === level.name)\n\t\t\tif (!child) {\n\t\t\t\tchild = { name: v, level: level.name, children: [] }\n\t\t\t\tnode.children.push(child)\n\t\t\t}\n\t\t\tnode = child\n\t\t}\n\t\tif (!node.children) node.children = []\n\t\tnode.children.push({ name: leafLabel(r, ui.leafLabel), cohort: r })\n\t}\n\tdisambiguateLeaves(root)\n\treturn root\n}\n\n/** sibling leaves sharing a label (e.g. two studies of the same disease and region) get\n *  their cohort key appended, so each wedge names the sample set it selects */\nfunction disambiguateLeaves(node: TreeNode) {\n\tconst leaves = (node.children || []).filter(c => c.cohort)\n\tconst seen = new Map<string, number>()\n\tfor (const l of leaves) seen.set(l.name, (seen.get(l.name) || 0) + 1)\n\tfor (const l of leaves) if (seen.get(l.name)! > 1) l.name = `${l.name} (${l.cohort!.cohort})`\n\tfor (const c of node.children || []) if (!c.cohort) disambiguateLeaves(c)\n}\n\n/** number of cohorts (leaves) under a node */\nfunction countLeaves(n: TreeNode): number {\n\tif (n.cohort) return 1\n\tlet s = 0\n\tfor (const c of n.children || []) s += countLeaves(c)\n\treturn s\n}\n\n/** every leaf under a node, in tree order */\nfunction leavesOf(n: TreeNode): TreeNode[] {\n\tif (n.cohort) return [n]\n\tconst out: TreeNode[] = []\n\tfor (const c of n.children || []) out.push(...leavesOf(c))\n\treturn out\n}\n\nconst cohortKey = (r: CatalogRow) => catalogRowKey(r.organism, r.assay, r.cohort)\n\n/*********** selection kind ***********/\n\n/** the kind of a cohort: its values of the selectionKind keys joined, e.g. \"Human Whole\";\n *  '' when no keys are configured, so every cohort is of one kind */\nfunction kindOf(r: CatalogRow, keys: string[] = []): string {\n\treturn keys\n\t\t.map(k => r[k])\n\t\t.filter(Boolean)\n\t\t.map(String)\n\t\t.join(' ')\n}\n\n/** the kind with the most leaves; first-seen wins a tie; '' for no leaves */\nfunction largestKind(leaves: TreeNode[], keys: string[] = []): string {\n\tconst counts = new Map<string, number>()\n\tfor (const l of leaves) {\n\t\tconst k = kindOf(l.cohort!, keys)\n\t\tcounts.set(k, (counts.get(k) || 0) + 1)\n\t}\n\tlet best = ''\n\tlet bestN = 0\n\tfor (const [k, n] of counts) {\n\t\tif (n > bestN) {\n\t\t\tbest = k\n\t\t\tbestN = n\n\t\t}\n\t}\n\treturn best\n}\n\n/*********** zoom geometry (d3 zoomable-sunburst) ***********/\n\n/** arc geometry of one wedge in partition units: angles in radians; y in ring units, where\n *  y=0 is the centre point, y=1 the edge of the centre circle and y=2 the outer edge of the\n *  first ring */\ntype Geom = { x0: number; x1: number; y0: number; y1: number }\n\n/** where a node lands once `focus` is the centre: its angles are rescaled to the focus's\n *  span (clamped, so wedges outside the focus collapse to zero width) and its rings shift\n *  inward by the focus depth (so the focus itself becomes the full centre disc, y 0..1,\n *  and its ancestors collapse onto the centre point). Interpolating a node's current\n *  geometry toward this is what makes a clicked wedge sweep into a circle. */\nfunction zoomTarget(d: Geom & { depth: number }, focus: Geom & { depth: number }): Geom {\n\tconst span = focus.x1 - focus.x0 || 1\n\tconst ang = (x: number) => Math.max(0, Math.min(1, (x - focus.x0) / span)) * 2 * Math.PI\n\treturn {\n\t\tx0: ang(d.x0),\n\t\tx1: ang(d.x1),\n\t\ty0: Math.max(0, d.y0 - focus.depth),\n\t\ty1: Math.max(0, d.y1 - focus.depth)\n\t}\n}\n\n/** a wedge is drawn when it lies within the `rings` shown around the centre and has width */\nfunction arcVisible(g: Geom, rings: number): boolean {\n\treturn g.y0 >= 1 && g.y1 <= rings + 1 && g.x1 > g.x0\n}\n\n/** break a label into at most `maxLines` lines of at most `maxChars` characters, splitting\n *  at spaces; a line that still does not fit is truncated with an ellipsis */\nfunction splitLabel(text: string, maxChars: number, maxLines: number): string[] {\n\tconst words = text.split(/\\s+/).filter(Boolean)\n\tconst lines: string[] = []\n\tlet cur = ''\n\tfor (const w of words) {\n\t\tif (!cur) cur = w\n\t\telse if ((cur + ' ' + w).length <= maxChars) cur += ' ' + w\n\t\telse {\n\t\t\tlines.push(cur)\n\t\t\tcur = w\n\t\t}\n\t}\n\tif (cur) lines.push(cur)\n\tif (lines.length > maxLines) {\n\t\tconst rest = lines.slice(maxLines - 1).join(' ')\n\t\tlines.length = maxLines - 1\n\t\tlines.push(rest)\n\t}\n\treturn lines.map(l => (l.length > maxChars ? l.slice(0, Math.max(1, maxChars - 1)) + '\u2026' : l))\n}\n\n/** value of a stat box over a set of leaves; null = not available (a sum with no data) */\nfunction computeStat(leaves: TreeNode[], def: ProteomeSunburstStat): number | null {\n\tconst rows = leaves.map(l => l.cohort!).filter(r => !def.where || cohortMatches(def.where, r.organism, r.assay, r))\n\tif (def.kind === 'count') return rows.length\n\tif (def.kind === 'distinct') {\n\t\tconst vals = new Set(rows.map(r => r[def.key || '']).filter(v => v !== undefined && v !== null && v !== ''))\n\t\treturn vals.size\n\t}\n\t// sum\n\tlet total = 0\n\tlet seen = false\n\tfor (const r of rows) {\n\t\tconst v = Number(r[def.key || ''])\n\t\tif (!Number.isFinite(v) || r[def.key || ''] === undefined || r[def.key || ''] === '') continue\n\t\ttotal += v\n\t\tseen = true\n\t}\n\treturn seen ? total : null\n}\n\nexport const componentInit = getCompInit(CohortSunburst)\n\nexport async function getPlotConfig(opts: any) {\n\tconst config = structuredClone(defaultConfig)\n\treturn copyMerge(config, opts)\n}\n"],
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+  "names": []
+}

