@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

package/dist/ProteomeInput-NYPUYVN5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/ProteomeInput.ts"],
+  "sourcesContent": ["import { PlotBase } from './PlotBase.ts'\nimport { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { NumericModes } from '#shared/terms.js'\nimport { sayerror, Menu } from '#dom'\nimport { TermTypeGroups } from '#shared/common.js'\nimport { getDefaultVolcanoSettings } from './volcano/settings/defaults.ts'\nimport { getDefaultGseaSettings } from './gsea/settings/defaults.ts'\nimport { dofetch3 } from '#common/dofetch'\nimport { PROTEOME_DAP, type ProteomeDetails, type DataQualityFigure } from '#types'\nimport { importPlot } from '#plots/importPlot.js'\nimport { axisBottom, axisLeft, scaleLinear } from 'd3'\nimport {\n\tmakeTileGrid,\n\tmakeTileCard,\n\ttileExpandState,\n\trenderTileError,\n\trenderPlaceholderTiles\n} from './proteinView.tiles'\n\n/*\nProteomeInput \u2014 the analysis tools for ONE sample set, laid out as\ntile cards like the Protein View and the multi-sample-set comparison. Each card's face previews\nthe tool; clicking a card expands it in place to the full tool (the rest of the grid shifts\naround it). The expanded volcano tile hosts the full differential analysis (volcano, GSEA) as a\nchild plot (parentId = this plot), so it lives inside the tile instead of its own sandbox. The\nprotein tools' plots open as new charts below, so this tool grid stays available.\n*/\n\ntype InputTool = {\n\tkey: string\n\ttitle: string\n\tsubtitle: string\n\tisVisible: () => boolean\n\t/** when set and false, the tool is shown as a greyed placeholder card with this note */\n\thasData?: () => boolean\n\tnoDataNote?: string\n\t/** card face (compact preview / quick entry) */\n\tface: (holder: any) => void | Promise<void>\n\t/** the full tool shown when the card is expanded */\n\texpanded: (holder: any) => void | Promise<void>\n}\n\n// volcano tile face: PNG size and axis margins; w + left + right margins fit the 230px card content\nconst VOLCANO_FACE = { w: 174, h: 150 }\nconst VOLCANO_MARGIN = { top: 8, right: 12, bottom: 34, left: 44 }\n// data quality: figure width in the expanded tile, and the thumbnail grid on the face\nconst QC_FIGURE_W = 460\nconst QC_THUMBS = 4\nconst QC_THUMB_W = 100\nconst UP_COLOR = '#b2182b'\nconst DOWN_COLOR = '#2166ac'\n\nexport class ProteomeInput extends PlotBase implements RxComponent {\n\tstatic type = 'ProteomeInput'\n\n\ttype: string\n\tdom!: { [index: string]: any }\n\ttools!: InputTool[]\n\t/** key of the in-place expanded tool tile */\n\texpandedTileKey: string | null = null\n\t/** memoized DAP volcano response for the tile face */\n\tvolcanoFace: Promise<any> | null = null\n\t/** the full differential analysis child plot, mounted into this persistent holder; the\n\t *  expanded volcano tile re-attaches the holder, so collapsing keeps the analysis and\n\t *  its settings alive */\n\tvolcanoHolder: any = null\n\tvolcanoComponent: any = null\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = ProteomeInput.type\n\t\tthis.components = {}\n\t}\n\n\tgetState(appState: any) {\n\t\tconst config = appState.plots.find((p: any) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\tconfig,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\t// the full differential analysis child plot; in state so its creation triggers main()\n\t\t\tvolcanoSubplotId: appState.plots.find(\n\t\t\t\t(p: any) => p.parentId === this.id && p.chartType === 'differentialAnalysis'\n\t\t\t)?.id\n\t\t}\n\t}\n\n\tasync init(appState: any) {\n\t\tconst state = this.getState(appState)\n\t\tconst proteomeDetails: ProteomeDetails = state.config.proteomeDetails\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst organisms = state.termdbConfig?.queries?.proteome?.organisms || {}\n\t\tconst cohortConfig = organisms[organism]?.assays?.