@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/chunk-DMG4ZMX5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/sunburst/sunburst.data.ts", "../plots/sunburst/SunburstChart.ts", "../plots/sunburst/sunburst.ts"],
+  "sourcesContent": ["import type { Filter, SunburstResponse, SunburstNode, SunburstCategory } from '#types'\nimport type { SunNode } from './SunburstRenderer'\n\n/*\nData helpers of the term-based sunburst, without any DOM code: the termdb/sunburst response as a renderer \ntree, and selected wedges as a group filter. Kept apart from sunburst.ts so they can be unit-tested directly.\n*/\n\n/** a wedge of the term sunburst. `id` names it by its path of [ring $id, key] pairs, as JSON so that no\n *  category key can make two paths alike, and a selection can survive a re-fetch; `ring`, `key` and\n *  `category` say which ring category it is */\nexport type TermSunNode = SunNode & {\n\tid: string\n\tring: number\n\tkey: string\n\tcategory: SunburstCategory\n\t/** samples under the wedge (SunNode.value is only those that end here) */\n\tcount: number\n\tchildren?: TermSunNode[]\n}\n\ntype TermSunRoot = SunNode & { children: TermSunNode[]; count: number }\n\n/** the response as a renderer tree; first-ring colours from the dataset (keyed by category key) win\n *  over the term's own */\nexport function buildTermTree(\n\tres: SunburstResponse,\n\ttwLst: any[],\n\trootName: string,\n\tcolors?: { [key: string]: string }\n): TermSunRoot {\n\tconst convert = (n: SunburstNode, ring: number, parentPath: string[][]): TermSunNode => {\n\t\tconst tw = twLst[ring]\n\t\tconst category = res.rings[ring].categories[n.key] || { label: n.key }\n\t\tconst path = [...parentPath, [tw.$id, n.key]]\n\t\tconst children = (n.children || []).map(c => convert(c, ring + 1, path))\n\t\tconst node: TermSunNode = {\n\t\t\tname: category.label,\n\t\t\tlevel: tw.term.name,\n\t\t\t// d3 adds the children to a node's own value, so it holds only the samples that end here\n\t\t\tvalue: n.count - children.reduce((s, c) => s + c.count, 0),\n\t\t\tcount: n.count,\n\t\t\tid: JSON.stringify(path),\n\t\t\tring,\n\t\t\tkey: n.key,\n\t\t\tcategory\n\t\t}\n\t\tconst color = (ring == 0 && colors?.[n.key]) || category.color\n\t\tif (color) node.color = color\n\t\tif (children.length) node.children = children\n\t\treturn node\n\t}\n\treturn { name: rootName, value: 0, count: res.total, children: res.nodes.map(n => convert(n, 0, [])) }\n}\n\n/** one ring category as a filter entry: the tvs of the ring's term, or a filter group's own filter */\nexport function categoryFilterItem(tw: any, category: SunburstCategory): any {\n\tif (category.filter) return structuredClone(category.filter)\n\tif (!category.tvs) throw `no filter for category '${category.label}' of ${tw.term.name}`\n\treturn { type: 'tvs', tvs: { term: tw.term, ...structuredClone(category.tvs) } }\n}\n\n/** the samples of one wedge: its categories along the path from the first ring, joined by \"and\" */\nexport function wedgeFilter(path: TermSunNode[], twLst: any[]): Filter {\n\tconst lst = path.map(n => categoryFilterItem(twLst[n.ring], n.category))\n\treturn { type: 'tvslst', in: true, join: lst.length > 1 ? 'and' : '', lst }\n}\n\n/** the samples of any of the selected wedges, each given as its path from the first ring. One wedge\n *  is just its own filter; several are joined by \"or\" */\nexport function selectionFilter(paths: TermSunNode[][], twLst: any[]): Filter {\n\tif (!paths.length) throw 'no wedge selected'\n\tif (paths.length == 1) return wedgeFilter(paths[0], twLst)\n\treturn { type: 'tvslst', in: true, join: 'or', lst: paths.map(p => wedgeFilter(p, twLst)) }\n}\n\n/** a readable name for a selection: the path of one wedge (e.g. \"BCP-ALL \u203A Hyperdiploid\"), or the\n *  wedge names joined when several are selected */\nexport function selectionName(paths: TermSunNode[][], maxLen = 60): string {\n\tconst names =\n\t\tpaths.length == 1 ? paths[0].map(n => n.name).join(' \u203A ') : paths.map(p => p[p.length - 1].name).join(' or ')\n\treturn names.length > maxLen ? names.slice(0, maxLen - 1) + '\u2026' : names\n}\n\n/** the sample types a new or replacing ring may have, given the other rings: the line of descent through\n *  the deepest of their sample types (its ancestors, itself and its descendants), since no value maps\n *  between sibling types such as primary and PDX samples. Undefined (any type) when the dataset has one\n *  sample type or no other ring is below the top level. `sampleTypes` is termdbConfig.sampleTypes */\nexport function allowedSampleTypes(otherTwLst: any[], sampleTypes?: { [id: string]: any }): number[] | undefined {\n\tif (!sampleTypes || Object.keys(sampleTypes).length < 2) return\n\tconst parent = (t: string) => {\n\t\tconst p = sampleTypes[t]?.parent_id\n\t\treturn p === null || p === undefined ? undefined : String(p)\n\t}\n\tconst ancestors = (t: string) => {\n\t\tconst lst: string[] = []\n\t\tfor (let p = parent(t); p !== undefined && !lst.includes(p); p = parent(p)) lst.push(p)\n\t\treturn lst\n\t}\n\tconst types = otherTwLst\n\t\t.map(tw => tw.term?.sample_type)\n\t\t.filter(t => t !== null && t !== undefined && sampleTypes[t])\n\t\t.map(String)\n\tconst below = types.filter(t => parent(t) !== undefined)\n\tif (!below.length) return\n\tconst deepest = below.reduce((a, b) => (ancestors(b).length > ancestors(a).length ? b : a))\n\tconst descendants = Object.keys(sampleTypes).filter(t => ancestors(t).includes(deepest))\n\treturn [...ancestors(deepest), deepest, ...descendants].map(Number)\n}\n", "import { dofetch3 } from '#common/dofetch'\nimport { select } from 'd3-selection'\nimport { escapeHtml, capitalizeFirstLetter, Menu } from '#dom'\nimport { getNormalRoot, filterJoin } from '#filter'\nimport {\n\taddNewGroup,\n\tgetGroupFilterOfConditions,\n\tgetSamplelstTWFromFilters,\n\tgetGeneExpressionPreAnalysis,\n\trenderPreAnalysisData\n} from '#mass/groups'\nimport { availabilitySections, fetchDataAvailability, type AvailabilityRow } from '#mass/groupDataAvailability'\nimport { TermTypes } from '#types'\nimport { getActiveCohortStr, getCurrentCohortChartTypes } from '#mass/charts'\nimport { dtsnvindel, dtcnv, dtfusionrna, dtsv } from '#shared/common.js'\nimport type { Filter, SunburstRequest, SunburstResponse } from '#types'\nimport {\n\tSunburstRenderer,\n\tcard,\n\tbadge,\n\tpill,\n\tSIZE,\n\tTEXT_DARK,\n\tTEXT_MUTED,\n\tLINK,\n\tRULE,\n\tSELECT_STROKE,\n\ticon,\n\ttype Card,\n\ttype HNode\n} from './SunburstRenderer'\nimport { buildTermTree, selectionFilter, selectionName, type TermSunNode } from './sunburst.data'\n\n/*\nThe term-based sunburst without its rx plot component: fetches the counts of the given rings, draws them,\nand keeps the wedge selection, one sample group. Below the selected wedges, \"Show available data\" lists how\nmany of the selected samples have each kind of data of the dataset (termdb/dataAvailability); a kind with a\nplot of its own opens that plot of the selected samples, which have the selection as the plot's filter.\nWhen enabled for the active cohort, GRIN2 is offered for a selection with SNV/indel, CNV or SV/fusion\ndata, alongside the mutation rows that open the genome browser.\nSummarize opens a dictionary popover beside its button to plot a term with the selection as its filter.\nGene Expression row likewise opens its gene-selection form beside the row, creating only the chosen plot.\nExactly two selected wedges can open the shared differential expression panel when supported and both\nhave RNA-seq counts; the first-selected wedge is the control and the second is the case.\nSurvival plots split two or more selected wedges into separate curves using a samplelst term, as custom variables do.\nThe selection can also become one sample group in the GROUPS tab. Used by the sunburst\nplot (sunburst.ts), which fills the Rings box with term pills, and by the About tab (about.ts), which\nlists the dataset's default rings.\n\nClick a wedge to zoom into it; a wedge without rings beneath it, a shift-click, or SELECT above the\nchart (for the wedge at the centre) selects it. Selecting a wedge drops its selected descendants, which\nit already contains.