@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/grin2-AJFEBD43.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/manhattan/manhattan.ts", "../plots/grin2/grin2.ts"],
+  "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport { select } from 'd3-selection'\nimport { Menu, icons, axisstyle, table2col } from '#dom'\nimport { to_svg } from '#src/client'\nimport { quadtree } from 'd3-quadtree'\nimport type { ManhattanPoint } from './manhattanTypes'\nimport { showResultsTable } from '../shared/resultsTable'\nimport { createLollipopFromGene } from '../shared/genePlotActions'\nimport { findPointsInRadius } from '../shared/quadtreeHitTest'\n\n/**\n * Creates an interactive Manhattan plot on top of a PNG background plot image.\n *\n * @param {Object} div - div element to contain the plot\n * @param {Object} data - Plot data\n * @param {Object} settings - Display configuration options:\n *   @param {number} [settings.plotWidth=500] - Plot area width\n *   @param {number} [settings.plotHeight=200] - Plot area height\n *   @param {boolean} [settings.showLegend=true] - Whether to display legend\n *   @param {boolean} [settings.showDownload=true] - Whether to show download button\n *   @param {boolean} [settings.showInteractiveDots=true] - Whether to show hoverable data points\n *   @param {number} [settings.yAxisX=70] - Y-axis positioning\n *   @param {number} [settings.yAxisSpace=40] - Space between Y-axis and plot\n *   @param {number} [settings.yAxisY=40] - Top margin\n *   @param {number} [settings.fontSize=12] - Base font size\n *   @param {number} [settings.pngDotRadius=2] - Radius of dots in PNG plot\n *   @param {number} [settings.legendItemWidth=80] - Horizontal space per legend item\n *   @param {number} [settings.legendDotRadius=3] - Size of legend dots\n *   @param {number} [settings.legendRightOffset=15] - Offset from right edge\n *   @param {number} [settings.legendTextOffset=12] - Distance between dot and text\n *   @param {number} [settings.legendVerticalOffset=4] - Vertical offset for legend items\n *   @param {number} [settings.legendFontSize=12] - Font size for legend text\n *   @param {number} [settings.interactiveDotRadius=2] - Radius of interactive dots\n *   @param {number} [settings.xAxisLabelPad=20] - Amount of padding we give for x-axis title padding\n *   @param {number} [settings.interactiveDotStrokeWidth=1] - Stroke width for interactive dots\n *   @param {string} [settings.axisColor='#545454'] - Color for y-axis\n *   @param {boolean} [settings.showYAxisLine=true] - Whether to show y-axis line\n *   @param {number} [settings.interactiveDotsCap=5000] - Interactive dots cap\n *   @param {number} [settings.maxTooltipGenes=5] - Maximum number of genes to show in tooltip\n * @param {Object} [app] - Optional app context for dispatching events\n *\n *\n * @description\n * Renders a genomic Manhattan plot by overlaying interactive elements on the base PNG plot image.\n * Features include chromosome labels, legend, hoverable data points with tooltips,\n * and proper axis scaling. The plot combines a static PNG plot image of all points with dynamic SVG elements\n * including axes, labels, legend, and top genes (represented as interactive dots) for detailed information on hover.\n */\n\nexport function plotManhattan(div: any, data: any, settings: any, app?: any) {\n\t// Get our settings\n\tsettings = {\n\t\t...settings\n\t}\n\n\t// Check size of interactive data\n\tlet interactivePoints = data.plotData.points\n\tif (data.plotData.points.length > settings.interactiveDotsCap) {\n\t\t// Sort points by y value (-log10(q-value)) descending and take top N up to interactiveDotsCap\n\t\tinteractivePoints = data.plotData.points.sort((a: any, b: any) => b.y - a.y).slice(0, settings.interactiveDotsCap)\n\t}\n\n\t// Set the  positioning up for download button to work properly\n\tdiv.style('position', 'relative')\n\n\t// Create tooltip menu\n\tconst geneTip = new Menu({ padding: '' })\n\t// Create click menu for showing all nearby genes\n\tlet clickMenuIsShown = false\n\tconst clickMenu = new Menu({\n\t\tpadding: '',\n\t\tonHide: () => {\n\t\t\tclickMenuIsShown = false\n\t\t}\n\t})\n\n\tconst svg = div\n\t\t.append('svg')\n\t\t.attr('data-testid', 'sjpp-manhattan')\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4) // Extra space for x-axis labels, legend, and title\n\n\t// Add y-axis\n\t// yPlot       \u2192 full padded scale, aligns exactly with PNG coordinates\n\t// yAxisScale  \u2192 trimmed scale for axis labels, ignores PNG padding\n\t// --- Y-Axis Setup ---\n\t// This section builds two linked scales:\n\t//\n\t//   1) yPlot       \u2192 full PNG-aligned scale (includes padding added by Rust)\n\t//   2) yAxisScale  \u2192 visual axis scale (no padding; shows only real data values)\n\t//\n\t// The reason for two scales is that the PNG image itself was rendered\n\t// with top/bottom padding for dot radius. We need one scale to stay\n\t// pixel-perfect with the PNG (for dots, overlays, etc.), and another\n\t// scale to make the visible y-axis line up only with the *real* data region.\n\n\t// 1) yPlot: true positioning scale used for all pixel-aligned elements\n\t//    - Domain = padded range from Rust (includes buffer above/below real data)\n\t//    - Range  = full PNG pixel height (0 is top, png_height is bottom)\n\tconst yPlot = scaleLinear()\n\t\t.domain([data.plotData.y_min, data.plotData.y_max]) // padded domain from Rust\n\t\t.range([settings.plotHeight + 2 * settings.pngDotRadius, 0]) // full PNG height\n\n\t// 2) yAxisScale: used only for the visible axis labels/ticks\n\t//    - Domain = true data values (no padding)\n\t//    - Range  = subset of pixel space between yPlot(0) and yPlot(realMax [data.plotData.y_max - data.plotData.png_dot_radius])\n\t//               so the axis sits entirely within the real data area\n\tconst yAxisScale = scaleLinear()\n\t\t.domain([0, data.plotData.y_max - settings.pngDotRadius])\n\t\t.range([yPlot(0), yPlot(data.plotData.y_max - settings.pngDotRadius)])\n\n\t// Axis group\n\tconst axisG = svg\n\t\t.append('g')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`)\n\n\taxisG.call(\n\t\td3axis.axisLeft(yAxisScale).tickSizeOuter(0) // removes top/bottom cap lines for clean look\n\t)\n\n\taxisstyle({\n\t\taxis: axisG,\n\t\tcolor: settings.axisColor,\n\t\tfontsize: settings.fontSize + 2,\n\t\tshowline: settings.showYAxisLine\n\t})\n\n\t// Add y-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY)\n\t\t.attr('y', settings.yAxisX / 2)\n\t\t.attr('transform', 'rotate(-90)')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text(data.plotData.has_capped_points ? '-log\u2081\u2080(q-value) [capped]' : '-log\u2081\u2080(q-value)')\n\n\t// Add png image\n\tsvg\n\t\t.append('image')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius)\n\t\t.attr('href', `data:image/png;base64,${data.pngImg || data.png}`)\n\n\t// Create scales for positioning elements\n\tconst xScale = scaleLinear()\n\t\t.domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer])\n\t\t.range([0, settings.plotWidth + 2 * settings.pngDotRadius])\n\n\t// Add interactive dots layer\n\tif (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {\n\t\t// Create a group for hover circles inside the SVG\n\t\tconst pointsLayer = svg\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\n\t\t// Create cover as a sibling div positioned over the plot area\n\t\t// This avoids mouse event issues when nested inside SVG\n\t\tconst cover = select(svg.node().parentNode as HTMLElement)\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('left', `${settings.yAxisX + settings.yAxisSpace}px`)\n\t\t\t.style('top', `${settings.yAxisY}px`)\n\t\t\t.style('width', `${settings.plotWidth + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('height', `${settings.plotHeight + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('pointer-events', 'all')\n\n\t\t// Track which dots are currently highlighted\n\t\tlet highlightedDots: ManhattanPoint[] = []\n\n\t\tconst normalizedPoints = interactivePoints\n\n\t\tconst pointQuadtree = quadtree<ManhattanPoint>()\n\t\t\t.x(d => d.pixel_x)\n\t\t\t.y(d => d.pixel_y)\n\t\t\t.addAll(normalizedPoints)\n\n\t\tcover\n\t\t\t.on('mousemove', event => {\n\t\t\t\t// Don't show hover tooltip if click menu is open\n\t\t\t\tif (clickMenuIsShown) return\n\t\t\t\t// Get mouse position relative to the cover