[assay]?.cohorts?.[cohort]\n\n\t\tthis.dom = this.initDom(proteomeDetails)\n\n\t\tconst activeCohort = state.activeCohort\n\t\t// the tile shows only when the dataset enables data quality\n\t\tconst dq = state.termdbConfig?.queries?.proteome?.dataQuality\n\t\tconst qcFigures: DataQualityFigure[] = cohortConfig?.qcFigures || []\n\t\tthis.tools = [\n\t\t\t{\n\t\t\t\tkey: 'volcano',\n\t\t\t\ttitle: 'DAP volcano',\n\t\t\t\tsubtitle: 'Differentially abundant proteins, case vs control',\n\t\t\t\tisVisible: () => !!cohortConfig?.DAPfile,\n\t\t\t\tface: holder => this.renderVolcanoFace(holder, proteomeDetails),\n\t\t\t\texpanded: holder => this.renderVolcanoExpanded(holder, proteomeDetails)\n\t\t\t},\n\t\t\t{\n\t\t\t\tkey: 'single',\n\t\t\t\ttitle: 'Single protein',\n\t\t\t\tsubtitle: 'Abundance of one protein across samples',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tface: holder => this.renderSingleProteinFace(holder, proteomeDetails),\n\t\t\t\texpanded: holder => this.renderSingleProtein(holder, proteomeDetails, activeCohort)\n\t\t\t},\n\t\t\t{\n\t\t\t\tkey: 'two',\n\t\t\t\ttitle: 'Two proteins',\n\t\t\t\tsubtitle: 'Abundance of one protein vs another',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tface: holder => toolGlyph(holder, 'scatter', 'Pick two proteins to compare their abundance per sample.'),\n\t\t\t\texpanded: holder => this.renderTwoProteinSelect(holder, proteomeDetails)\n\t\t\t},\n\t\t\t{\n\t\t\t\tkey: 'cluster',\n\t\t\t\ttitle: 'Hierarchical clustering',\n\t\t\t\tsubtitle: 'Protein \u00D7 sample abundance heatmap',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tface: holder => toolGlyph(holder, 'cluster', 'Pick three or more proteins to cluster samples by abundance.'),\n\t\t\t\texpanded: holder => this.renderMultiProteinSelect(holder, proteomeDetails, activeCohort)\n\t\t\t},\n\t\t\t{\n\t\t\t\tkey: 'dataQuality',\n\t\t\t\ttitle: 'Data quality',\n\t\t\t\tsubtitle: 'QC figures provided for this sample set',\n\t\t\t\tisVisible: () => !!dq,\n\t\t\t\thasData: () => qcFigures.length > 0,\n\t\t\t\tnoDataNote: 'No data quality figures have been provided for this sample set yet',\n\t\t\t\tface: holder => renderQcFace(holder, qcFigures),\n\t\t\t\texpanded: holder => {\n\t\t\t\t\tif (dq.description)\n\t\t\t\t\t\tholder\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('max-width', '900px')\n\t\t\t\t\t\t\t.style('margin-bottom', '12px')\n\t\t\t\t\t\t\t.style('color', '#555')\n\t\t\t\t\t\t\t.text(dq.description)\n\t\t\t\t\trenderQcFigures(holder, qcFigures, QC_FIGURE_W)\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\t// config.expandedTile opens one tool on arrival (e.g. from the Data quality card)\n\t\tif (state.config.expandedTile) this.expandedTileKey = state.config.expandedTile\n\t\tconst grid = makeTileGrid(this.dom.tiles)\n\t\tconst missing: InputTool[] = []\n\t\tfor (const tool of this.tools) {\n\t\t\tif (!tool.isVisible()) continue\n\t\t\tif (tool.hasData && !tool.hasData()) {\n\t\t\t\tmissing.push(tool)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst face = makeTileCard(grid, {\n\t\t\t\ttitle: tool.title,\n\t\t\t\tsubtitle: tool.subtitle,\n\t\t\t\tuniform: true,\n\t\t\t\texpand: { render: tool.expanded, ...tileExpandState(this, tool.key) }\n\t\t\t})\n\t\t\ttry {\n\t\t\t\tconst p = tool.face(face)\n\t\t\t\tif (p instanceof Promise) p.catch(err => renderTileError(face, err, this))\n\t\t\t} catch (err: any) {\n\t\t\t\trenderTileError(face, err, this)\n\t\t\t}\n\t\t}\n\t\t// data-first ordering, as in the Protein View: no-data placeholders after the live cards\n\t\trenderPlaceholderTiles(\n\t\t\tgrid,\n\t\t\tmissing.map(t => ({ title: t.title, note: t.noDataNote }))\n\t\t)\n\t}\n\n\tinitDom(proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tthis.opts.header.append('span').style('padding-right', '5px').text(`${organism} ${assay}: ${cohort}`)\n\t\tthis.opts.header.append('span').text('PROTEOME').style('font-size', '0.7em').style('opacity', '0.6')\n\n\t\treturn {\n\t\t\ttiles: this.opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.attr('data-testid', 'sjpp-proteome-input-tiles-wrapper')\n\t\t}\n\t}\n\n\tprivate getUsecase(proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\treturn {\n\t\t\ttarget: 'proteomeAbundance',\n\t\t\tdetail: 'term',\n\t\t\tproteomeDetails: { organism, assay, cohort },\n\t\t\tlabel: `Organism: ${organism}; Assay: ${assay}; Sample set: ${cohort}`\n\t\t}\n\t}\n\n\t/** face: a quick protein search that opens the single-protein plot directly */\n\trenderSingleProteinFace(holder: any, proteomeDetails: ProteomeDetails) {\n\t\ttoolGlyph(holder, 'violin', 'Search a protein to plot its abundance:')\n\t\tconst row = holder.append('div').style('margin-top', '6px')\n\t\tthis.addProteinSearchbox(row, proteomeDetails, (term: any) => this.launchSingleProtein(term, proteomeDetails), {\n\t\t\twidth: '150px'\n\t\t})\n\t}\n\n\tlaunchSingleProtein(term: any, proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst t = structuredClone(term.term || term)\n\t\tt.dataTypeDetails = { organism, assay, cohort }\n\t\tconst config: any = {\n\t\t\tchartType: 'summary',\n\t\t\tterm: { term: t, q: { mode: NumericModes.continuous } },\n\t\t\tassayCohortTitle: `${organism} ${assay}: ${cohort}`,\n\t\t\tproteomeDetails: { organism, assay, cohort }\n\t\t}\n\t\tconst overlayTerm = this.getState(this.app.getState()).termdbConfig?.queries?.proteome?.organisms?.[organism]\n\t\t\t?.overlayTerm\n\t\tif (overlayTerm) config.term2 = { term: structuredClone(overlayTerm), q: {} }\n\t\tthis.launchPlot(config)\n\t}\n\n\tasync renderSingleProtein(holder: any, proteomeDetails: ProteomeDetails, activeCohort: number) {\n\t\tconst row = holder.style('padding', '10px')\n\t\trow.append('div').style('padding', '5px').style('margin-bottom', '5px').text('Select a protein:')\n\n\t\tconst treeHolder = row.append('div')\n\t\tconst termdb = await import('../termdb/app')\n\t\ttermdb.appInit({\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tholder: treeHolder,\n\t\t\tstate: {\n\t\t\t\tactiveCohort,\n\t\t\t\tnav: { header_mode: 'search_only' },\n\t\t\t\ttree: { usecase: this.getUsecase(proteomeDetails) }\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tclick_term: (term: any) => this.launchSingleProtein(term, proteomeDetails)\n\t\t\t}\n\t\t})\n\t}\n\n\tprivate addProteinSearchbox(\n\t\trow: any,\n\t\tproteomeDetails: ProteomeDetails,\n\t\tonSelect: (term: any) => void,\n\t\topts: { width?: string } = {}\n\t) {\n\t\tconst usecase = this.getUsecase(proteomeDetails)\n\t\tconst tip = new Menu({ padding: '0px' })\n\t\tconst searchbox = row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'search')\n\t\t\t.attr('placeholder', 'Protein')\n\t\t\t.attr('class', 'sja_genesearchinput')\n\t\t\t.style('width', opts.width || '200px')\n\t\tconst mark = row.append('span').style('margin-left', '5px')\n\t\tconst word = row.append('span').style('margin-left', '5px').style('font-size', '.8em').style('opacity', 0.6)\n\n\t\tlet debounceTimer: ReturnType<typeof setTimeout>\n\t\tconst doSearch = async () => {\n\t\t\tconst v = searchbox.property('value').trim()\n\t\t\tif (v.length < 2) {\n\t\t\t\ttip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\ttry {\n\t\t\t\tconst data = await this.app.vocabApi.findTerm(v, '', usecase, TermTypeGroups.PROTEOME_ABUNDANCE)\n\t\t\t\tif (!data.lst?.length) {\n\t\t\t\t\tmark.style('color', 