\n\nA sample with no value for a ring, or a value the ring hides (tw.q.hiddenValues, e.g. set in the dataset's\ndefault rings), ends at the previous ring, leaving a gap in the outer ring of its wedge; samples with no\nor a hidden value for the first ring are not in the chart.\n*/\n\n// stat box keys; their titles follow the unit\nconst STAT_SAMPLES = 'Samples'\nconst STAT_SELECTED = 'Selected samples'\n/** indent per ring in the Rings box, so the rings read as a path from the first to the last */\nconst RING_STEP = 6\nconst RING_LINE = '#cbd5e1'\n\nexport type SunburstChartOpts = {\n\tholder: any\n\t/** the mass app, for the term pickers and the created groups */\n\tapp: any\n\t/** px between the chart and its side columns (SunburstRendererOpts.gap) */\n\tgap?: number\n\t/** called before a plot of the selection is created, e.g. to show the plots tab */\n\tbeforeLaunch?: () => Promise<any> | void\n}\n\nexport type SunburstUpdateArg = {\n\tgenome: string\n\tdslabel: string\n\t/** ring term wrappers, inside out, filled */\n\ttwLst: any[]\n\t/** the filter the counts are of: the global filter, joined with the plot's own if any */\n\ttermfilter?: { filter?: Filter; filter0?: any }\n\t/** the plot's own filter, which a created group also has; the global filter is joined where the\n\t *  group is used */\n\tgroupFilter?: Filter\n\t/** first-ring colours from the dataset, keyed by category key */\n\tcolors?: { [key: string]: string }\n}\n\nexport class SunburstChart {\n\tapp: any\n\tdom: {\n\t\terrdiv: any\n\t\tloadingDiv: any\n\t\tnoteDiv: any\n\t\t/** the rings, left of the chart; filled by the caller (ringRow) */\n\t\trings: Card\n\t\t/** the selected wedges, with the create-group action */\n\t\tsel: Card\n\t\t/** selects the wedge at the centre, in the toolbar above the chart */\n\t\tselectFocus: any\n\t}\n\trenderer: SunburstRenderer\n\ttwLst: any[] = []\n\tgroupFilter?: Filter\n\t/** selected wedges by node id, in selection order */\n\tselected: Map<string, HNode> = new Map()\n\t/** note shown in the selection card after a group is created */\n\tcreatedNote = ''\n\t/** the counted unit, from the server */\n\tunit = { one: 'sample', many: 'samples' }\n\t/** number of the latest update(), so that the response of an earlier one that arrives later is dropped */\n\tupdateId = 0\n\tbeforeLaunch?: () => Promise<any> | void\n\t/** whether the available data of the selection is shown; a change of the selection hides it */\n\tdataShown = false\n\t/** number of the latest renderData(), so that the response of an earlier one is dropped */\n\tdataId = 0\n\tdataMenu?: Menu\n\tdataPicker?: { destroy: () => void }\n\n\tconstructor(opts: SunburstChartOpts) {\n\t\tthis.app = opts.app\n\t\tthis.beforeLaunch = opts.beforeLaunch\n\t\tconst holder = opts.holder\n\t\tconst errdiv = holder.append('div').attr('class', 'sja_errorbar').style('display', 'none')\n\t\tconst loadingDiv = holder.append('div').style('display', 'none').style('padding', '24px').text('Loading ...')\n\t\tconst noteDiv = holder\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.85em')\n\t\t\t.style('color', TEXT_MUTED)\n\t\t\t.style('margin-bottom', '6px')\n\t\tconst chartHolder = holder.append('div').attr('data-testid', 'sjpp-sunburst-chart')\n\t\tthis.renderer = new SunburstRenderer({\n\t\t\tholder: chartHolder,\n\t\t\tunit: this.unit,\n\t\t\trootName: 'All samples',\n\t\t\tstatLabels: [STAT_SAMPLES, STAT_SELECTED],\n\t\t\tpathCard: false,\n\t\t\tgap: opts.gap,\n\t\t\thooks: {\n\t\t\t\tonClick: (d: HNode, event: any) => this.onWedgeClick(d, event),\n\t\t\t\tisSelected: (d: HNode) => this.selected.has(d.data.id),\n\t\t\t\tcursor: (d: HNode) => (d.children ? 'zoom-in' : 'pointer'),\n\t\t\t\ttooltip: (d: HNode, box: any) => this.tooltip(d, box),\n\t\t\t\tonFocus: () => {\n\t\t\t\t\tthis.renderStats()\n\t\t\t\t\tthis.renderSidebar()\n\t\t\t\t\tthis.renderSelectFocus()\n\t\t\t\t\tthis.markShownRings()\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\tconst rings = card(this.renderer.dom.left, 'Rings')\n\t\trings.body.attr('data-testid', 'sjpp-sunburst-rings')\n\t\tconst selectFocus = this.renderer\n\t\t\t.addControl()\n\t\t\t.attr('data-testid', 'sjpp-sunburst-select-focus')\n\t\t\t.on('click', () => {\n\t\t\t\tconst f = this.renderer.focus\n\t\t\t\tif (f?.depth && !this.selectedAncestor(f)) this.toggle(f)\n\t\t\t})\n\t\tthis.dom = {\n\t\t\terrdiv,\n\t\t\tloadingDiv,\n\t\t\tnoteDiv,\n\t\t\trings,\n\t\t\tsel: card(this.renderer.dom.right, 'Selected wedges'),\n\t\t\tselectFocus\n\t\t}\n\t}\n\n\t/** fetch and draw the counts of the rings; with no rings, an empty chart and `emptyNote`. Resolves true\n\t *  when drawn, false when the request failed (the error is shown), and undefined when a later update\n\t *  replaced this one, which then has its own outcome */\n\tasync update(arg: SunburstUpdateArg, emptyNote = ''): Promise<boolean | undefined> {\n\t\tthis.closeDataPicker()\n\t\tconst id = ++this.updateId\n\t\tthis.twLst = arg.twLst\n\t\tthis.groupFilter = arg.groupFilter\n\t\tthis.dom.errdiv.style('display', 'none')\n\t\tthis.dom.noteDiv.text('')\n\t\tif (!this.twLst.length) {\n\t\t\t// an earlier update may still be loading; its response is dropped\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tthis.selected.clear()\n\t\t\tthis.renderer.setTree({ name: this.renderer.opts.rootName, children: [] })\n\t\t\tthis.dom.noteDiv.text(emptyNote)\n\t\t\treturn true\n\t\t}\n\t\ttry {\n\t\t\tthis.dom.loadingDiv.style('display', '')\n\t\t\tconst res = await fetchSunburst({\n\t\t\t\tgenome: arg.genome,\n\t\t\t\tdslabel: arg.dslabel,\n\t\t\t\ttwLst: this.twLst,\n\t\t\t\tfilter: getNormalRoot(arg.termfilter?.filter),\n\t\t\t\tfilter0: arg.termfilter?.filter0\n\t\t\t})\n\t\t\tif (id != this.updateId) return\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tthis.render(res, arg.colors)\n\t\t\treturn true\n\t\t} catch (e: any) {\n\t\t\tif (id != this.updateId) return\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tthis.dom.errdiv.style('display', '').text(e?.message || String(e))\n\t\t\tif (e instanceof Error) console.error(e)\n\t\t\treturn false\n\t\t}\n\t}\n\n\trender(res: SunburstResponse, colors?: { [key: string]: string }) {\n\t\tthis.setUnit(res.unit || { one: 'sample', many: 'samples' })\n\t\tif (res.noFirstRingValue) {\n\t\t\tconst n = res.noFirstRingValue\n\t\t\tthis.dom.noteDiv.text(\n\t\t\t\t`${n.toLocaleString()} ${n == 1 ? this.unit.one : this.unit.many} with ${noValue(this.twLst[0])} ${\n\t\t\t\t\tn == 1 ? 'is' : 'are'\n\t\t\t\t} not shown.`\n\t\t\t)\n\t\t}\n\t\tconst focusId = this.renderer.focus?.data.id\n\t\tconst selectedIds = [...this.selected.keys()]\n\t\tthis.renderer.setTree(buildTermTree(res, this.twLst, this.renderer.opts.rootName, colors))\n\t\t// keep the selection and the centre of a re-fetch (e.g. after a filter change) where their\n\t\t// wedges still exist\n\t\tconst byId = new Map(this.renderer.root.descendants().map((d: HNode) => [d.data.id, d]))\n\t\tthis.selected = new Map(selectedIds.filter(id => byId.has(id)).map(id => [id, byId.get(id)]))\n\t\tthis.renderer.refresh()\n\t\tconst focus = focusId && byId.get(focusId)\n\t\tif (focus?.children) this.renderer.zoomTo(focus)\n\t\telse this.renderSidebar()\n\t}\n\n\t/** wording of the counted unit: centre, stat box titles, tooltip and the create-group action */\n\tsetUnit(unit: { one: string; many: string }) {\n\t\tthis.unit = unit\n\t\tthis.renderer.opts.unit = unit\n\t\tthis.renderer.opts.rootName = `All ${unit.many}`\n\t\tthis.renderer.setStatTitle(STAT_SAMPLES, capitalizeFirstLetter(unit.many))\n\t\tthis.renderer.setStatTitle(STAT_SELECTED, `Selected ${unit.many}`)\n\t}\n\n\t/** SELECT above the chart, for the wedge at the centre (which cannot be clicked) */\n\trenderSelectFocus() {\n\t\tconst f = this.renderer.focus\n\t\tconst el = this.dom.selectFocus\n\t\tif (!f?.depth) {\n\t\t\tel.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tconst anc = this.selectedAncestor(f)\n\t\tconst on = this.selected.has(f.data.id)\n\t\tel.style('display', '')\n\t\t\t.style('opacity', anc ? 