@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/brainRegions-YA2H2QOI.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/brainRegions.ts"],
+  "sourcesContent": ["import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { PlotBase } from './PlotBase'\nimport { Menu, addGeneSearchbox } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { scaleLinear } from 'd3'\nimport { loadBrainAssets, renderBrainSvg, type BrainAssets } from './brainRegions.svg'\n\nconst defaultConfig = {\n\tchartType: 'brainRegions'\n}\n\nconst P_VALUE_THRESHOLD = 0.05\nconst NONSIG_COLOR = '#ccc'\n\nconst BRAIN_RENDER_W = 520\n\n// Monotonic counter for unique <linearGradient> ids (Date.now() can collide when\n// two legends render within the same millisecond).\nlet gradientSeq = 0\n\nclass BrainRegions extends PlotBase implements RxComponent {\n\tstatic type = 'brainRegions'\n\ttype: string\n\tdom!: {\n\t\tholder: any\n\t\tbody: any\n\t\ttip: Menu\n\t\theader?: any\n\t}\n\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = BrainRegions.type\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div').style('padding', '10px')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tbody: holder.append('div'),\n\t\t\ttip: new Menu({ padding: '' }),\n\t\t\theader: this.opts.header\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Brain Regional Proteome')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config: any = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\tasync main() {\n\t\tconst gene = this.state.config?.gene\n\t\tif (!gene) throw new Error('brainRegions: gene is missing')\n\n\t\tif (this.dom.header) this.dom.header.text(`Brain Regional Proteome: ${gene}`)\n\n\t\tconst body = {\n\t\t\tgenome: this.app.opts.state.vocab.genome,\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tgene\n\t\t}\n\n\t\tconst data = await dofetch3('termdb/brainRegions', { body })\n\t\tif (data.error) throw data.error\n\n\t\tthis.dom.body.selectAll('*').remove()\n\n\t\t// Intro paragraph (config-driven), styled like the gene-ranking description note.\n\t\tconst description = this.app.vocabApi.termdbConfig?.queries?.proteome?.brainRegions?.description\n\t\tif (description) {\n\t\t\tthis.dom.body\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t.style('color', '#555')\n\t\t\t\t.style('margin-bottom', '10px')\n\t\t\t\t.style('line-height', '1.4')\n\t\t\t\t.style('max-width', '600px')\n\t\t\t\t.style('white-space', 'normal')\n\t\t\t\t.style('overflow-wrap', 'break-word')\n\t\t\t\t.text(description)\n\t\t}\n\n\t\tconst isoformIds = Object.keys(data.isoforms)\n\t\tif (isoformIds.length === 0) {\n\t\t\tthis.dom.body\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.style('color', '#666')\n\t\t\t\t.text(`No brain-region data found for gene \"${gene}\".`)\n\t\t\treturn\n\t\t}\n\n\t\tconst brainAssets = await loadBrainAssets(data.svgUrl, Object.keys(data.regions))\n\n\t\tconst controlRow = this.dom.body.append('div').style('margin-bottom', '15px')\n\t\tcontrolRow.append('span').style('font-weight', 'bold').text('Isoform: ')\n\n\t\tconst selectedIsoform = isoformIds[0]\n\t\tif (isoformIds.length > 1) {\n\t\t\tconst sel = controlRow\n\t\t\t\t.append('select')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.style('padding', '3px 6px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tthis.renderBrains(data, sel.node().value, brainAssets)\n\t\t\t\t})\n\n\t\t\tsel\n\t\t\t\t.selectAll('option')\n\t\t\t\t.data(isoformIds)\n\t\t\t\t.enter()\n\t\t\t\t.append('option')\n\t\t\t\t.attr('value', (d: string) => d)\n\t\t\t\t.text((d: string) => `${data.isoforms[d].gene_name} \u2014 ${d}`)\n\t\t} else {\n\t\t\tcontrolRow\n\t\t\t\t.append('span')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.text(`${data.isoforms[selectedIsoform].gene_name} \u2014 ${selectedIsoform}`)\n\t\t}\n\n\t\tthis.renderBrains(data, selectedIsoform, brainAssets)\n\t}\n\n\trenderBrains(data: any, selectedIsoform: string, brainAssets: BrainAssets) {\n\t\tconst existing = this.dom.body.select('.sjpp-brain-regions-container')\n\t\tif (!existing.empty()) existing.remove()\n\n\t\tconst container = this.dom.body\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-brain-regions-container')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', '40px')\n\t\t\t.style('flex-wrap', 'wrap')\n\n\t\tconst isoformData = data.isoforms[selectedIsoform]\n\t\tif (!isoformData) return\n\n\t\tconst allFCs: number[] = []\n\t\tfor (const disease of data.diseases) {\n\t\t\tconst regionData = isoformData.data[disease] || {}\n\t\t\tfor (const entry of Object.values(regionData) as any[]) {\n\t\t\t\tif (entry.p_value < P_VALUE_THRESHOLD) {\n\t\t\t\t\tallFCs.push(entry.fold_change)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst maxAbsFC = allFCs.length > 0 ? Math.max(...allFCs.map(v => Math.abs(v))) : 1\n\t\tconst colorScale = scaleLinear<string>()\n\t\t\t.domain([-maxAbsFC, 0, maxAbsFC])\n\t\t\t.range(['#2166ac', '#f7f7f7', '#b2182b'])\n\t\t\t.clamp(true)\n\n\t\tfor (const disease of data.diseases) {\n\t\t\tconst regionData = isoformData.data[disease] || {}\n\t\t\trenderBrainSvg({\n\t\t\t\tholder: container,\n\t\t\t\twidth: BRAIN_RENDER_W,\n\t\t\t\ttemplateUrl: data.templateUrl,\n\t\t\t\tassets: brainAssets,\n\t\t\t\tregions: data.regions,\n\t\t\t\ttitle: disease,\n\t\t\t\ttip: this.dom.tip,\n\t\t\t\tfillByRegion: (code: string) => {\n\t\t\t\t\tconst entry = regionData[code]\n\t\t\t\t\tif (entry && entry.p_value < P_VALUE_THRESHOLD) return colorScale(entry.fold_change) as string\n\t\t\t\t\treturn NONSIG_COLOR\n\t\t\t\t},\n\t\t\t\ttooltipByRegion: (code: string, label: string) => {\n\t\t\t\t\tconst entry = regionData[code]\n\t\t\t\t\tif (!entry) return `${label} (${code})\\nNo data`\n\t\t\t\t\tconst fc = entry.fold_change.toFixed(4)\n\t\t\t\t\tconst p = entry.p_value >= 0.0001 ? entry.p_value.toFixed(4) : entry.p_value.toExponential(3)\n\t\t\t\t\treturn `${label} (${code})\\nlog\u2082 fold change: ${fc}\\np-value: ${p}`\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tthis.renderLegend(container, colorScale, maxAbsFC)\n\t}\n\n\trenderLegend(container: any, colorScale: any, maxAbsFC: number) {\n\t\tconst legendDiv = container\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-direction', 'column')\n\t\t\t.style('justify-content', 'center')\n\t\t\t.style('padding', '10px')\n\n\t\tlegendDiv\n\t\t\t.append('div')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-size', '13px')\n\t\t\t.style('margin-bottom', '8px')\n\t\t\t.text('Fold Change (log\u2082)')\n\n\t\tconst legendWidth = 20\n\t\tconst legendHeight = 200\n\t\tconst svg = legendDiv\n\t\t\t.append('svg')\n\t\t\t.attr('width', legendWidth + 60)\n\t\t\t.attr('height', legendHeight + 30)\n\n\t\tconst defs = svg.append('defs')\n\t\tconst gradientId = `brain-fc-gradient-${gradientSeq++}`\n\t\tconst gradient = defs\n\t\t\t.append('linearGradient')\n\t\t\t.attr('id', gradientId)\n\t\t\t.attr('x1', '0')\n\t\t\t.attr('y1', '0')\n\t\t\t.attr('x2', '0')\n\t\t\t.attr('y2', '1')\n\n\t\tconst steps = 10\n\t\tfor (let i = 0; i <= steps; i++) {\n\t\t\tconst t = i / steps\n\t\t\tconst val = maxAbsFC * (1 - 2 * t)\n\t\t\tgradient\n\t\t\t\t.append('stop')\n\t\t\t\t.attr('offset', `${t * 100}%`)\n\t\t\t\t.attr('stop-color', colorScale(val))\n\t\t}\n\n\t\tsvg\n\t\t\t.append('rect')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', 10)\n\t\t\t.attr('width', legendWidth)\n\t\t\t.attr('height', legendHeight)\n\t\t\t.style('fill', `url(#${gradientId})`)\n\t\t\t.attr('stroke', '#999')\n\n\t\tconst legendScale = scaleLinear()\n\t\t\t.domain([maxAbsFC, -maxAbsFC])\n\t\t\t.range([10, legendHeight + 10])\n\n\t\tconst ticks = [-maxAbsFC, -maxAbsFC / 2, 0, maxAbsFC / 2, maxAbsFC]\n\t\tfor (const tick of ticks) {\n\t\t\tconst y = legendScale(tick)\n\t\t\tsvg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('x1', legendWidth)\n\t\t\t\t.attr('y1', y)\n\t\t\t\t.attr('x2', legendWidth + 5)\n\t\t\t\t.attr('y2', y)\n\t\t\t\t.attr('stroke', '#666')\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', legendWidth + 8)\n\t\t\t\t.attr('y', y)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('font-size', '10px')\n\t\t\t\t.text(tick.toFixed(2))\n\t\t}\n\n\t\tlegendDiv\n\t\t\t.append('div')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('font-size', '12px')\n\t\t\t.style('color', '#666')\n\t\t\t.html(\n\t\t\t\t`<span style=\"display:inline-block;width:14px;height:14px;background:${NONSIG_COLOR};border:1px solid #999;vertical-align:middle;margin-right:4px\"></span> Not significant (p \u2265 0.05)`\n\t\t\t)\n\t}\n}\n\nexport const componentInit = getCompInit(BrainRegions)\n\nexport async function getPlotConfig(opts: any) {\n\tconst config = structuredClone(defaultConfig)\n\tif (!opts.gene) throw new Error('brainRegions requires opts.gene')\n\treturn copyMerge(config, opts)\n}\n\nexport function makeChartBtnMenu(holder: any, chartsInstance: any) {\n\tconst row = holder.append('div').style('padding', '5px')\n\trow.append('span').style('font-weight', 'bold').text('Enter a gene name:')\n\n\tconst geneSearch = addGeneSearchbox({\n\t\trow,\n\t\tgenome: chartsInstance.app.opts.genome,\n\t\ttip: new Menu({ padding: '0px' }),\n\t\tsearchOnly: 'gene',\n\t\tcallback: async () => {\n\t\t\tif (!geneSearch.geneSymbol) throw new Error('A valid gene selection is required')\n\t\t\tchartsInstance.dom.tip.hide()\n\t\t\tchartsInstance.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'brainRegions',\n\t\t\t\t\tgene: geneSearch.geneSymbol\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t})\n}\n"],
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