'red').html('&cross;')\n\t\t\t\t\tword.text('No match')\n\t\t\t\t\ttip.hide()\n\t\t\t\t} else {\n\t\t\t\t\ttip.clear().showunder(searchbox.node())\n\t\t\t\t\tfor (const term of data.lst) {\n\t\t\t\t\t\ttip.d\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t.style('border-radius', '0px')\n\t\t\t\t\t\t\t.text(term.name)\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\t\tsearchbox.property('value', term.name)\n\t\t\t\t\t\t\t\tmark.style('color', 'green').html('&check;')\n\t\t\t\t\t\t\t\tword.text(term.name)\n\t\t\t\t\t\t\t\tonSelect(term)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (e: any) {\n\t\t\t\tmark.style('color', 'red').html('&cross;')\n\t\t\t\tword.text(e.message || 'Error')\n\t\t\t}\n\t\t}\n\n\t\tsearchbox.on('keyup', async (event: any) => {\n\t\t\tif (event.key === 'Escape') {\n\t\t\t\ttip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tclearTimeout(debounceTimer)\n\t\t\tmark.html('')\n\t\t\tword.text('')\n\t\t\tdebounceTimer = setTimeout(doSearch, 300)\n\t\t})\n\n\t\treturn { searchbox, mark, word }\n\t}\n\n\tasync renderTwoProteinSelect(holder: any, proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tholder.style('padding', '10px')\n\t\tlet selectedTerm1: any = null\n\t\tlet selectedTerm2: any = null\n\n\t\tconst gene1row = holder.append('div').style('padding', '5px')\n\t\tconst gene2row = holder.append('div').style('padding', '5px').style('display', 'none')\n\t\tconst submitBtn = holder.append('button').attr('type', 'button').attr('disabled', true)\n\n\t\tgene1row.append('span').text('Select the first protein:')\n\t\tthis.addProteinSearchbox(gene1row, proteomeDetails, (term: any) => {\n\t\t\tselectedTerm1 = term\n\t\t\tgene2row.style('display', 'block')\n\t\t})\n\n\t\tgene2row.append('span').text('Select the second protein:')\n\t\tthis.addProteinSearchbox(gene2row, proteomeDetails, (term: any) => {\n\t\t\tselectedTerm2 = term\n\t\t\tsubmitBtn.attr('disabled', null)\n\t\t})\n\n\t\tsubmitBtn\n\t\t\t.text('Submit')\n\t\t\t.style('border', 'none')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('padding', '10px 15px')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.on('click', async () => {\n\t\t\t\tif (!selectedTerm1 || !selectedTerm2) {\n\t\t\t\t\tsayerror(holder, 'Please select two proteins.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst t1 = structuredClone(selectedTerm1)\n\t\t\t\tconst t2 = structuredClone(selectedTerm2)\n\t\t\t\tt1.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\tt2.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\tawait this.launchPlot({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: { term: t1, q: { mode: NumericModes.continuous } },\n\t\t\t\t\tterm2: { term: t2, q: { mode: NumericModes.continuous } },\n\t\t\t\t\tassayCohortTitle: `${organism} ${assay}: ${cohort}`,\n\t\t\t\t\tproteomeDetails: { organism, assay, cohort }\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\tasync renderMultiProteinSelect(holder: any, proteomeDetails: ProteomeDetails, activeCohort: number) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tholder.style('padding', '10px')\n\n\t\tconst usecase = this.getUsecase(proteomeDetails)\n\t\tconst termdb = await import('../termdb/app')\n\n\t\tconst treeHolder = holder.append('div')\n\n\t\ttermdb.appInit({\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tholder: treeHolder,\n\t\t\tstate: {\n\t\t\t\tactiveCohort,\n\t\t\t\tnav: { header_mode: 'search_only' },\n\t\t\t\ttree: { usecase }\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tsubmit_lst: (termlst: any[]) => {\n\t\t\t\t\tconst twlst = termlst.map((term: any) => {\n\t\t\t\t\t\tconst t = structuredClone(term)\n\t\t\t\t\t\tt.