0.35 : 1)\n\t\t\t.style('cursor', anc ? 'default' : 'pointer')\n\t\t\t.style('color', on ? SELECT_STROKE : TEXT_MUTED)\n\t\t\t.attr('title', anc ? `Included in the selected ${anc.data.name}` : null)\n\t\t\t.html(\n\t\t\t\ton\n\t\t\t\t\t? `${icon('<polyline points=\"5 12 10 17 19 7\"/>')}SELECTED \u00B7 ${escapeHtml(f.data.name.toUpperCase())}`\n\t\t\t\t\t: `${icon('<circle cx=\"12\" cy=\"12\" r=\"9\"/><path d=\"M12 8v8M8 12h8\"/>')}SELECT ${escapeHtml(\n\t\t\t\t\t\t\tf.data.name.toUpperCase()\n\t\t\t\t\t  )}`\n\t\t\t)\n\t}\n\n\t/************ rings box ************/\n\n\t/** a line of the Rings box, indented by its ring, with an elbow from the line above */\n\tringRow(level: number) {\n\t\tconst row = this.dom.rings.body\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('margin', '2px 0')\n\t\t\t.style('margin-left', `${level * RING_STEP}px`)\n\t\tif (level) {\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('left', `${-RING_STEP + 4}px`)\n\t\t\t\t.style('top', '-6px')\n\t\t\t\t.style('width', `${RING_STEP - 6}px`)\n\t\t\t\t.style('height', '18px')\n\t\t\t\t.style('border-left', `1px solid ${RING_LINE}`)\n\t\t\t\t.style('border-bottom', `1px solid ${RING_LINE}`)\n\t\t\t\t.style('border-bottom-left-radius', '4px')\n\t\t}\n\t\treturn row\n\t}\n\n\t/** the line of ring i: its number, which is marked while the ring is in the chart (markShownRings),\n\t *  then a slot for the caller's term pill or name */\n\tringLine(i: number) {\n\t\tconst row = this.ringRow(i)\n\t\t\t.attr('class', 'sjpp-sunburst-ring')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '4px')\n\t\trow\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sjpp-sunburst-ringnum')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('width', '14px')\n\t\t\t.style('flex', '0 0 auto')\n\t\t\t.style('padding-left', '4px')\n\t\t\t.style('border-left', '3px solid transparent')\n\t\t\t.style('border-radius', '2px')\n\t\t\t.text(i + 1)\n\t\treturn row\n\t}\n\n\t/** mark the two rings around the current centre: a bar beside the ring number, which is bold */\n\tmarkShownRings() {\n\t\tconst first = this.renderer.focus?.depth || 0\n\t\tconst shown = (i: number) => i == first || i == first + 1\n\t\tthis.dom.rings.body\n\t\t\t.selectAll('.sjpp-sunburst-ring')\n\t\t\t.attr('title', (_: any, i: number) => (shown(i) ? 'Shown in the chart' : null))\n\t\t\t.select('.sjpp-sunburst-ringnum')\n\t\t\t.style('border-left-color', (_: any, i: number) => (shown(i) ? LINK : 'transparent'))\n\t\t\t.style('color', (_: any, i: number) => (shown(i) ? TEXT_DARK : TEXT_MUTED))\n\t\t\t.style('font-weight', (_: any, i: number) => (shown(i) ? 'bold' : 'normal'))\n\t}\n\n\t/************ selection ************/\n\n\t/** the selected ancestor that already contains a wedge, if any */\n\tselectedAncestor(d: HNode): HNode | undefined {\n\t\tfor (let a = d.parent; a?.depth; a = a.parent) if (this.selected.has(a.data.id)) return a\n\t}\n\n\ttoggle(d: HNode) {\n\t\tif (!d.depth) return\n\t\tconst id = d.data.id\n\t\tthis.createdNote = ''\n\t\tif (this.selected.has(id)) this.selected.delete(id)\n\t\telse {\n\t\t\tif (this.selectedAncestor(d)) return // already in the selection; the tooltip says so\n\t\t\t// a selected wedge contains its descendants, so drop any that were selected\n\t\t\tfor (const [k, n] of this.selected) if (n.ancestors().includes(d)) this.selected.delete(k)\n\t\t\tthis.selected.set(id, d)\n\t\t}\n\t\tthis.refreshSelection()\n\t}\n\n\trefreshSelection() {\n\t\tthis.dataShown = false\n\t\tthis.renderer.refresh()\n\t\tthis.renderStats()\n\t\tthis.renderSidebar()\n\t\tthis.renderSelectFocus()\n\t}\n\n\t/** wedge paths from the first ring, in selection order */\n\tselectedPaths(): TermSunNode[][] {\n\t\treturn [...this.selected.values()].map(\n\t\t\t(d: HNode) =>\n\t\t\t\td\n\t\t\t\t\t.ancestors()\n\t\t\t\t\t.reverse()\n\t\t\t\t\t.slice(1)\n\t\t\t\t\t.map((a: HNode) => a.data) as TermSunNode[]\n\t\t)\n\t}\n\n\tselectedCount(): number {\n\t\tlet n = 0\n\t\tfor (const d of this.selected.values()) n += d.value || 0\n\t\treturn n\n\t}\n\n\trenderStats() {\n\t\tconst r = this.renderer\n\t\tr.setStats(\n\t\t\tnew Map([\n\t\t\t\t[STAT_SAMPLES, r.focus.value || 0],\n\t\t\t\t[STAT_SELECTED, this.selectedCount()]\n\t\t\t])\n\t\t)\n\t}\n\n\t/************ interaction ************/\n\n\tonWedgeClick(d: HNode, event: any) {\n\t\tif (event?.shiftKey || !d.children) this.toggle(d)\n\t\telse this.renderer.zoomTo(d)\n\t}\n\n\ttooltip(d: HNode, box: any) {\n\t\tconst line = (text: string, color = '#6b7280') => box.append('div').style('color', color).text(text)\n\t\tline(d.data.level)\n\t\tconst total = this.renderer.root.value || 0\n\t\tconst pct = total ? ` (${((100 * (d.value || 0)) / total).toFixed(1)}%)` : ''\n\t\tconst s = box.append('div').style('color', '#374151')\n\t\ts.append('span').text(`${capitalizeFirstLetter(this.unit.many)}: `)\n\t\ts.append('b').text((d.value || 0).toLocaleString())\n\t\ts.append('span').text(pct)\n\t\tconst ended = d.data.value || 0\n\t\tconst next = this.twLst[d.data.ring + 1]\n\t\tif (d.children && ended && next) line(`${ended.toLocaleString()} with ${noValue(next)}`)\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 anc = this.selectedAncestor(d)\n\t\tif (anc) note(`Included in the selected ${anc.data.name}`, TEXT_MUTED)\n\t\telse if (this.selected.has(d.data.id))\n\t\t\tnote(d.children ? 'click to zoom in \u00B7 shift-click to deselect' : 'click to deselect', LINK)\n\t\telse note(d.children ? 'click to zoom in \u00B7 shift-click to select' : 'click to select', LINK)\n\t}\n\n\t/** the selected-wedges card: one line per wedge with its path and count, and the create-group\n\t *  action as the footer */\n\trenderSidebar() {\n\t\tthis.closeDataPicker()\n\t\tconst sel = this.dom.sel\n\t\tconst { title, headRight, body } = sel\n\t\theadRight.selectAll('*').remove()\n\t\tbody.selectAll('*').remove()\n\t\theadRight.style('margin-bottom', '8px')\n\t\tconst n = this.selected.size\n\t\ttitle.text(n ? 'Selected wedges' : 'No wedges selected')\n\t\tif (n) {\n\t\t\tpill(headRight).text(n)\n\t\t\theadRight\n\t\t\t\t.append('span')\n\t\t\t\t.style('font-size', '11px')\n\t\t\t\t.style('color', LINK)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text('Clear')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.selected.clear()\n\t\t\t\t\tthis.refreshSelection()\n\t\t\t\t})\n\t\t}\n\t\tconst list = body\n\t\t\t.append('div')\n\t\t\t.style('max-height', `${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('Shift-click a wedge, click an outermost one, or zoom into one and click SELECT above the chart.')\n\t\t}\n\t\tfor (const [id, d] of this.selected) {\n\t\t\tconst path = d\n\t\t\t\t.ancestors()\n\t\t\t\t.reverse()\n\t\t\t\t.slice(1)\n\t\t\t\t.map((a: HNode) => a.data.name)\n\t\t\tconst row = 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\tbadge(row, d.data.name, this.renderer.color(d), 24)\n\t\t\tconst text = row.