div\n\t\t\t\tconst rect = (cover.node() as HTMLElement).getBoundingClientRect()\n\t\t\t\tconst mx = event.clientX - rect.left\n\t\t\t\tconst my = event.clientY - rect.top\n\n\t\t\t\t// Find all dots within hit radius\n\t\t\t\t// TODO: Make hit radius user configurable with its own setting\n\t\t\t\tconst hitRadius = settings.pngDotRadius + 3\n\n\t\t\t\t// Find all points within hit radius with their distances\n\t\t\t\tconst candidates = findPointsInRadius(pointQuadtree, mx, my, hitRadius)\n\n\t\t\t\t// Sort by distance and take the closest points based on settings.maxTooltipGenes setting\n\t\t\t\tcandidates.sort((a, b) => a.distance - b.distance)\n\t\t\t\tconst nearbyDots = candidates.slice(0, settings.maxTooltipGenes).map(c => c.point)\n\t\t\t\tconst additionalCount = candidates.length - settings.maxTooltipGenes\n\n\t\t\t\t// Always remove old circles first\n\t\t\t\tpointsLayer.selectAll('.hover-circle').remove()\n\n\t\t\t\tif (nearbyDots.length > 0) {\n\t\t\t\t\t// Add hover circles for all nearby dots\n\t\t\t\t\tnearbyDots.forEach(d => {\n\t\t\t\t\t\tpointsLayer\n\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t.attr('class', 'hover-circle')\n\t\t\t\t\t\t\t.attr('cx', d.pixel_x)\n\t\t\t\t\t\t\t.attr('cy', d.pixel_y)\n\t\t\t\t\t\t\t.attr('r', settings.pngDotRadius)\n\t\t\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t\t\t.attr('stroke-width', settings.interactiveDotStrokeWidth)\n\t\t\t\t\t})\n\n\t\t\t\t\thighlightedDots = nearbyDots\n\n\t\t\t\t\t// Show tooltip\n\t\t\t\t\tgeneTip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\tif (nearbyDots.length > 1) {\n\t\t\t\t\t\t// Multiple genes\n\t\t\t\t\t\tconst holder = geneTip.d.append('div').style('margin', '10px')\n\n\t\t\t\t\t\tshowResultsTable({ tableDiv: holder, hits: nearbyDots })\n\n\t\t\t\t\t\t// Show message if there are more dots beyond the settings.maxTooltipGenes shown\n\t\t\t\t\t\t// TODO: Make these settings abstracted out and can improve this later\n\t\t\t\t\t\tif (additionalCount > 0) {\n\t\t\t\t\t\t\tholder\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t\t\t\t\t.style('color', '#666')\n\t\t\t\t\t\t\t\t.style('font-style', 'italic')\n\t\t\t\t\t\t\t\t.text(`and ${additionalCount} more gene${additionalCount > 1 ? 's' : ''}...`)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// Single gene - use table2col format\n\t\t\t\t\t\tconst d = nearbyDots[0]\n\t\t\t\t\t\tconst table = table2col({\n\t\t\t\t\t\t\tholder: geneTip.d.append('div'),\n\t\t\t\t\t\t\tmargin: '10px'\n\t\t\t\t\t\t})\n\t\t\t\t\t\ttable.addRow('Gene', d.gene)\n\t\t\t\t\t\ttable.addRow('Position', `${d.chrom}:${d.start}-${d.end}`)\n\t\t\t\t\t\tconst [t1, t2] = table.addRow()\n\t\t\t\t\t\tt1.text('Type')\n\t\t\t\t\t\tt2.html(`<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`)\n\t\t\t\t\t\ttable.addRow('Q-value', d.q_value.toPrecision(3))\n\t\t\t\t\t\ttable.addRow('Subject count', d.nsubj)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// No dots nearby, hide tooltip\n\t\t\t\t\thighlightedDots = []\n\t\t\t\t\tgeneTip.hide()\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('mouseleave', () => {\n\t\t\t\t// Remove all hover circles and hide tooltip\n\t\t\t\tpointsLayer.selectAll('.hover-circle').remove()\n\t\t\t\thighlightedDots = []\n\t\t\t\tgeneTip.hide()\n\t\t\t})\n\t\t\t.on('click', event => {\n\t\t\t\t// Don't do anything if no dots nearby or no app context\n\t\t\t\tif (highlightedDots.length === 0 || !app) return\n\n\t\t\t\t// Hide the hover tooltip\n\t\t\t\tgeneTip.hide()\n\n\t\t\t\t// Get ALL candidates within hit radius (reusing the quadtree search)\n\t\t\t\tconst rect = (cover.node() as HTMLElement).getBoundingClientRect()\n\t\t\t\tconst mx = event.clientX - rect.left\n\t\t\t\tconst my = event.clientY - rect.top\n\t\t\t\tconst hitRadius = settings.pngDotRadius + 3\n\n\t\t\t\tconst allCandidates = findPointsInRadius(pointQuadtree, mx, my, hitRadius)\n\n\t\t\t\tallCandidates.sort((a, b) => a.distance - b.distance)\n\t\t\t\tconst allNearbyDots = allCandidates.map(c => c.point)\n\n\t\t\t\tif (allNearbyDots.length === 1) {\n\t\t\t\t\t// Single gene - launch directly\n\t\t\t\t\tcreateLollipopFromGene(allNearbyDots[0].gene, app)\n\t\t\t\t} else if (allNearbyDots.length > 1) {\n\t\t\t\t\t// Multiple genes - show click menu with table\n\t\t\t\t\tclickMenu.clear().show(event.clientX, event.clientY)\n\t\t\t\t\tclickMenuIsShown = true\n\n\t\t\t\t\tconst holder = clickMenu.d.append('div').style('margin', '10px')\n\n\t\t\t\t\tshowResultsTable({ tableDiv: holder, hits: allNearbyDots, app, clickMenu })\n\t\t\t\t}\n\t\t\t})\n\t}\n\n\t// Add chromosome labels\n\tif (data.plotData.chrom_data) {\n\t\tconst chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10\n\n\t\tObject.entries(data.plotData.chrom_data).forEach(([chrom, chromData]: [string, any]) => {\n\t\t\tconst chromLabel = chrom.replace('chr', '')\n\n\t\t\t// Skip chrM\n\t\t\tif (chromLabel === 'M') return\n\n\t\t\t// Calculate center position for label\n\t\t\tconst centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center)\n\n\t\t\t// Append chromosome label\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', centerPos)\n\t\t\t\t.attr('y', chromLabelY)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t\t\t.text(chromLabel)\n\t\t})\n\t}\n\n\t// Add x-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2)\n\t\t.attr('y', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text('Chromosomes')\n\n\t// Add title\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('y', settings.yAxisY / 2)\n\t\t.attr('font-weight', 'bold')\n\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t.text('Manhattan Plot')\n\n\tif (settings.showDownload) {\n\t\tconst downloadDiv = div\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('top', '5px')\n\t\t\t.style('left', `${settings.yAxisX + settings.yAxisSpace + 108}px`)\n\n\t\ticons['download'](downloadDiv, {\n\t\t\twidth: 16,\n\t\t\theight: 16,\n\t\t\ttitle: 'Download Manhattan plot',\n\t\t\thandler: () => {\n\t\t\t\t// Clone the SVG to avoid modifying the displayed version\n\t\t\t\tconst svgNode = svg.node() as SVGSVGElement\n\t\t\t\tconst clone = svgNode.cloneNode(true) as SVGSVGElement\n\n\t\t\t\t// Get the bounding box of all content\n\t\t\t\tconst bbox = svgNode.getBBox()\n\n\t\t\t\t// Set the clone's dimensions to match the full content\n\t\t\t\tclone.setAttribute('width', bbox.width.toString())\n\t\t\t\tclone.setAttribute('height', bbox.height.toString())\n\t\t\t\tclone.setAttribute('viewBox', `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`)\n\n\t\t\t\tto_svg(clone, `manhattan_plot_${new Date().toISOString().replace(/[:.]/g, '-').slice(0, -5)}`, {\n\t\t\t\t\tapply_dom_styles: true\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\t// Generate legend data\n\tconst mutationTypes = [...new Set(data.plotData.points.map((p: any) => p.type))]\n\tconst legendData = mutationTypes.map(type => {\n\t\tconst point = data.plotData.points.find((p: any) => p.type === type)\n\t\treturn {\n\t\t\ttype: String(type).charAt(0).toUpperCase() + String(type).slice(1),\n\t\t\tcolor: point?.color\n\t\t}\n\t})\n\n\t// Add legend\n\tif (settings.showLegend && legendData.length > 0) {\n\t\tconst legendY = settings.yAxisY / 2\n\t\tconst totalWidth = legendData.length * settings.legendItemWidth\n\t\tconst legendX =\n\t\t\tsettings.yAxisX +\n\t\t\tsettings.yAxisSpace +\n\t\t\t(settings.plotWidth + 2 * settings.pngDotRadius) -\n\t\t\ttotalWidth -\n\t\t\tsettings.legendRightOffset\n\n\t\tlegendData.forEach((item, i) => {\n\t\t\tconst x = legendX + i * settings.legendItemWidth\n\n\t\t\t// Legend dot\n\t\t\tsvg\n\t\t\t\t.append('circle')\n\t\t\t\t.attr('cx', x + 8)\n\t\t\t\t.attr('cy', legendY)\n\t\t\t\t.attr('r', settings.legendDotRadius)\n\t\t\t\t.attr('fill', item.color)\n\n\t\t\t// Legend text\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', x + 8 + settings.legendTextOffset)\n\t\t\t\t.attr('y', legendY + settings.legendVerticalOffset)\n\t\t\t\t.attr('font-size', `${settings.legendFontSize + 2}px`)\n\t\t\t\t.text(item.type)\n\t\t})\n\t}\n}\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport type { BasePlotConfig, MassAppApi, MassState } from '#mass/types/mass'\nimport type { GRIN2Dom, GRIN2Opts } from './GRIN2Types'\nimport { getCombinedTermFilter, getNormalRoot, filterInit } from '#filter'\nimport { Menu, table2col, make_one_checkbox, sayerror } from '#dom'\nimport { dtsnvindel, mclass, dtcnv, dtfusionrna, dtsv, proteinChangingMutations, dt2lesion } from '#shared/common.js'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { plotManhattan } from '#plots/manhattan/manhattan.ts'\nimport { showResultsTable } from '../shared/resultsTable'\nimport { controlsInit } from '#plots/controls.js'\n\nclass GRIN2 extends PlotBase implements RxComponent {\n\tstatic type = 'grin2'\n\treadonly type = 'grin2'\n\tdom: GRIN2Dom\n\tcomponents: { controls: ComponentApi }\n\tprivate snvindelMafFilter: any // active MAF filter state, updated by filterInit UI\n\n\t// Colors\n\treadonly borderColor = '#eee'\n\treadonly backgroundColor = '#f8f8f8'\n\treadonly optionsTextColor = '#666'\n\treadonly btnBackgroundColor = '#f0f0f0'\n\treadonly btnBorderColor = '#ccc'\n\treadonly btnTextColor = '#333'\n\treadonly btnHoverBackgroundColor = '#e0e0e0'\n\n\t// Typography\n\treadonly optionsTextFontSize: number = 12\n\treadonly btnFontSize: number = 12\n\treadonly headerFontSize: number = 14\n\treadonly headerFontWeight: number = 600\n\treadonly tableFontSize: number = 11\n\treadonly statsTableFontWeight: string = 'bold'\n\n\t// Spacing & Layout\n\treadonly btnPadding = '8px 16px'\n\treadonly btnSmallPadding = '2px 8px' // for Select All/Clear All\n\treadonly btnBorderRadius = '3px'\n\treadonly btnMargin = '10px'\n\treadonly tableCellPadding = '8px'\n\treadonly controlsMargin = '5px'\n\treadonly controlsPadding = '10px'\n\n\t// Input fields\n\treadonly inputWidth = '80px'\n\treadonly inputPadding = '2px 4px'\n\treadonly inputBorderColor = '#ddd'\n\treadonly inputBorderRadius = '2px'\n\n\t// Containers\n\treadonly checkboxContainerMaxHeight = '150px'\n\treadonly checkboxContainerBackground = '#fafafa'\n\treadonly checkboxContainerBorder = '1px solid #ddd'\n\treadonly checkboxContainerPadding = '4px'\n\treadonly checkboxContainerBorderRadius = '3px'\n\n\t// Interactive states\n\treadonly disabledOpacity = '0.6'\n\treadonly enabledOpacity = '1'\n\n\t// Gaps and offsets\n\treadonly controlGap = '8px'\n\treadonly checkboxMarginBottom = '2px'\n\treadonly headerMargin = '0 10px 0 0'\n\treadonly sectionMargin = '20px 0'\n\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.opts = opts\n\t\tthis.components = {\n\t\t\tcontrols: {} as ComponentApi\n\t\t}\n\t\topts.holder.classed('sjpp-grin2-main', true)\n\t\tthis.dom = {\n\t\t\tmassControls: opts.holder.append('div').style('display', 'inline-block'),\n\t\t\theaderText: opts.holder.append('div').style('display', 'inline-block'),\n\t\t\tcontrols: opts.holder.append('div'), // controls ui on top\n\t\t\tdiv: opts.holder.append('div').style('margin', '20px'), // result ui on bottom\n\t\t\ttip: new Menu({ padding: '' }),\n\t\t\tgeneTip: new Menu({ padding: '' }),\n\t\t\tsnvindelCheckbox: null,\n\t\t\tcnvCheckbox: null,\n\t\t\tfusionCheckbox: null,\n\t\t\tsvCheckbox: null,\n\t\t\trunButton: null,\n\t\t\tconsequenceCheckboxes: {},\n\t\t\tsnvindelSelectAllBtn: null,\n\t\t\tsnvindelClearAllBtn: null,\n\t\t\tsnvindelDefaultBtn: null\n\t\t}\n\t\tif (opts.header) this.dom.header = opts.header.text('GRIN2')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => 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\tconst parentConfig = appState.plots.find((p: BasePlotConfig) => p.id === this.parentId)\n\t\t// Get combined term filter from global app state and plot-specific config\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermfilter\n\t\t}\n\t}\n\n\tprivate addSnvindelRow = (table: any) => {\n\t\tconst [left, right] = table.addRow()\n\n\t\t// Options table\n\t\tconst t2 = table2col({ holder: right })\n\n\t\t// if 5/3 flanking size will be needed in future, can create a helper this.addFlankingOption() to dedup\n\n\t\t// TODO: Enable once talk to collaborators about supporting these options\n\t\t// // 5' flanking size\n\t\t// this.dom.snvindel_five_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"5' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\t\t// // 3' flanking size\n\t\t// this.dom.snvindel_three_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"3' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\t// Consequences section header + checkbox