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\t\t\treturn { term: t, q: { mode: NumericModes.continuous } }\n\t\t\t\t\t})\n\n\t\t\t\t\tif (twlst.length < 3) {\n\t\t\t\t\t\talert('At least three proteins are required for hierarchical clustering. Please select more proteins.')\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\tthis.launchPlot({\n\t\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\t\tdataType: 'proteomeAbundance',\n\t\t\t\t\t\ttermgroups: [{ name: 'Protein Abundance Cluster', lst: twlst, type: 'hierCluster' }],\n\t\t\t\t\t\tassayCohortTitle: `${organism} ${assay}: ${cohort}`,\n\t\t\t\t\t\tproteomeDetails: { organism, assay, cohort }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tconst enforceMinAndLayout = () => {\n\t\t\tconst submitBtn = treeHolder.select('button').node() as HTMLButtonElement | null\n\t\t\tif (submitBtn) {\n\t\t\t\tconst selectedCount = treeHolder.selectAll('.sja_menuoption[aria-label=\"Click to delete\"]').size()\n\t\t\t\tsubmitBtn.disabled = selectedCount < 3\n\t\t\t}\n\n\t\t\tconst node = treeHolder.node() as HTMLElement\n\t\t\tconst divs = node.querySelectorAll('div')\n\t\t\tfor (const div of divs) {\n\t\t\t\tif (div.style.flexWrap === 'wrap' && div.style.display === 'inline-block') {\n\t\t\t\t\tdiv.style.display = 'flex'\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst observer = new MutationObserver(enforceMinAndLayout)\n\t\tobserver.observe(treeHolder.node(), {\n\t\t\tchildList: true,\n\t\t\tsubtree: true,\n\t\t\tattributes: true,\n\t\t\tattributeFilter: ['style']\n\t\t})\n\t}\n\n\t/** tile-face DAP volcano: the server-rendered PNG of every protein, no interactive dots */\n\tgetVolcanoFace(proteomeDetails: ProteomeDetails) {\n\t\tif (!this.volcanoFace) {\n\t\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\t\tconst s = this.volcanoSettings()\n\t\t\tthis.volcanoFace = dofetch3('termdb/dapVolcano', {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\t\torganism,\n\t\t\t\t\tassay,\n\t\t\t\t\tcohort,\n\t\t\t\t\tvolcanoRender: {\n\t\t\t\t\t\tsignificanceThresholds: {\n\t\t\t\t\t\t\tpValueCutoff: s.pValue,\n\t\t\t\t\t\t\tpValueType: s.pValueType,\n\t\t\t\t\t\t\tfoldChangeCutoff: s.foldChangeCutoff\n\t\t\t\t\t\t},\n\t\t\t\t\t\tpixelWidth: VOLCANO_FACE.w,\n\t\t\t\t\t\tpixelHeight: VOLCANO_FACE.h,\n\t\t\t\t\t\tdotRadius: Math.max(VOLCANO_FACE.w, VOLCANO_FACE.h) / 160,\n\t\t\t\t\t\tcolorSignificantUp: UP_COLOR,\n\t\t\t\t\t\tcolorSignificantDown: DOWN_COLOR,\n\t\t\t\t\t\tcolorNonsignificant: '#9ca3af',\n\t\t\t\t\t\tmaxInteractiveDots: 0,\n\t\t\t\t\t\tdevicePixelRatio: Math.max(1, Math.min(window.devicePixelRatio || 1, 3))\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}).then(res => {\n\t\t\t\tif (res.error) throw res.error\n\t\t\t\tif (!res.data?.volcanoPng) throw 'No volcano data for this sample set'\n\t\t\t\treturn res\n\t\t\t})\n\t\t\t// a failed request must not stay cached\n\t\t\tthis.volcanoFace.catch(() => (this.volcanoFace = null))\n\t\t}\n\t\treturn this.volcanoFace\n\t}\n\n\tvolcanoSettings() {\n\t\treturn { ...getDefaultVolcanoSettings({}, { termType: PROTEOME_DAP }), pValueType: 'original' as const }\n\t}\n\n\t/** PNG + axes */\n\tdrawVolcano(holder: any, res: any) {\n\t\tconst ext = res.data.plotExtent\n\t\tconst m = VOLCANO_MARGIN\n\t\tconst svg = holder\n\t\t\t.append('svg')\n\t\t\t.attr('width', ext.pixelWidth + m.left + m.right)\n\t\t\t.attr('height', ext.pixelHeight + m.top + m.bottom)\n\t\tconst g = svg.append('g').attr('transform', `translate(${m.left},${m.top})`)\n\t\tg.append('image')\n\t\t\t.attr('href', `data:image/png;base64,${res.data.volcanoPng}`)\n\t\t\t.attr('width', ext.pixelWidth)\n\t\t\t.attr('height', ext.pixelHeight)\n\t\t\t.attr('preserveAspectRatio', 'none')\n\t\tconst x = scaleLinear().domain([ext.xMin, ext.xMax]).range([0, ext.pixelWidth])\n\t\tconst y = scaleLinear().domain([ext.yMin, ext.yMax]).range([ext.pixelHeight, 0])\n\t\tconst xAxis = scaleLinear()\n\t\t\t.domain([ext.xMinUnpadded, ext.xMaxUnpadded])\n\t\t\t.range([x(ext.xMinUnpadded), x(ext.xMaxUnpadded)])\n\t\tconst yAxis = scaleLinear()\n\t\t\t.domain([ext.yMinUnpadded, ext.yMaxUnpadded])\n\t\t\t.range([y(ext.yMinUnpadded), y(ext.yMaxUnpadded)])\n\t\tg.append('g')\n\t\t\t.attr('transform', `translate(0,${ext.pixelHeight})`)\n\t\t\t.call(axisBottom(xAxis).ticks(4) as any)\n\t\t\t.selectAll('text')\n\t\t\t.style('font-size', '8.5px')\n\t\tg.append('g')\n\t\t\t.call(axisLeft(yAxis).ticks(4) as any)\n\t\t\t.selectAll('text')\n\t\t\t.style('font-size', '8.5px')\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.attr('x', m.left + ext.pixelWidth / 2)\n\t\t\t.attr('y', m.top + ext.pixelHeight + 30)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.style('font-size', '10px')\n\t\t\t.text('log2FC')\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(11,${m.top + ext.pixelHeight / 2}) rotate(-90)`)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.style('font-size', '10px')\n\t\t\t.text('\\u2212log\\u2081\\u2080(FDR)')\n\t}\n\n\tvolcanoCountsLine(holder: any, res: any) {\n\t\tconst d = res.data\n\t\tconst line = holder.append('div').style('font-size', '.75em').style('color', '#374151').style('margin-top', '2px')\n\t\tline.append('span').style('color', UP_COLOR).text(`${d.totalSignificantUp} up`)\n\t\tline.append('span').text(' \u00B7 ')\n\t\tline.append('span').style('color', DOWN_COLOR).text(`${d.totalSignificantDown} down`)\n\t\tline.append('span').style('color', '#6b7280').text(` of ${d.totalRows.toLocaleString()} proteins`)\n\t}\n\n\tasync renderVolcanoFace(holder: any, proteomeDetails: ProteomeDetails) {\n\t\tconst wait = holder.append('div').style('font-size', '.75em').style('color', '#9ca3af').text('Loading\u2026')\n\t\ttry {\n\t\t\tconst res = await this.getVolcanoFace(proteomeDetails)\n\t\t\twait.remove()\n\t\t\tthis.drawVolcano(holder, res)\n\t\t\tthis.volcanoCountsLine(holder, res)\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('color', '#9ca3af')\n\t\t\t\t.text(`${res.sample_size2} case \u00B7 ${res.sample_size1} control samples`)\n\t\t} catch (e: any) {\n\t\t\twait.remove()\n\t\t\tthrow e\n\t\t}\n\t}\n\n\t/** expanded volcano tile: the full differential analysis plot. Created as a child plot on\n\t *  first expand; later expands re-attach the same live component. */\n\tasync renderVolcanoExpanded(holder: any, proteomeDetails: ProteomeDetails) {\n\t\tif (!this.volcanoHolder) this.volcanoHolder = holder.append('div')\n\t\telse holder.node().appendChild(this.volcanoHolder.node())\n\t\tif (this.volcanoComponent) return\n\t\tif (this.getVolcanoSubplot()) {\n\t\t\tawait this.mayMountVolcano()\n\t\t\treturn\n\t\t}\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\t// main() mounts it once the store has the config\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tparentId: this.id,\n\t\t\tconfig: {\n\t\t\t\tchartType: 'differentialAnalysis',\n\t\t\t\tchildType: 'volcano',\n\t\t\t\tparentId: this.id,\n\t\t\t\ttermType: PROTEOME_DAP,\n\t\t\t\theaderText: `${organism} ${assay}: ${cohort}`,\n\t\t\t\tproteomeDetails: { organism, assay, cohort },\n\t\t\t\tsettings: {\n\t\t\t\t\tvolcano: this.volcanoSettings(),\n\t\t\t\t\tgsea: getDefaultGseaSettings({})\n\t\t\t\t},\n\t\t\t\thighlightedData: [],\n\t\t\t\thidePlotFilter: true\n\t\t\t}\n\t\t})\n\t}\n\n\tgetVolcanoSubplot() {\n\t\tconst id = this.getState(this.app.getState()).volcanoSubplotId\n\t\treturn id ? this.app.getState().plots.find((p: any) => p.id === id) : undefined\n\t}\n\n\t/** mount the differential analysis child plot into the volcano holder, only while the\n\t *  holder is on the page (the volcano measures