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.attr('title', path.join(' \u203A '))\n\t\t\t\t.text(path.join(' \u203A '))\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(this.renderer.unitText(d.value || 0))\n\t\t\trow\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(id)\n\t\t\t\t\tthis.refreshSelection()\n\t\t\t\t})\n\t\t}\n\n\t\tconst count = this.selectedCount()\n\t\tif (n) void this.renderData(body, count)\n\t\tif (!n && !this.createdNote) return\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\tif (n) {\n\t\t\tpill(footer, { button: true })\n\t\t\t\t.attr('data-testid', 'sjpp-sunburst-create-group')\n\t\t\t\t.text(`Create group of ${this.renderer.unitText(count)}`)\n\t\t\t\t.on('click', () => this.createGroup())\n\t\t}\n\t\tif (this.createdNote) {\n\t\t\tfooter\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t.style('margin-top', '6px')\n\t\t\t\t.text(this.createdNote)\n\t\t}\n\t}\n\n\t/** \"Show available data\", then how many of the selected samples have each kind of data of the dataset;\n\t *  a kind with a plot of the selected samples opens it */\n\tasync renderData(body: any, count: number) {\n\t\tconst div = body\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-group-data')\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\tif (!this.dataShown) {\n\t\t\tpill(div, { button: true })\n\t\t\t\t.attr('data-testid', 'sjpp-sunburst-show-data')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text('Show available data')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.dataShown = true\n\t\t\t\t\tthis.renderSidebar()\n\t\t\t\t})\n\t\t\treturn\n\t\t}\n\t\tconst id = ++this.dataId\n\t\tconst head = div\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('justify-content', 'space-between')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('margin-bottom', '6px')\n\t\thead\n\t\t\t.append('span')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-data-title')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('font-size', '0.95em')\n\t\t\t.style('font-weight', 600)\n\t\t\t.style('color', TEXT_DARK)\n\t\t\t.text(capitalizeFirstLetter(this.renderer.unitText(count)))\n\t\t// back to the button\n\t\thead\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-hide-data')\n\t\t\t.style('flex', '0 0 auto')\n\t\t\t.style('font-size', '11px')\n\t\t\t.style('padding', '1px 10px')\n\t\t\t.style('border', `1px solid ${RULE}`)\n\t\t\t.style('border-radius', '10px')\n\t\t\t.style('background', 'white')\n\t\t\t.style('color', LINK)\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.text('Hide \u25B4')\n\t\t\t.on('click', () => this.hideData())\n\t\tthis.dataRow(\n\t\t\tdiv.append('div').style('font-size', '0.85em'),\n\t\t\t{ kind: 'data', key: 'summarize', label: 'Summarize', counts: [] },\n\t\t\tfalse,\n\t\t\tundefined,\n\t\t\tanchor => this.showDataPicker(anchor)\n\t\t)\n\t\tconst list = div.append('div').text('Loading ...').style('font-size', '0.85em').style('color', TEXT_MUTED)\n\t\ttry {\n\t\t\tconst appState = this.app.getState()\n\t\t\tconst termfilter = appState.termfilter || {}\n\t\t\tconst filter = filterJoin([this.plotFilter(), termfilter.filter].filter(f => f?.lst?.length))\n\t\t\tconst chartTypes = getCurrentCohortChartTypes(appState)\n\t\t\tconst queries = this.app.vocabApi.termdbConfig?.queries || {}\n\t\t\tconst canCompare = this.selected.size == 2 && chartTypes.includes('DA') && queries.rnaseqGeneCount\n\t\t\tconst comparison = canCompare ? this.comparisonGroups() : []\n\t\t\tconst groups = [\n\t\t\t\t{ name: 'selection', filter },\n\t\t\t\t...comparison.map(g => ({\n\t\t\t\t\t...g,\n\t\t\t\t\tfilter: filterJoin([g.filter, termfilter.filter].filter(f => f?.lst?.length))\n\t\t\t\t}))\n\t\t\t]\n\t\t\tconst res = await fetchDataAvailability(\n\t\t\t\tthis.app.vocabApi,\n\t\t\t\tgroups,\n\t\t\t\ttermfilter.filter0,\n\t\t\t\tgetActiveCohortStr(appState)\n\t\t\t)\n\t\t\tif (id != this.dataId) return\n\t\t\tlist.text('').style('color', null)\n\t\t\tconst comparisonCounts = res.groups.slice(1)\n\t\t\tif (\n\t\t\t\tcanCompare &&\n\t\t\t\tcomparisonCounts.length == 2 &&\n\t\t\t\tcomparisonCounts.every(g => (g.data.rnaseqGeneCount || 0) > 0)\n\t\t\t) {\n\t\t\t\tconst tw = getSamplelstTWFromFilters(groups.slice(1))\n\t\t\t\tthis.dataRow(\n\t\t\t\t\tlist,\n\t\t\t\t\t{ kind: 'data', key: 'differentialExpression', label: 'Differential Gene Expression Analysis', counts: [] },\n\t\t\t\t\tfalse,\n\t\t\t\t\tundefined,\n\t\t\t\t\tanchor => this.showDataPicker(anchor, 'differentialExpression', tw)\n\t\t\t\t)\n\t\t\t}\n\t\t\tconst sections = availabilitySections({ ...res, groups: res.groups.slice(0, 1) }, ['rnaseqGeneCount'])\n\t\t\tif (!sections.length) {\n\t\t\t\tif (list.selectAll('*').empty()) list.style('color', TEXT_MUTED).text(`No data for these ${this.unit.many}`)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tfor (const section of sections) {\n\t\t\t\tif (section.title) {\n\t\t\t\t\tlist\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('data-testid', `sjpp-sunburst-section-${section.key}`)\n\t\t\t\t\t\t.style('margin', '8px 0 2px 0')\n\t\t\t\t\t\t.style('padding', '0 6px')\n\t\t\t\t\t\t.style('font-size', '10px')\n\t\t\t\t\t\t.style('font-weight', 600)\n\t\t\t\t\t\t.style('letter-spacing', '.06em')\n\t\t\t\t\t\t.style('text-transform', 'uppercase')\n\t\t\t\t\t\t.style('color', TEXT_MUTED)\n\t\t\t\t\t\t.text(section.title)\n\t\t\t\t}\n\t\t\t\tfor (const row of section.rows) {\n\t\t\t\t\tconst launch = this.dataPlot(row)\n\t\t\t\t\tthis.dataRow(\n\t\t\t\t\t\tlist,\n\t\t\t\t\t\trow,\n\t\t\t\t\t\t!!section.title,\n\t\t\t\t\t\tlaunch,\n\t\t\t\t\t\trow.kind == 'data' && row.key == 'geneExpression'\n\t\t\t\t\t\t\t? anchor => this.showDataPicker(anchor, 'geneExpression')\n\t\t\t\t\t\t\t: undefined\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\tif (\n\t\t\t\t\tsection.key == 'mutations' &&\n\t\t\t\t\tchartTypes.includes('grin2') &&\n\t\t\t\t\tsection.rows.some(row => {\n\t\t\t\t\t\tconst dt = Number(row.key.split('.')[0])\n\t\t\t\t\t\tif (dt == dtsnvindel) return !!queries.snvindel\n\t\t\t\t\t\tif (dt == dtcnv) return !!(queries.cnv || queries.singleSampleMutation?.cnvTypes?.length)\n\t\t\t\t\t\treturn (dt == dtfusionrna || dt == dtsv) && queries.svfusion?.dtLst?.includes(dt)\n\t\t\t\t\t})\n\t\t\t\t) {\n\t\t\t\t\tpill(list, { button: true })\n\t\t\t\t\t\t.attr('data-testid', 'sjpp-sunburst-grin2')\n\t\t\t\t\t\t.style('font-family', 'inherit')\n\t\t\t\t\t\t.style('font-weight', 'normal')\n\t\t\t\t\t\t.style('width', 'auto')\n\t\t\t\t\t\t.style('padding', '2px 8px')\n\t\t\t\t\t\t.style('margin', '4px 6px 4px 16px')\n\t\t\t\t\t\t.text('Run GRIN2')\n\t\t\t\t\t\t.on('click', () => this.launchPlot({ chartType: 'grin2', filter: this.plotFilter() }))\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\tif (id != this.dataId) return\n\t\t\tlist.attr('class', 'sja_errorbar').text(e?.message || String(e))\n\t\t}\n\t}\n\n\t/** Separate groups in selection order; for differential analysis, first control, then case. */\n\tcomparisonGroups() {\n\t\tconst termfilter = this.app.getState().termfilter || {}\n\t\tconst nodes = [...this.selected.values()]\n\t\treturn this.selectedPaths().map((path, i) => ({\n\t\t\tname: `${i + 1}: ${selectionName([path])}`,\n\t\t\tfilter: filterJoin([selectionFilter([path], this.twLst), this.groupFilter].filter(f => f?.lst?.length)),\n\t\t\tfilter0: termfilter.filter0,\n\t\t\tsampleCount: nodes[i].value || 0,\n\t\t\tcolor: this.renderer.color(nodes[i])\n\t\t}))\n\t}\n\n\tasync showDataPicker(\n\t\tanchor: HTMLElement,\n\t\tkind: 'summary' | 'geneExpression' | 'differentialExpression' = 'summary',\n\t\tsamplelstTW?: ReturnType<typeof getSamplelstTWFromFilters>\n\t) {\n\t\tthis.closeDataPicker()\n\t\tconst menu = new Menu({\n\t\t\tpadding: '8px',\n\t\t\ttestid:\n\t\t\t\tkind == 'geneExpression'\n\t\t\t\t\t? 'sjpp-sunburst-expression-menu'\n\t\t\t\t\t: kind == 'differentialExpression'\n\t\t\t\t\t? 'sjpp-sunburst-differential-menu'\n\t\t\t\t\t: 'sjpp-sunburst-summary-menu'\n\t\t})\n\t\tthis.dataMenu = menu\n\t\tconst position = () => {\n\t\t\tif (!menu.dnode) throw new Error('Missing data picker menu element')\n\t\t\tconst rect = anchor.getBoundingClientRect()\n\t\t\tconst width = menu.dnode.getBoundingClientRect().width\n\t\t\tconst x = rect.right + 5 + width <= window.innerWidth ? rect.right + 5 : Math.max(0, rect.left - width - 5)\n\t\t\tmenu.showunder(anchor, { offsetX: x - rect.left, offsetY: -rect.height - 5 })\n\t\t}\n\t\tconst loading = menu.d.append('div').text('Loading ...')