package/dist/condition-QROUALBG.js

@@ -0,0 +1,323 @@
+import {
+  getPillNameDefault,
+  make_radios,
+  sayerror,
+  set_hiddenvalues,
+  throwMsgWithFilePathAndFnName
+} from "./chunk-YS7Y257H.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-PITPUAWX.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-K6CZAEBF.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-XJYVMXMZ.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-ZSNZPH6G.js";
+import "./chunk-ET2KFCXK.js";
+import "./chunk-LMG7Y5IN.js";
+import {
+  copyMerge
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// termsetting/handlers/condition.ts
+var cutoffGrades = [1, 2, 3, 4, 5];
+function getHandler(self) {
+  return {
+    getPillName(d) {
+      return getPillNameDefault(self, d);
+    },
+    getPillStatus() {
+      return getPillStatus(self);
+    },
+    showEditMenu(div) {
+      if (self.q.mode == "discrete") {
+        return showMenu_discrete(self, div);
+      }
+      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
+        return showMenu_cutoff(self, div);
+      }
+      console.error("invalid q.mode:", self.q.mode);
+      throw "invalid q.mode";
+    }
+    // async postMain() {
+    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
+    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
+    // 	//not really sure this is necessary but it's consistent across other handlers
+    // 	self.category2samplecount = []
+    // 	for (const d of data.lst) {
+    // 		self.category2samplecount.push({
+    // 			key: d.key,
+    // 			label: d.label,
+    // 			count: d.samplecount
+    // 		})
+    // 		// }
+    // 	}
+    // }
+  };
+}
+function getPillStatus(self) {
+  const text = self.q?.name;
+  if (text) return { text };
+  if (self.q.mode == "discrete") {
+    if (self.q.breaks?.length) {
+      return { text: self.q.breaks.length + 1 + " groups" };
+    } else {
+      if (self.q.bar_by_grade) {
+        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
+        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
+        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
+        return { text: "Error: unknown grade setting", bgcolor: "red" };
+      }
+      if (self.q.bar_by_children) return { text: "Sub-condition" };
+    }
+  }
+  if (self.q.mode == "binary") {
+    return {
+      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
+    };
+  }
+  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    return { text: `Grades ${self.q.breaks[0]}-5` };
+  }
+  return {};
+}
+async function showMenu_discrete(self, div) {
+  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
+  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
+    const i = value_type_select.property("selectedIndex");
+    self.q.bar_by_grade = i != 3;
+    self.q.bar_by_children = i == 3;
+    self.q.value_by_max_grade = i == 0;
+    self.q.value_by_most_recent = i == 1;
+    self.q.value_by_computable_grade = i == 2 || i == 3;
+    self.dom.tip.hide();
+    self.api.runCallback();
+  });
+  value_type_select.append("option").text("Max grade per patient");
+  value_type_select.append("option").text("Most recent grade per patient");
+  value_type_select.append("option").text("Any grade per patient");
+  if (self.term.subconditions) {
+    value_type_select.append("option").text("Sub-conditions");
+  }
+  value_type_select.property(
+    "selectedIndex",
+    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
+  );
+  if (self.q.bar_by_children) {
+    return;
+  }
+  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
+  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
+  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
+  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
+  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
+  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
+  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+  if (self.q.breaks?.length) {
+    textarea.property("value", self.q.breaks.join("\n"));
+  }
+  textarea2gradeUI();
+  function textarea2gradeUI() {
+    rangeNameDiv.selectAll("*").remove();
+    const breaks = textarea2breaks();
+    if (!breaks.length) {
+      delete self.q.breaks;
+      delete self.q.groups;
+      return;
+    }
+    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
+    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
+    const groups = getGroups(grades, breaks);
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
+    for (const [i, g] of groups.entries()) {
+      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
+      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
+        groups[i].name = this.value;
+      });
+    }
+    self.q.breaks = breaks;
+    self.q.groups = groups;
+  }
+  function textarea2breaks() {