grid\n\t\t{\n\t\t\tconst [labelCell, containerCell] = t2.addRow()\n\t\t\tlabelCell.text('Consequences').style('padding-top', '8px')\n\n\t\t\t// Build the consequence checkboxes in the right cell\n\t\t\tthis.createConsequenceCheckboxes(containerCell)\n\t\t}\n\n\t\t// MAF filter UI, if mafFilter is defined in the dataset config\n\t\tconst mafFilterConfig = this.app.vocabApi.termdbConfig.queries?.snvindel?.mafFilter\n\t\tif (mafFilterConfig) {\n\t\t\tthis.snvindelMafFilter = structuredClone(\n\t\t\t\tthis.state.config.settings?.snvindelOptions?.mafFilter || mafFilterConfig.filter\n\t\t\t)\n\t\t\tconst [td1, td2] = t2.addRow()\n\t\t\ttd1.text('MAF filter')\n\t\t\tfilterInit({\n\t\t\t\temptyLabel: '+',\n\t\t\t\tholder: td2,\n\t\t\t\theader_mode: 'hide_search',\n\t\t\t\tvocab: { terms: mafFilterConfig.terms },\n\t\t\t\tcallback: async (filter: any) => {\n\t\t\t\t\tthis.snvindelMafFilter = filter\n\t\t\t\t}\n\t\t\t}).main(this.snvindelMafFilter)\n\t\t}\n\n\t\t// ----- Left-side SNV/INDEL checkbox -----\n\t\tconst isChecked = this.state.config.settings.dtUsage[dtsnvindel].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\t\tthis.dom.snvindelCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtsnvindel].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-snvindel',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\t// Add CNV row\n\tprivate addCnvRow = (table: any) => {\n\t\tconst [left, right] = table.addRow()\n\n\t\t// CNV options table\n\t\tconst t2 = table2col({ holder: right })\n\n\t\t// We need this extra useSaved because of having a ds specific value set. Only use saved CNV settings if we know they came from a completed run\n\t\t// TODO: Long term we will need to do this for snvindel once we support ds specific values there also\n\t\tconst useSaved = this.state.config.settings.runAnalysis === true\n\t\tconst savedCnv = useSaved ? this.state.config.settings.cnvOptions : undefined\n\n\t\t// Loss Threshold\n\t\tthis.dom.cnv_lossThreshold = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Loss Threshold',\n\t\t\tsavedCnv?.lossThreshold ?? this.app.vocabApi.termdbConfig.queries.cnv?.cnvLossCutoff ?? -0.4, // default. We first check if we have saved state, then we check the ds specific value, if that is undefined we fall back to the hardcoded default value\n\t\t\t-5, // min\n\t\t\t0, // max\n\t\t\t0.05 // step\n\t\t)\n\n\t\t// Gain Threshold\n\t\tthis.dom.cnv_gainThreshold = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Gain Threshold',\n\t\t\tsavedCnv?.gainThreshold ?? this.app.vocabApi.termdbConfig.queries.cnv?.cnvGainCutoff ?? 0.4, // default. We first check if we have saved state, then we check the ds specific value, if that is undefined we fall back to the hardcoded default value\n\t\t\t0, // min\n\t\t\t5, // max\n\t\t\t0.05 // step\n\t\t)\n\n\t\t// Max Segment Length (0 = no cap)\n\t\tthis.dom.cnv_maxSegLength = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Max Segment Length',\n\t\t\tsavedCnv?.maxSegLength ?? this.app.vocabApi.termdbConfig.queries.cnv?.cnvMaxLength ?? 2e6, // default 2Mb. We first check if we have saved state, then we check the ds specific value, if that is undefined we fall back to the hardcoded default value\n\t\t\t0, // min\n\t\t\t1e9, // max\n\t\t\t1000 // step\n\t\t)\n\n\t\t// // 5' flanking size\n\t\t// this.dom.cnv_five_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"5' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\t// // 3' flanking size\n\t\t// this.dom.cnv_three_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"3' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\t// ----- Left-side CNV checkbox -----\n\t\tconst dtUsage = this.state.config.settings.dtUsage\n\t\tconst isChecked =\n\t\t\tuseSaved && dtUsage[dtcnv]?.checked !== undefined\n\t\t\t\t? dtUsage[dtcnv].checked\n\t\t\t\t: !!this.app.vocabApi.termdbConfig.queries.cnv\n\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\n\t\tthis.dom.cnvCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtcnv].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-cnv',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\t// Add Fusion row\n\tprivate addFusionRow = (table: any) => {\n\t\tconst [left, right] = table.addRow()\n\n\t\t// Fusion options table\n\t\tconst t2 = table2col({ holder: right })\n\n\t\t// // 5' flanking size\n\t\t// this.dom.fusion_five_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"5' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\t// // 3' flanking size\n\t\t// this.dom.fusion_three_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"3' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\tconst isChecked = this.state.config.settings.dtUsage[dtfusionrna].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\n\t\tthis.dom.fusionCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtfusionrna].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'grin2-checkbox-fusion',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\t// Add SV row\n\tprivate addSvRow = (table: any) => {\n\t\tconst [left, right] = table.addRow()\n\n\t\t// SV options table\n\t\tconst t2 = table2col({ holder: right })\n\n\t\t// // 5' flanking size\n\t\t// this.dom.sv_five_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"5' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\t// // 3' flanking size\n\t\t// this.dom.sv_three_prime_flank_size = this.addOptionRowToTable(\n\t\t// \tt2,\n\t\t// \t\"3' Flanking Size\",\n\t\t// \t500, // default\n\t\t// \t0, // min\n\t\t// \t1e9, // max\n\t\t// \t500 // step\n\t\t// )\n\n\t\tconst isChecked = this.state.config.settings.dtUsage[dtsv].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\n\t\tthis.dom.svCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtsv].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-sv',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\t// Enable the run button only if at least one data type is checked\n\tprivate updateRunButtonState(dtu?: Record<number, { checked: boolean; label: string }>) {\n\t\tconst dtUsage = dtu || (this.state.config.settings.dtUsage as Record<number, { checked: boolean; label: string }>)\n\t\tconst anyChecked = Object.values(dtUsage).some(info => info.checked)\n\t\tthis.dom.runButton.property('disabled', !anyChecked)\n\t}\n\n\tprivate createConfigTable() {\n\t\t// Add citation text\n\t\tthis.dom.headerText\n\t\t\t.style('margin', '15px')\n\t\t\t.html(\n\t\t\t\t'GRIN2 stands for Genomic Random Interval (GRIN) statistical model. For details, see <a href=https://pubmed.ncbi.nlm.nih.gov/23842812/ target=_blank>Pounds, S. et al. Bioinformatics 2013</a>.'\n\t\t\t)\n\n\t\tconst table = table2col({ holder: this.dom.controls, disableScroll: true })\n\t\tconst queries = this.app.vocabApi.termdbConfig.queries\n\t\tif (queries.snvindel) {\n\t\t\tthis.addSnvindelRow(table)\n\t\t}\n\n\t\tif (queries.cnv) {\n\t\t\tthis.addCnvRow(table)\n\t\t}\n\t\tif (queries.svfusion?.dtLst?.includes(dtfusionrna)) {\n\t\t\tthis.addFusionRow(table)\n\t\t}\n\t\tif (queries.svfusion?.dtLst?.includes(dtsv)) {\n\t\t\tthis.addSvRow(table)\n\t\t}\n\n\t\t// Run Button\n\t\tthis.dom.runButton = this.dom.controls\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-grin2-run-button')\n\t\t\t.style('margin-left', '100px')\n\t\t\t.text('Run GRIN2')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.runAnalysis()\n\t\t\t})\n\n\t\tif (this.state.config.settings.runAnalysis) {\n\t\t\tthis.runAnalysis()\n\t\t} else {\n\t\t\t// Set initial button state\n\t\t\tthis.updateRunButtonState()\n\t\t}\n\t}\n\n\t// Helper method to add option rows to table2col instances\n\tprivate addOptionRowToTable(\n\t\ttable: any,\n\t\tlabel: string,\n\t\tdefaultValue: number,\n\t\tmin?: number,\n\t\tmax?: number,\n\t\tstep?: number\n\t) {\n\t\tconst [labelCell, inputCell] = table.addRow()\n\t\tlabelCell.text(label)\n\n\t\tconst input = inputCell\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('value', defaultValue)\n\t\t\t.style('width', this.inputWidth)\n\t\t\t.style('padding', this.inputPadding)\n\t\t\t.style('border', `1px solid ${this.inputBorderColor}`)\n\t\t\t.style('border-radius', this.inputBorderRadius)\n\t\t\t.style('font-size', `${this.optionsTextFontSize}px`)\n\n\t\tif (min !== null && min !== undefined) input.attr('min', min)\n\t\tif (max !== null && max !== undefined) input.attr('max', max)\n\t\tif (step !== null && step !