\n\t\tposition()\n\t\ttry {\n\t\t\tconst state = this.app.getState()\n\t\t\tconst filter = this.plotFilter()\n\t\t\tif (kind == 'differentialExpression') {\n\t\t\t\tif (!samplelstTW) throw new Error('Missing differential analysis groups')\n\t\t\t\tconst preAnalysisData = await getGeneExpressionPreAnalysis(this.app, samplelstTW, state.termfilter)\n\t\t\t\tif (this.dataMenu != menu) return\n\t\t\t\trenderPreAnalysisData({\n\t\t\t\t\tpreAnalysisData,\n\t\t\t\t\tsamplelstTW,\n\t\t\t\t\tgroups: samplelstTW.q.groups,\n\t\t\t\t\ttip: menu,\n\t\t\t\t\tself: { app: this.app, state: { termfilter: state.termfilter } },\n\t\t\t\t\tonLaunch: async config => {\n\t\t\t\t\t\tthis.closeDataPicker()\n\t\t\t\t\t\tawait this.launchPlot(config)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t} else if (kind == 'geneExpression') {\n\t\t\t\tconst { geneExpInputInit } = await import('#plots/GeneExpInput.ts')\n\t\t\t\tif (this.dataMenu != menu) return\n\t\t\t\tconst picker = await geneExpInputInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tholder: menu.d.append('div'),\n\t\t\t\t\theader: menu.d.insert('div', ':first-child'),\n\t\t\t\t\tconfig: { termType: TermTypes.GENE_EXPRESSION, spawnConfig: { filter } },\n\t\t\t\t\tonSubmit: async config => {\n\t\t\t\t\t\tthis.closeDataPicker()\n\t\t\t\t\t\tawait this.launchPlot(config)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tif (this.dataMenu != menu) {\n\t\t\t\t\tpicker.destroy()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.dataPicker = picker\n\t\t\t\tawait picker.update({ appState: state })\n\t\t\t} else {\n\t\t\t\tconst { appInit } = await import('#termdb/app')\n\t\t\t\tif (this.dataMenu != menu) return\n\t\t\t\tconst tree = await appInit({\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tholder: menu.d.append('div'),\n\t\t\t\t\tstate: {\n\t\t\t\t\t\tvocab: state.vocab,\n\t\t\t\t\t\tactiveCohort: state.activeCohort,\n\t\t\t\t\t\ttermfilter: {\n\t\t\t\t\t\t\t...state.termfilter,\n\t\t\t\t\t\t\tfilter: filterJoin([filter, state.termfilter?.filter].filter(f => f?.lst?.length))\n\t\t\t\t\t\t},\n\t\t\t\t\t\tcustomTerms: state.customTerms,\n\t\t\t\t\t\ttree: { usecase: { target: 'dictionary' } }\n\t\t\t\t\t},\n\t\t\t\t\ttree: {\n\t\t\t\t\t\tclick_term: selected => {\n\t\t\t\t\t\t\tconst term = selected.term || selected\n\t\t\t\t\t\t\tthis.closeDataPicker()\n\t\t\t\t\t\t\tvoid this.launchPlot(\n\t\t\t\t\t\t\t\tterm.type == 'survival'\n\t\t\t\t\t\t\t\t\t? this.survivalConfig(selected.term ? selected : { term })\n\t\t\t\t\t\t\t\t\t: { chartType: 'summary', term: selected.term ? selected : { term }, filter }\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\tif (this.dataMenu != menu) {\n\t\t\t\t\ttree.destroy()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.dataPicker = tree\n\t\t\t}\n\t\t\tif (this.dataMenu != menu) return\n\t\t\tloading.remove()\n\t\t\tif (menu.d.style('display') != 'none') position()\n\t\t} catch (e: any) {\n\t\t\tif (this.dataMenu != menu) return\n\t\t\tloading.attr('class', 'sja_errorbar').text(e?.message || String(e))\n\t\t}\n\t}\n\n\tcloseDataPicker() {\n\t\tthis.dataPicker?.destroy()\n\t\tthis.dataPicker = undefined\n\t\tthis.dataMenu?.destroy()\n\t\tthis.dataMenu = undefined\n\t}\n\n\thideData() {\n\t\tthis.dataShown = false\n\t\t// a response still on its way is not drawn\n\t\tthis.dataId++\n\t\tthis.renderSidebar()\n\t}\n\n\t/** a line of the available data: the kind of data and its count (omitted for empty counts), which opens `launch`, a plot_create config,\n\t *  when given; a row of a section is indented under the section's title */\n\tdataRow(\n\t\tlist: any,\n\t\trow: AvailabilityRow,\n\t\tinSection: boolean,\n\t\tlaunch?: any,\n\t\tonActivate?: (anchor: HTMLElement) => void\n\t) {\n\t\tconst n = row.counts.length ? row.counts[0] || 0 : undefined\n\t\tconst clickable = !!launch || !!onActivate\n\t\tconst div = list\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', `sjpp-sunburst-data-${row.kind == 'data' ? '' : row.kind + '-'}${row.key}`)\n\t\t\t.style('display', 'flex')\n\t\t\t.style('justify-content', 'space-between')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('padding', `3px 6px 3px ${inSection ? 16 : 6}px`)\n\t\t\t.style('margin', '1px 0')\n\t\t\t.style('border-radius', '6px')\n\t\t\t.style('color', TEXT_DARK)\n\t\tdiv.append('span').text(row.label)\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('color', clickable ? LINK : null)\n\t\t\t.text(`${n === undefined ? '' : n.toLocaleString()}${row.unit ? ' ' + row.unit : ''}${clickable ? ' \u203A' : ''}`)\n\t\tif (!clickable) return\n\t\tconst activate = (anchor: HTMLElement) => (onActivate ? onActivate(anchor) : this.launchPlot(launch))\n\t\tdiv\n\t\t\t.attr('role', 'button')\n\t\t\t.attr('tabindex', 0)\n\t\t\t.attr('title', `Open the ${row.label} of these ${this.unit.many}`)\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.on('mouseenter', (event: any) => select(event.currentTarget).style('background', '#f3f4f6'))\n\t\t\t.on('mouseleave', (event: any) => select(event.currentTarget).style('background', 'transparent'))\n\t\t\t.on('click', (event: MouseEvent) => activate(event.currentTarget as HTMLElement))\n\t\t\t.on('keydown', (event: KeyboardEvent) => {\n\t\t\t\tif (event.key == 'Enter' || event.key == ' ') {\n\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\tactivate(event.currentTarget as HTMLElement)\n\t\t\t\t}\n\t\t\t})\n\t}\n\n\t/** the filter of the selected samples: the selection with the plot's own filter. A plot that is given it as\n\t *  its own filter joins the global filter to it */\n\tplotFilter(): Filter {\n\t\tconst filters = [selectionFilter(this.selectedPaths(), this.twLst), this.groupFilter]\n\t\treturn filterJoin(filters.filter(f => f?.lst?.length)) as Filter\n\t}\n\n\tsurvivalConfig(term: any) {\n\t\treturn {\n\t\t\tchartType: 'survival',\n\t\t\tterm,\n\t\t\tfilter: this.plotFilter(),\n\t\t\t...(this.selected.size > 1 ? { term2: getSamplelstTWFromFilters(this.comparisonGroups()) } : {})\n\t\t}\n\t}\n\n\t/** the plot of the selected samples for a row of the available data, as a plot_create config; undefined\n\t *  when the row has no plot of its own */\n\tdataPlot(row: AvailabilityRow): any {\n\t\tconst filter = this.plotFilter()\n\t\tconst q = this.app.vocabApi.termdbConfig?.queries || {}\n\t\t// the mutations of the selected samples, in the genome browser after a gene is entered\n\t\tif (row.kind == 'assay')\n\t\t\treturn q.snvindel || q.svfusion || q.cnv\n\t\t\t\t? {\n\t\t\t\t\t\tchartType: 'genomeBrowser',\n\t\t\t\t\t\tfilter,\n\t\t\t\t\t\t/* the mutation track shown, which the genome browser hides by default when the dataset also has\n\t\t\t\t\t\ttrackLst. The query is copied as the browser's config replaces it, not merged */\n\t\t\t\t\t\t...(q.snvindel ? { snvindel: { ...structuredClone(q.snvindel), shown: true } } : {})\n\t\t\t\t  }\n\t\t\t\t: undefined\n\t\tif (row.kind == 'survival') return this.survivalConfig({ id: row.key })\n\t\t// the term search, whose DNA methylation tab lists methylation terms; a term opens its summary with the filter\n\t\tif (row.key == 'dnaMethylation') return { chartType: 'dictionary', spawnConfig: { filter } }\n\t\t// the table of the imaging samples that pass the filter, to render on a brain template\n\t\tif (row.key == 'NIdata') return { chartType: 'brainImaging', filter }\n\t\t// the lanes of the patients of the selected samples\n\t\tif (row.key == 'longitudinal') return { chartType: 'swimmer', filter }\n\t}\n\n\tasync launchPlot(config: any) {\n\t\ttry {\n\t\t\tawait this.beforeLaunch?.()\n\t\t\tawait this.app.dispatch({ type: 'plot_create', config })\n\t\t} catch (e: any) {\n\t\t\tthis.dom.errdiv.style('display', '').text(e?.message || String(e))\n\t\t}\n\t}\n\n\t/** one group of the union of the selected wedges, added to the GROUPS tab; the group also has the\n\t *  plot's own filter, which the counts are of. The global filter is joined where the group is used */\n\tcreateGroup() {\n\t\tconst paths = this.selectedPaths()\n\t\tif (!paths.length) return\n\t\ttry {\n\t\t\tconst name = selectionName(paths)\n\t\t\tconst groups = this.app.getState().groups || []\n\t\t\tconst filter = getGroupFilterOfConditions([this.groupFilter, selectionFilter(paths, this.twLst)])\n\t\t\taddNewGroup(this.app, filter, groups, name)\n\t\t\tthis.selected.clear()\n\t\t\tthis.createdNote = `Group \"${name}\" added; find it in the GROUPS tab.