+    const str = textarea.property("value").trim();
+    if (!str) return [];
+    const lst = [...new Set(str.split("\n"))];
+    const breaks = [];
+    for (const x of lst) {
+      const b = Number(x);
+      if (!Number.isInteger(b)) {
+        sayerror(div, "cutoff grade must be an integer value");
+        return [];
+      }
+      if (b < 1 || b > 5) {
+        sayerror(div, `cutoff grade must be within grades 1-5`);
+        return [];
+      }
+      breaks.push(b);
+    }
+    if (!breaks.length) return [];
+    return breaks.sort((i, j) => i - j);
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function showMenu_cutoff(self, div) {
+  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
+  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
+  const sd = holder.append("div");
+  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
+  for (const i of cutoffGrades) {
+    gradeSelect.append("option").text(self.term.values?.[i].label);
+  }
+  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
+  const g1n = holder.append("div").style("opacity", 0.4);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
+  const g2n = holder.append("div").style("opacity", 0.4);
+  changeGradeSelect();
+  function changeGradeSelect() {
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    g1n.selectAll("*").remove();
+    g2n.selectAll("*").remove();
+    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+    for (const i of grades) {
+      if (i < grade) {
+        g1n.append("div").text(self.term.values?.[i].label);
+      } else {
+        g2n.append("div").text(self.term.values?.[i].label);
+      }
+    }
+  }
+  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
+  let timeScaleChoice;
+  if (self.q.mode == "cox") {
+    timeScaleChoice = self.q.timeScale;
+    holder.append("div").text("Time axis").style("opacity", 0.4);
+    const options = [
+      {
+        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
+        value: "time"
+      },
+      { label: "Age", value: "age" }
+    ];
+    if (self.q.timeScale == "age") {
+      options[1].checked = true;
+    } else {
+      options[0].checked = true;
+    }
+    make_radios({
+      holder: holder.append("div"),
+      options,
+      styles: { padding: "" },
+      callback: (v) => timeScaleChoice = v
+    });
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    self.q.breaks[0] = grade;
+    if (self.q.mode == "binary") {
+      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+      self.q.groups = getGroups(grades, self.q.breaks);
+      self.refGrp = self.q.groups[0].name;
+    }
+    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function getGroups(grades, breaks) {
+  grades.sort((a, b2) => a - b2);
+  const groups = [];
+  let group = { values: [] };
+  let b;
+  for (const g of grades) {
+    if (breaks.includes(g)) {
+      b = g;
+      const max = Math.max(...group.values);
+      if (!groups.length) {
+        if (group.values.length == 1) {
+          if (group.values[0] !== 0) throw "unexpected group value";
+          group.name = "Grade 0";
+        } else {
+          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
+            group.name = "Not tested/Grade 0";
+          } else {
+            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
+          }
+        }
+      } else {
+        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
+      }
+      groups.push(group);
+      group = {
+        name: `Grade ${b}`,
+        values: [g]
+      };
+    } else {
+      group.values.push(g);
+    }
+  }
+  group.name = `Grades ${b}-5`;
+  groups.push(group);
+  return groups;
+}
+function fillTW(tw, vocabApi, defaultQ) {
+  set_hiddenvalues(tw.q, tw.term);
+  if (defaultQ) {
+    copyMerge(tw.q, defaultQ);
+  }
+  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
+  if (!tw.q.valueFor) {
+    const q = tw.q;
+    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
+    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
+    } else {
+      tw.q.value_by_max_grade = true;
+    }
+  }
+  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
+    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
+    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
+    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.breaks?.length) {
+      if (!tw.term.values) throw "missing term.values";
+      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
+        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
+        tw.q.groups = getGroups(grades, tw.q.breaks);
+      }
+    }
+    if (tw.q.mode == "cox") {
+      if (!tw.q.timeScale) tw.q.timeScale = "time";
+      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
+    }
+  }
+}
+export {
+  fillTW,
+  getHandler
+};
+//# sourceMappingURL=condition-QROUALBG.js.map