its layout) */\n\tasync mayMountVolcano() {\n\t\tif (this.volcanoComponent || !this.volcanoHolder?.node()?.isConnected) return\n\t\tconst subplot = this.getVolcanoSubplot()\n\t\tif (!subplot) return\n\t\tconst { componentInit } = await importPlot(subplot.chartType)\n\t\tthis.volcanoComponent = await componentInit({\n\t\t\tapp: this.app,\n\t\t\tholder: this.volcanoHolder,\n\t\t\tid: subplot.id,\n\t\t\tparentId: this.id\n\t\t})\n\t\t// as a sub-component it gets later state updates (filters, its own setting edits);\n\t\t// the first render is forced here since mounting can happen outside a dispatch\n\t\tthis.components.volcano = this.volcanoComponent\n\t\tawait this.volcanoComponent.update({ appState: this.app.getState() })\n\t}\n\n\t/** open a tool's plot as a new chart; this tool grid stays so other tools remain one click away */\n\tasync launchPlot(config: any) {\n\t\tawait this.app.dispatch({ type: 'plot_create', config })\n\t}\n\n\tasync main() {\n\t\tawait this.mayMountVolcano()\n\t}\n\n\t/** remove the differential analysis child config here\n\t *  Deferred until app.main() has finished destroying the deleted plots\n\t *  skipped if the child is already gone (e.g. every plot was deleted). */\n\tdestroy() {\n\t\tconst app = this.app\n\t\tconst parentId = this.id\n\t\tconst childIds = app\n\t\t\t.getState()\n\t\t\t.plots.filter((p: any) => p.parentId === parentId && p.chartType === 'differentialAnalysis')\n\t\t\t.map((p: any) => p.id)\n\t\tif (!childIds.length) return\n\t\tqueueMicrotask(() => {\n\t\t\tconst ids = new Set(app.getState().plots.map((p: any) => p.id))\n\t\t\t// only when this plot's own config is gone, so a child still in use is never removed\n\t\t\tif (ids.has(parentId)) return\n\t\t\tfor (const id of childIds) if (ids.has(id)) app.dispatch({ type: 'plot_delete', id })\n\t\t})\n\t}\n}\n\nexport const proteomeInputInit = getCompInit(ProteomeInput)\nexport const componentInit = proteomeInputInit\n\nexport function getPlotConfig(opts: any) {\n\tconst config = {\n\t\tchartType: 'ProteomeInput',\n\t\thidePlotFilter: true\n\t}\n\treturn copyMerge(config, opts)\n}\n\n/** a small static glyph + hint for tool cards whose output needs a protein choice first */\nfunction toolGlyph(holder: any, kind: 'violin' | 'scatter' | 'cluster', hint: string) {\n\tconst W = 200,\n\t\tH = 110\n\tconst svg = holder.append('svg').attr('width', W).attr('height', H).style('display', 'block')\n\tconst g = svg.append('g')\n\tif (kind === 'violin') {\n\t\tfor (const [cx, h, c] of [\n\t\t\t[60, 80, DOWN_COLOR],\n\t\t\t[140, 60, UP_COLOR]\n\t\t] as [number, number, string][]) {\n\t\t\tconst top = (H - h) / 2\n\t\t\tg.append('path')\n\t\t\t\t.attr(\n\t\t\t\t\t'd',\n\t\t\t\t\t`M${cx},${top} C${cx + 28},${top + h * 0.35} ${cx + 22},${top + h * 0.8} ${cx},${top + h} ` +\n\t\t\t\t\t\t`C${cx - 22},${top + h * 0.8} ${cx - 28},${top + h * 0.35} ${cx},${top} Z`\n\t\t\t\t)\n\t\t\t\t.attr('fill', c)\n\t\t\t\t.attr('fill-opacity', 0.25)\n\t\t\t\t.attr('stroke', c)\n\t\t\tg.append('line')\n\t\t\t\t.attr('x1', cx - 10)\n\t\t\t\t.attr('x2', cx + 10)\n\t\t\t\t.attr('y1', top + h * 0.55)\n\t\t\t\t.attr('y2', top + h * 0.55)\n\t\t\t\t.attr('stroke', c)\n\t\t\t\t.attr('stroke-width', 2)\n\t\t}\n\t} else if (kind === 'scatter') {\n\t\t// deterministic pseudo-random cloud along a diagonal\n\t\tfor (let i = 0; i < 40; i++) {\n\t\t\tconst t = (i * 37) % 40\n\t\t\tconst jitter = (((i * 53) % 17) - 8) * 2.2\n\t\t\tg.append('circle')\n\t\t\t\t.attr('cx', 20 + t * 4)\n\t\t\t\t.attr('cy', H - 12 - t * 2.1 + jitter)\n\t\t\t\t.attr('r', 2.6)\n\t\t\t\t.attr('fill', '#6b7280')\n\t\t\t\t.attr('fill-opacity', 0.55)\n\t\t}\n\t\tg.append('line')\n\t\t\t.attr('x1', 16)\n\t\t\t.attr('y1', H - 10)\n\t\t\t.attr('x2', 184)\n\t\t\t.attr('y2', 