`\n\t\t\tthis.refreshSelection()\n\t\t} catch (e: any) {\n\t\t\tthis.dom.errdiv.style('display', '').text(e?.message || String(e))\n\t\t}\n\t}\n\n\tdestroy() {\n\t\tthis.closeDataPicker()\n\t\tthis.renderer?.destroy()\n\t}\n}\n\n/** why a sample is not in a ring: \"no X value\", or \"no or a hidden X value\" when the ring hides some\n *  categories (tw.q.hiddenValues), which the server treats as missing. The term's uncomputable values,\n *  which fillTermWrapper puts in hiddenValues by default, are missing values anyway, so they do not count */\nfunction noValue(tw: any): string {\n\tconst values = tw.term.values || {}\n\tconst hidden = Object.keys(tw.q?.hiddenValues || {}).some(k => !values[k]?.uncomputable)\n\treturn `no ${hidden ? 'or a hidden ' : ''}${tw.term.name} value`\n}\n\n/** termdb/sunburst request; errors are thrown */\nasync function fetchSunburst(body: SunburstRequest): Promise<SunburstResponse> {\n\tconst res: any = await dofetch3('termdb/sunburst', { body })\n\tif (res?.error) throw res.error\n\tif (!res?.nodes) throw 'invalid response from termdb/sunburst'\n\treturn res\n}\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { getCombinedTermFilter } from '#filter'\nimport { fillTermWrapper, termsettingInit } from '#termsetting'\nimport { SunburstChart } from './SunburstChart'\nimport { allowedSampleTypes } from './sunburst.data'\n\n/*\nSunburst of nested sample counts, one dictionary term per ring (categorical, or numeric binned),\ninside out. The dataset sets the default rings (termdb.sunburst.twLst); the Rings box left of the\nchart switches, edits, adds and removes them (from each term pill's menu). Counts follow the\nglobal and plot filters.\n\nThe chart itself, its wedge selection and the sample group made from it are in SunburstChart.ts, which\nthe About tab also uses.\n\nIn a dataset with a sample hierarchy, the rings are patient terms and the terms of one sample type (no\nvalue maps between sibling types such as primary and PDX samples): once a ring is of a sample type, the\npickers offer only terms of its line of descent. The server returns the counted unit (e.g. patients,\nprimary samples), which the chart's wording follows.\n*/\n\nclass Sunburst extends PlotBase implements RxComponent {\n\tstatic type = 'sunburst'\n\ttype: string\n\tchart!: SunburstChart\n\ttwLst: any[] = []\n\t/** the rings the Rings box shows, to rebuild its pills only when they change */\n\tringsShown = ''\n\t/** the Rings box pills and their main() argument without the filter, which follows the state */\n\tringPills: { pill: any; arg: any }[] = []\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = Sunburst.type\n\t\tif (this.opts.header)\n\t\t\tthis.opts.header.style('padding-left', '7px').style('color', 'rgb(85, 85, 85)').html('Sunburst')\n\t}\n\n\tgetState(appState: any) {\n\t\tconst config = appState.plots.find((p: any) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig,\n\t\t\t// global mass filter combined with this plot's local filter\n\t\t\ttermfilter: getCombinedTermFilter(appState, config.filter),\n\t\t\tgenome: appState.vocab.genome,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\tsunburst: appState.termdbConfig?.sunburst || {}\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// the plot holder inherits nowrap from the sandbox; the cards need their text to wrap\n\t\tconst holder = this.opts.holder\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-sunburst-holder')\n\t\t\t.style('white-space', 'normal')\n\t\t\t.style('padding', '10px')\n\t\tthis.chart = new SunburstChart({ holder, app: this.app })\n\t\t// a ring pill is only the term: termsetting's info button (its holder's 4th child) is hidden\n\t\tthis.chart.dom.rings.box\n\t\t\t.append('style')\n\t\t\t.text('.sjpp-sunburst-ringpill > div:nth-child(4) { display: none !important; }')\n\t}\n\n\tasync main() {\n\t\tconst config = this.state.config\n\t\tthis.twLst = config.twLst || []\n\t\tawait this.renderRings()\n\t\tawait this.chart.update(\n\t\t\t{\n\t\t\t\tgenome: this.state.genome,\n\t\t\t\tdslabel: this.state.dslabel,\n\t\t\t\ttwLst: this.twLst,\n\t\t\t\ttermfilter: this.state.termfilter,\n\t\t\t\tgroupFilter: config.filter,\n\t\t\t\tcolors: this.state.sunburst.colors\n\t\t\t},\n\t\t\t'Add a ring in the Rings box to draw the sunburst.'\n\t\t)\n\t}\n\n\t/************ rings box ************/\n\n\t/** one line per ring: its number and a term pill, whose menu switches, edits or removes the\n\t *  term; then + Add ring. Rebuilt only when the rings change; otherwise the pills get the current\n\t *  filter, which their term pickers use */\n\tasync renderRings() {\n\t\tconst twLst = this.twLst\n\t\tconst filter = this.state.termfilter?.filter\n\t\tconst sig = JSON.stringify(twLst.map(tw => [tw.$id, tw.q]))\n\t\tif (sig == this.ringsShown) {\n\t\t\tawait Promise.all(this.ringPills.map(({ pill, arg }) => pill.main({ ...arg, filter })))\n\t\t\treturn\n\t\t}\n\t\tthis.ringsShown = sig\n\t\tthis.ringPills = []\n\t\tthis.chart.dom.rings.body.selectAll('*').remove()\n\t\tconst disable_terms = twLst.map(tw => tw.term)\n\t\tconst sampleTypes = this.app.vocabApi.termdbConfig?.sampleTypes\n\t\tconst edit = (lst: any[]) => this.app.dispatch({ type: 'plot_edit', id: this.id, config: { twLst: lst } })\n\t\tfor (const [i, tw] of twLst.entries()) {\n\t\t\tconst pillDiv = this.chart\n\t\t\t\t.ringLine(i)\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-sunburst-ringpill')\n\t\t\t\t.style('min-width', '0')\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.style('font-size', '.9em')\n\t\t\t\t.style('text-overflow', 'ellipsis')\n\t\t\t\t.attr('title', tw.term.name)\n\t\t\tconst others = twLst.filter((_, j) => j != i)\n\t\t\tconst p = await this.ringPill(\n\t\t\t\tpillDiv,\n\t\t\t\tnewTw => {\n\t\t\t\t\tconst lst = twLst.slice()\n\t\t\t\t\tif (newTw?.term) lst[i] = newTw\n\t\t\t\t\telse lst.splice(i, 1)\n\t\t\t\t\tedit(lst)\n\t\t\t\t},\n\t\t\t\tallowedSampleTypes(others, sampleTypes)\n\t\t\t)\n\t\t\tthis.ringPills.push({ pill: p, arg: { term: tw.term, q: tw.q, $id: tw.$id, disable_terms } })\n\t\t}\n\t\tconst addDiv = this.chart\n\t\t\t.ringRow(twLst.length)\n\t\t\t.style('margin-top', '6px')\n\t\t\t.append('div')\n\t\t\t.style('margin-left', '21px')\n\t\tconst add = await this.ringPill(\n\t\t\taddDiv,\n\t\t\tnewTw => {\n\t\t\t\tif (newTw?.term) edit([...twLst, newTw])\n\t\t\t},\n\t\t\tallowedSampleTypes(twLst, sampleTypes),\n\t\t\t'+ Add ring'\n\t\t)\n\t\tthis.ringPills.push({ pill: add, arg: { term: null, q: null, disable_terms } })\n\t\tawait Promise.all(this.ringPills.map(({ pill, arg }) => pill.main({ ...arg, filter })))\n\t\tthis.chart.markShownRings()\n\t}\n\n\t/** a ring term pill; `sampleTypes` limits the terms it offers (see allowedSampleTypes) */\n\tasync ringPill(holder: any, callback: (tw: any) => void, sampleTypes?: number[], placeholder?: string) {\n\t\treturn await termsettingInit({\n\t\t\tholder,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tusecase: { target: 'sunburst', ...(sampleTypes ? { sampleTypes } : {}) },\n\t\t\t// the full term name; a name too long for the box is clipped, with the name as its tooltip\n\t\t\tabbrCutoff: 1000,\n\t\t\tmenuOptions: '*',\n\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\tdefaultQ4fillTW: { numeric: { mode: 'discrete' } },\n\t\t\t...(placeholder ? { placeholder } : {}),\n\t\t\tdebug: this.app.opts.debug,\n\t\t\tcallback\n\t\t})\n\t}\n\n\tdestroy() {\n\t\tthis.chart?.destroy()\n\t}\n}\n\n/** the plot config, with the dataset's default rings unless `opts` gives its own; also used by the\n *  About tab for the same rings */\nexport async function getPlotConfig(opts: any, app: any) {\n\tconst config: any = {\n\t\tchartType: 'sunburst',\n\t\tsettings: {}\n\t}\n\tcopyMerge(config, opts)\n\t// default rings from the dataset; a saved session or another chart may give its own\n\tif (!config.twLst) config.twLst = structuredClone(app.vocabApi.termdbConfig?.sunburst?.twLst || [])\n\tconfig.twLst = await Promise.all(\n\t\tconfig.twLst.map((tw: any) => fillTermWrapper(tw, app.vocabApi, { numeric: { mode: 'discrete' } } as any))\n\t)\n\treturn config\n}\n\nexport const sunburstInit = getCompInit(Sunburst)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = sunburstInit\n"],
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+  "names": ["pill"]
+}

package/dist/chunk-DYX6B6RN.js

@@ -0,0 +1,328 @@
+import {
+  first_genetrack_tolist
+} from "./chunk-CXCAQOFB.js";
+import {