package/dist/controls-GH37YWOP.js

@@ -0,0 +1,30 @@
+import {
+  controlsInit,
+  renderTerm1Label
+} from "./chunk-YS7Y257H.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-PITPUAWX.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-K6CZAEBF.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-XJYVMXMZ.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-ZSNZPH6G.js";
+import "./chunk-ET2KFCXK.js";
+import "./chunk-LMG7Y5IN.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  controlsInit,
+  renderTerm1Label
+};
+//# sourceMappingURL=controls-GH37YWOP.js.map

package/dist/controls.config-ZYCDICYF.js

@@ -0,0 +1,30 @@
+import {
+  configUiInit,
+  initByInput
+} from "./chunk-YS7Y257H.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-PITPUAWX.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-K6CZAEBF.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-XJYVMXMZ.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-ZSNZPH6G.js";
+import "./chunk-ET2KFCXK.js";
+import "./chunk-LMG7Y5IN.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  configUiInit,
+  initByInput
+};
+//# sourceMappingURL=controls.config-ZYCDICYF.js.map

package/dist/correlation-JESMUFS6.js

@@ -0,0 +1,91 @@
+import {
+  appInit
+} from "./chunk-M2XWAAIZ.js";
+import "./chunk-M5SJ42E2.js";
+import "./chunk-PVXG2BRT.js";
+import "./chunk-C7O67FZJ.js";
+import "./chunk-LPDQ26OP.js";
+import "./chunk-HNMKK33Y.js";
+import "./chunk-4E2F26CC.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-3QZHRQ55.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-YS7Y257H.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-PITPUAWX.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-K6CZAEBF.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-XJYVMXMZ.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-ZSNZPH6G.js";
+import "./chunk-ET2KFCXK.js";
+import "./chunk-LMG7Y5IN.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// gdc/correlation.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  if (!genomes[useGenome]) throw useGenome + " missing";
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome: genomes[useGenome],
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: window.location.pathname.includes("example.gdc") ? void 0 : "only_buttons" },
+      plots: arg.state?.plots || [
+        { chartType: "summaryInput" }
+        // default shows summaryInput ui, can change
+        //{ chartType: 'barchart', term: {id: 'case.demographic.gender'} }, // uncomment for quicker testing
+      ]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    barchart: arg.opts?.barchart || {},
+    violin: arg.opts?.violin || {},
+    boxplot: arg.opts?.boxplot || {},
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=correlation-JESMUFS6.js.map