12)\n\t\t\t.attr('stroke', UP_COLOR)\n\t} else {\n\t\t// dendrogram over a mini heatmap\n\t\tconst cols = 8,\n\t\t\trows = 5,\n\t\t\tcw = 18,\n\t\t\tch = 12,\n\t\t\tx0 = (W - cols * cw) / 2,\n\t\t\ty0 = 40\n\t\tconst palette = [DOWN_COLOR, '#92c5de', '#f7f7f7', '#f4a582', UP_COLOR]\n\t\tfor (let r = 0; r < rows; r++)\n\t\t\tfor (let c = 0; c < cols; c++)\n\t\t\t\tg.append('rect')\n\t\t\t\t\t.attr('x', x0 + c * cw)\n\t\t\t\t\t.attr('y', y0 + r * ch)\n\t\t\t\t\t.attr('width', cw - 1)\n\t\t\t\t\t.attr('height', ch - 1)\n\t\t\t\t\t.attr('fill', palette[(r * 3 + c * 2 + (c > 3 ? 2 : 0)) % palette.length])\n\t\tconst leaf = (c: number) => x0 + c * cw + cw / 2\n\t\tconst link = (a: number, b: number, yTop: number, yA: number, yB: number) =>\n\t\t\tg.append('path').attr('d', `M${a},${yA} V${yTop} H${b} V${yB}`).attr('fill', 'none').attr('stroke', '#6b7280')\n\t\tfor (let c = 0; c < cols; c += 2) link(leaf(c), leaf(c + 1), 30, y0, y0)\n\t\tlink((leaf(0) + leaf(1)) / 2, (leaf(2) + leaf(3)) / 2, 20, 30, 30)\n\t\tlink((leaf(4) + leaf(5)) / 2, (leaf(6) + leaf(7)) / 2, 20, 30, 30)\n\t\tlink((leaf(0) + leaf(3)) / 2, (leaf(4) + leaf(7)) / 2, 8, 20, 20)\n\t}\n\tholder.append('div').style('font-size', '.75em').style('color', '#6b7280').style('margin-top', '4px').text(hint)\n}\n\n/** data quality face: up to QC_THUMBS figure thumbnails in a 2-column grid + the figure count */\nfunction renderQcFace(holder: any, figures: DataQualityFigure[]) {\n\tconst grid = holder\n\t\t.append('div')\n\t\t.style('display', 'grid')\n\t\t.style('grid-template-columns', `repeat(2, ${QC_THUMB_W}px)`)\n\t\t.style('gap', '6px')\n\t\t.style('margin-top', '4px')\n\tfor (const fig of figures.slice(0, QC_THUMBS)) {\n\t\tconst cell = grid\n\t\t\t.append('div')\n\t\t\t.attr('title', fig.title)\n\t\t\t.style('height', '78px')\n\t\t\t.style('overflow', 'hidden')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('justify-content', 'center')\n\t\t\t.style('border', '1px solid #f3f4f6')\n\t\tloadQcFigure(cell, fig, '100%')\n\t}\n\tholder\n\t\t.append('div')\n\t\t.style('font-size', '.75em')\n\t\t.style('color', '#6b7280')\n\t\t.style('margin-top', '6px')\n\t\t.text(`${figures.length} QC figure${figures.length === 1 ? '' : 's'}`)\n}\n\n/** the figures of one sample set as a wrapping grid of captioned images, each `width` px wide */\nfunction renderQcFigures(holder: any, figures: DataQualityFigure[], width: number) {\n\tconst grid = holder.append('div').style('display', 'flex').style('flex-wrap', 'wrap').style('gap', '16px')\n\tfor (const fig of figures) {\n\t\tconst cell = grid.append('div').style('width', `${width}px`)\n\t\tcell.append('div').style('font-size', '0.9em').style('margin-bottom', '4px').text(fig.title)\n\t\tloadQcFigure(cell.append('div'), fig)\n\t}\n}\n\n/** load one figure into holder through the img route; each figure loads on its own, so one\n *  missing file only blanks its own cell */\nfunction loadQcFigure(holder: any, fig: DataQualityFigure, maxHeight?: string) {\n\tholder.style('color', '#888').style('font-size', '0.85em').text('Loading\u2026')\n\tdofetch3(`img?file=${encodeURIComponent(fig.file)}`)\n\t\t.then((img: any) => {\n\t\t\tif (!img || img.error) throw img?.error || 'no image'\n\t\t\tholder\n\t\t\t\t.text('')\n\t\t\t\t.append('img')\n\t\t\t\t.attr('src', img.src)\n\t\t\t\t.attr('alt', fig.title)\n\t\t\t\t.style('max-width', '100%')\n\t\t\t\t.style('max-height', maxHeight || null)\n\t\t})\n\t\t.catch((e: any) => {\n\t\t\t// the img route's error names the server file path; log it, don't show it\n\t\t\tconsole.error('dataQuality figure', fig.file, e)\n\t\t\tholder.text('Figure not available')\n\t\t})\n}\n"],
+  "mappings": 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+  "names": ["componentInit"]
+}