+  HYPER_COLOR,
+  HYPO_COLOR
+} from "./chunk-VVWZ4BOI.js";
+import {
+  clearsMinDeltaBeta
+} from "./chunk-2N345NXD.js";
+
+// plots/dmr/settings/defaults.ts
+function getDefaultDMRSettings(opts) {
+  const overrides = opts.settings || {};
+  const dm = opts?.app?.vocabApi?.termdbConfig?.queries?.dnaMethylation;
+  const chr = opts?.coordinateOverride?.chr;
+  const elementScale = dm?.regionAnalysis == "element" || Array.isArray(dm?.cpgChroms) && !!chr && !dm.cpgChroms.includes(chr);
+  const defaults = {
+    blockWidth: 800,
+    pad: elementScale ? 1e5 : 2e3,
+    lambda: elementScale ? 5e4 : 1e3,
+    C: 2,
+    fdr_cutoff: 0.05,
+    colors: {
+      group1: "#3b5ee6",
+      group2: "#c04e00",
+      hyper: HYPER_COLOR,
+      hypo: HYPO_COLOR
+    },
+    maxLoessRegion: 25e4,
+    minProbesForCi: 10,
+    maxRegionSize: 5e6,
+    minDeltaBeta: 0
+  };
+  if (overrides.colors) {
+    Object.assign(defaults.colors, overrides.colors);
+    delete overrides.colors;
+  }
+  return Object.assign(defaults, overrides);
+}
+
+// plots/dmr/viewModel/DmrViewModel.ts
+var CCRE_TRACK_NAME = "ENCODE cCREs";
+var MASKED_COLOR = "#aaaaaa";
+var signed = (v) => `${(v ?? 0) >= 0 ? "+" : ""}${(v ?? 0).toFixed(3)}`;
+var BELOW_FLOOR_COLOR = "#d9d9d9";
+var DmrViewModel = class {
+  constructor(dmrResult, config, genomeObj, queryChr, queryStart, queryStop) {
+    const { settings } = config;
+    const dmrBedItems = this.makeDmrBedItems(dmrResult, settings);
+    const sigCpgBedItems = this.makeSigCpgBedItems(dmrResult, settings, queryChr, queryStart, queryStop);
+    const xRange = (queryStop ?? 0) - (queryStart ?? 0);
+    const loess = dmrResult.diagnostic?.loess;
+    const showLoess = !!(loess && loess.group1_fitted.length > 0 && loess.group2_fitted.length > 0);
+    const showDots = xRange <= settings.dmr.maxLoessRegion;
+    const betaTrackResult = dmrResult.diagnostic ? this.renderBetaTrack(
+      dmrResult.diagnostic,
+      config,
+      settings.dmr.blockWidth,
+      showLoess,
+      showDots,
+      queryStart,
+      queryStop
+    ) : void 0;
+    this.viewData = {
+      tklst: this.buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackResult?.img),
+      legendRows: this.buildLegendData(
+        config,
+        dmrResult.dmrs,
+        dmrResult.maskedDmrs || [],
+        sigCpgBedItems,
+        showLoess,
+        showDots,
+        betaTrackResult?.showCi ?? false
+      ),
+      diagnostic: dmrResult.diagnostic,
+      dmrs: dmrResult.dmrs,
+      dmrBedItems,
+      showLoess,
+      showDots,
+      notes: this.buildNotes(config, dmrResult, showDots)
+    };
+  }
+  /* Plain sentences for what the view cannot say by color alone: why a DMR is gray, and when to zoom.
+  A gray DMR with significant CpGs under it otherwise reads as a contradiction. */
+  buildNotes(config, dmrResult, showDots) {
+    const notes = [];
+    const floor = config.settings.dmr.minDeltaBeta || 0;
+    const below = dmrResult.dmrs.filter((d) => !clearsMinDeltaBeta(d.delta_beta_mean, floor));
+    if (below.length) {
+      const g1 = config.group1Name || "group 1";
+      const g2 = config.group2Name || "group 2";
+      const one = below.length == 1;
+      let text = `Light gray: ${one ? "a DMR" : `${below.length} DMRs`} that DMRcate called, but where methylation barely changes between the groups (${one ? `\u0394\u03B2 ${signed(below[0].delta_beta_mean)}` : "each"} under the volcano's minimum of ${floor}), so the volcano does not count ${one ? "it" : "them"}.`;
+      const d = config.readDepth;
+      if (d && Math.min(d.control, d.case) > 0 && Math.max(d.control, d.case) / Math.min(d.control, d.case) > 1.5) {
+        const [deep, shallow, dv, sv] = d.case > d.control ? [g2, g1, d.case, d.control] : [g1, g2, d.control, d.case];
+        text += ` In this comparison ${deep} has ${(dv / sv).toFixed(1)}\xD7 the reads per CpG of ${shallow} (${dv.toFixed(
+          2
+        )} vs ${sv.toFixed(2)}). DMRcate compares ratios of methylated to unmethylated reads, which shift with read depth, so a depth difference alone can produce a call like this, and its CpGs show as significant below.`;
+      }
+      notes.push(text);
+    }
+    const masked = dmrResult.maskedDmrs || [];
+    if (masked.length) {
+      const by = [...new Set(masked.flatMap((m) => m.maskedBy))].join(", ").toLowerCase() || "an artifact-prone region";
+      notes.push(
+        `Dark gray: ${masked.length == 1 ? "a DMR" : `${masked.length} DMRs`} in ${by}, where reads from near-identical copies of the sequence can mix and the methylation measured can be wrong, so the volcano does not count ${masked.length == 1 ? "it" : "them"}.`
+      );
+    }
+    if (!showDots) notes.push("Zoom in to see per-CpG dots.");
+    if (!config.scanChromosomes?.length)
+      notes.push(
+        "This view was saved before region views were opened from a DMR scan. Its DMRs come from DMRcate run over the whole genome at default settings, with no minimum CpG count or Min \u0394\u03B2, so they can differ from those it showed when saved. Open the region from a DMR scan to match the scan."
+      );
+    return notes;
+  }
+  buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackImg) {
+    const tklst = [];
+    first_genetrack_tolist(genomeObj, tklst);
+    const ccre = (genomeObj?.tracks || []).find((t) => t.name == CCRE_TRACK_NAME);
+    if (ccre) tklst.push(structuredClone(ccre));
+    tklst.push({ type: "bedj", name: "DMRs", bedItems: dmrBedItems });
+    tklst.push({ type: "bedj", name: "Sig. CpGs", bedItems: sigCpgBedItems });
+    if (betaTrackImg) {
+      tklst.push({
+        type: "bigwig",
+        name: "Per-CpG Means",
+        height: 150,
+        imgData: betaTrackImg
+      });
+    }
+    return tklst;
+  }
+  buildLegendData(config, dmrs, masked, sigCpgBedItems, showLoess, showDots, showCi) {
+    const { colors } = config.settings.dmr;
+    const g1 = config.group1Name || "Group 1";
+    const g2 = config.group2Name || "Group 2";
+    const meansItems = [];
+    if (showDots) {
+      meansItems.push({ text: `${g1} (control)`, color: colors.group1 }, { text: `${g2} (case)`, color: colors.group2 });
+    }
+    if (showLoess) {
+      const ciLabel = showCi ? " + 95% CI" : "";
+      meansItems.push(
+        { text: `${g1} LOESS trend${ciLabel}`, color: colors.group1, style: showCi ? "shaded" : "dashed" },
+        { text: `${g2} LOESS trend${ciLabel}`, color: colors.group2, style: showCi ? "shaded" : "dashed" }
+      );
+    }
+    const rows = [{ label: "Per-CpG Means", items: meansItems }];
+    const floor = config.settings.dmr.minDeltaBeta || 0;
+    const counted = dmrs.filter((d) => clearsMinDeltaBeta(d.delta_beta_mean, floor));
+    const hasHyper = counted.some((d) => d.direction === "hyper");
+    const hasHypo = counted.some((d) => d.direction === "hypo");
+    const below = dmrs.length > counted.length;
+    if (hasHyper || hasHypo || below || masked.length) {
+      const items = [];
+      if (hasHyper) items.push({ text: "Hypermethylated", color: colors.hyper });
+      if (hasHypo) items.push({ text: "Hypomethylated", color: colors.hypo });
+      if (below)
+        items.push({ text: `Methylation change below ${floor}: not counted (see note)`, color: BELOW_FLOOR_COLOR });
+      if (masked.length)
+        items.push({ text: "In an artifact-prone region: not counted (see note)", color: MASKED_COLOR });
+      rows.push({ label: "DMR", items });
+    }
+    if (sigCpgBedItems.length) {
+      const items = [];
+      const hasHyperCpg = sigCpgBedItems.some((b) => b.color === colors.hyper);
+      const hasHypoCpg = sigCpgBedItems.some((b) => b.color === colors.hypo);
+      if (hasHyperCpg) items.push({ text: "Hyper (FDR sig.)", color: colors.hyper });
+      if (hasHypoCpg) items.push({ text: "Hypo (FDR sig.)", color: colors.hypo });
+      rows.push({ label: "Sig. CpGs", items });
+    }
+    return rows;
+  }
+  /**
+   * Render the per-CpG means scatter plot to an offscreen canvas and return
+   * a data URI suitable for the bigwig imgData track.
+   */
+  renderBetaTrack(diagnostic, config, blockWidth, showLoess, showDots, queryStart, queryStop) {
+    const { probes } = diagnostic;
+    if (!probes.positions.length) return void 0;
+    const { colors, minProbesForCi } = config.settings.dmr;
+    const dpr = typeof window !== "undefined" && window.devicePixelRatio > 1 ? window.devicePixelRatio : 1;
+    const width = blockWidth;
+    const height = 150;
+    const canvas = document.createElement("canvas");
+    canvas.width = width * dpr;
+    canvas.height = height * dpr;
+    const ctx = canvas.getContext("2d");
+    if (!ctx) return void 0;
+    ctx.scale(dpr, dpr);
+    const xMin = queryStart ?? probes.positions[0];
+    const xMax = queryStop ?? probes.positions[probes.positions.length - 1];
+    const xRange = xMax - xMin || 1;
+    const scaleX = (val) => (val - xMin) / xRange * width;
+    const scaleY = (val) => height - val * height;
+    ctx.clearRect(0, 0, width, height);
+    let showCi = false;
+    if (showLoess && diagnostic.loess) {
+      const { loess } = diagnostic;
+      const firstProbePos = probes.positions[0];
+      const lastProbePos = probes.positions[probes.positions.length - 1];
+      showCi = probes.positions.length >= minProbesForCi;
+      for (const [fitted, ciLower, ciUpper, color] of [
+        [loess.group1_fitted, loess.group1_ci_lower, loess.group1_ci_upper, colors.group1],
+        [loess.group2_fitted, loess.group2_ci_lower, loess.group2_ci_upper, colors.group2]
+      ]) {
+        if (!fitted.length) continue;
+        const lPos = loess.positions;
+        let iStart = 0;
+        let iEnd = lPos.length - 1;
+        while (iStart < lPos.length && lPos[iStart] < firstProbePos) iStart++;
+        while (iEnd >= 0 && lPos[iEnd] > lastProbePos) iEnd--;
+        if (iStart > iEnd) continue;
+        if (showCi) {
+          ctx.globalAlpha = 0.12;
+          ctx.fillStyle = color;
+          ctx.beginPath();
+          for (let i = iStart; i <= iEnd; i++) {
+            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciUpper[i]))));
+          }
+          for (let i = iEnd; i >= iStart; i--) {
+            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciLower[i]))));
+          }
+          ctx.closePath();
+          ctx.fill();
+        }
+        ctx.globalAlpha = 0.8;
+        ctx.strokeStyle = color;
+        ctx.lineWidth = 2;
+        ctx.setLineDash(showCi ? [] : [6, 4]);
+        ctx.beginPath();
+        for (let i = iStart; i <= iEnd; i++) {
+          ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, fitted[i]))));
+        }
+        ctx.stroke();
+        ctx.setLineDash([]);
+      }
+    }
+    if (!showDots) {
+      ctx.globalAlpha = 1;
+      return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
+    }
+    for (let i = 0; i < probes.positions.length; i++) {
+      const x = scaleX(probes.positions[i]);
+      const isSig = probes.sig[i];
+      const alpha = isSig ? 0.85 : 0.3;
+      ctx.globalAlpha = alpha;
+      ctx.fillStyle = colors.group1;
+      const m1 = probes.mean_group1[i];
+      if (m1 != null) {
+        ctx.beginPath();
+        ctx.arc(x, scaleY(m1), 4, 0, Math.PI * 2);
+        ctx.fill();
+      }
+      ctx.fillStyle = colors.group2;
+      const m2 = probes.mean_group2[i];
+      if (m2 != null) {
+        ctx.beginPath();
+        ctx.arc(x, scaleY(m2), 4, 0, Math.PI * 2);
+        ctx.fill();
+      }
+    }
+    ctx.globalAlpha = 1;
+    return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
+  }
+  makeDmrBedItems(dmrResult, settings) {
+    const floor = settings.dmr.minDeltaBeta || 0;
+    const items = dmrResult.dmrs.map((dmr) => {
+      if (!clearsMinDeltaBeta(dmr.delta_beta_mean, floor))
+        return {
+          chr: dmr.chr,
+          start: dmr.start,
+          stop: dmr.stop,
+          color: BELOW_FLOOR_COLOR,
+          name: `\u0394\u03B2 ${signed(dmr.delta_beta_mean)}, under ${floor}: not counted`
+        };
+      const negLog = -Math.log10(Math.max(dmr.min_smoothed_fdr, 1e-300));
+      const alpha = Math.round(Math.min(255, Math.max(50, negLog / 10 * 255)));
+      const hex = alpha.toString(16).padStart(2, "0");
+      const base = dmr.direction === "hyper" ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
+      return {
+        chr: dmr.chr,
+        start: dmr.start,
+        stop: dmr.stop,
+        color: base + hex,
+        name: `\u0394\u03B2 ${signed(dmr.delta_beta_mean)}, ${dmr.no_cpgs} CpGs`
+      };
+    });
+    for (const d of dmrResult.maskedDmrs || [])
+      items.push({
+        chr: d.chr,
+        start: d.start,
+        stop: d.stop,
+        color: MASKED_COLOR,
+        name: `masked: ${d.maskedBy.join(", ").toLowerCase() || "artifact-prone region"}`
+      });
+    return items;
+  }
+  makeSigCpgBedItems(dmrResult, settings, chr, queryStart, queryStop) {
+    const diag = dmrResult.diagnostic;
+    if (!diag) return [];
+    const { probes } = diag;
+    const items = [];
+    const minDeltaBeta = 0.05;
+    for (let i = 0; i < probes.positions.length; i++) {
+      if (!probes.sig[i]) continue;
+      const pos = probes.positions[i];
+      if (queryStart != null && queryStop != null && (pos < queryStart || pos > queryStop)) continue;
+      const mg1 = probes.mean_group1[i];
+      const mg2 = probes.mean_group2[i];
+      if (mg1 == null || mg2 == null) continue;
+      const deltaBeta = mg2 - mg1;
+      if (Math.abs(deltaBeta) < minDeltaBeta) continue;
+      const color = deltaBeta >= 0 ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
+      items.push({ chr, start: pos, stop: pos + 1, color });
+    }
+    return items;
+  }
+};
+
+export {
+  getDefaultDMRSettings,
+  CCRE_TRACK_NAME,
+  DmrViewModel
+};
+//# sourceMappingURL=chunk-DYX6B6RN.js.map

package/dist/chunk-FA2B6PKK.js

@@ -0,0 +1,42 @@
+import {
+  defaultMaxPairwiseTestGroups
+} from "./chunk-VVWZ4BOI.js";
+import {
+  plotColor
+} from "./chunk-2N345NXD.js";
+
+// plots/violin/settings/defaults.ts
+function getDefaultViolinSettings(app, overrides = {}) {
+  const defaults = {
+    orientation: "horizontal",
+    rowlabelw: 250,
+    brushRange: null,
+    //object with start and end if there is a brush selection
+    svgw: 500,
+    // span length of a plot/svg, not including margin
+    datasymbol: "rug",
+    radius: 10,
+    axisHeight: 60,
+    rightMargin: 50,
+    lines: [],
+    isLogScale: false,
+    // false: linear scale, true: log scale
+    rowSpace: 10,
+    medianLength: 7,
+    medianColor: "#FF0000",
+    medianThickness: 3,
+    ticks: 15,
+    defaultColor: plotColor,
+    method: 0,
+    orderByMedian: false,
+    showStats: true,
+    showAssociationTests: true,
+    maxPairwiseTestGroups: defaultMaxPairwiseTestGroups
+  };
+  return Object.assign(defaults, overrides);
+}
+
+export {
+  getDefaultViolinSettings
+};
+//# sourceMappingURL=chunk-FA2B6PKK.js.map