== undefined) input.attr('step', step)\n\n\t\treturn input\n\t}\n\n\tprivate createConsequenceCheckboxes(container: any) {\n\t\tconst snvIndelClasses = Object.entries(mclass).filter(\n\t\t\t([key, cls]: [string, any]) => cls.dt === dtsnvindel && key !== 'Blank' && key !== 'WT'\n\t\t)\n\n\t\tconst saved = this.state.config.settings.snvindelOptions?.consequences as string[] | undefined\n\t\tconst useSaved = this.state.config.settings.runAnalysis === true && !!saved && saved.length > 0\n\n\t\t// Canonical default set = protein-changing + StartLost + StopLost\n\t\tconst canonicalDefault = new Set<string>([...proteinChangingMutations, 'StartLost', 'StopLost'])\n\n\t\t// What we use for initial rendering:\n\t\tconst initialChecked = useSaved ? new Set<string>(saved!) : canonicalDefault\n\n\t\t// --- Controls row ---\n\t\tconst controlDiv = container\n\t\t\t.append('div')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', this.controlGap)\n\n\t\tthis.dom.snvindelSelectAllBtn = controlDiv\n\t\t\t.append('button')\n\t\t\t.style('font-size', `${this.tableFontSize}px`)\n\t\t\t.text('Select All')\n\n\t\tthis.dom.snvindelClearAllBtn = controlDiv\n\t\t\t.append('button')\n\t\t\t.style('font-size', `${this.tableFontSize}px`)\n\t\t\t.text('Clear All')\n\n\t\tthis.dom.snvindelDefaultBtn = controlDiv\n\t\t\t.append('button')\n\t\t\t.style('font-size', `${this.tableFontSize}px`)\n\t\t\t.text('Default')\n\n\t\t// --- Checkbox list ---\n\t\tconst checkboxContainer = container\n\t\t\t.append('div')\n\t\t\t.style('max-height', this.checkboxContainerMaxHeight)\n\t\t\t.style('overflow-y', 'auto')\n\t\t\t.style('border', this.checkboxContainerBorder)\n\n\t\tthis.dom.consequenceCheckboxes = {}\n\n\t\tsnvIndelClasses.forEach(([classKey, classInfo]: [string, any]) => {\n\t\t\tconst checkboxDiv = checkboxContainer.append('div').style('margin-bottom', this.checkboxMarginBottom)\n\n\t\t\tconst checkbox = make_one_checkbox({\n\t\t\t\tholder: checkboxDiv,\n\t\t\t\tlabeltext: classInfo.label,\n\t\t\t\tchecked: initialChecked.has(classKey),\n\t\t\t\tdivstyle: { 'font-size': `${this.tableFontSize}px` },\n\t\t\t\tcallback: () => {}\n\t\t\t})\n\n\t\t\tcheckboxDiv.select('label').attr('title', classInfo.desc)\n\t\t\tthis.dom.consequenceCheckboxes[classKey] = checkbox\n\t\t})\n\n\t\t// Select All\n\t\tthis.dom.snvindelSelectAllBtn.on('click', () => {\n\t\t\tObject.values(this.dom.consequenceCheckboxes).forEach(cb => cb.property('checked', true))\n\t\t})\n\n\t\t// Clear All\n\t\tthis.dom.snvindelClearAllBtn.on('click', () => {\n\t\t\tObject.values(this.dom.consequenceCheckboxes).forEach(cb => cb.property('checked', false))\n\t\t})\n\n\t\t// Default: always reset to canonical (protein-changing + StartLost + StopLost)\n\t\tthis.dom.snvindelDefaultBtn.on('click', () => {\n\t\t\tObject.entries(this.dom.consequenceCheckboxes).forEach(([classKey, checkbox]) => {\n\t\t\t\tcheckbox.property('checked', canonicalDefault.has(classKey))\n\t\t\t})\n\t\t})\n\t}\n\n\tprivate getConfigValues(dtUsage: Record<number, { checked: boolean; label: string }>): any {\n\t\tconst requestConfig: any = {}\n\t\tconst usage = dtUsage || this.state.config.settings.dtUsage\n\n\t\tif (usage[dtsnvindel]?.checked) {\n\t\t\trequestConfig.snvindelOptions = {\n\t\t\t\t// minTotalDepth: parseFloat(this.dom.snvindel_minTotalDepth.property('value')),\n\t\t\t\t// minAltAlleleCount: parseFloat(this.dom.snvindel_minAltAlleleCount.property('value')),\n\t\t\t\tconsequences: this.getSelectedConsequences()\n\t\t\t}\n\t\t\tif (this.snvindelMafFilter) {\n\t\t\t\trequestConfig.snvindelOptions.mafFilter = this.snvindelMafFilter\n\t\t\t}\n\t\t}\n\n\t\tif (usage[dtcnv]?.checked) {\n\t\t\trequestConfig.cnvOptions = {\n\t\t\t\tlossThreshold: parseFloat(this.dom.cnv_lossThreshold.property('value')),\n\t\t\t\tgainThreshold: parseFloat(this.dom.cnv_gainThreshold.property('value')),\n\t\t\t\tmaxSegLength: parseFloat(this.dom.cnv_maxSegLength.property('value'))\n\t\t\t}\n\t\t}\n\n\t\tif (usage[dtfusionrna]?.checked) {\n\t\t\trequestConfig.fusionOptions = {}\n\t\t}\n\n\t\tif (usage[dtsv]?.checked) {\n\t\t\trequestConfig.svOptions = {}\n\t\t}\n\n\t\treturn requestConfig\n\t}\n\n\tprivate getDtUsageFromCheckboxes(): Record<number, { checked: boolean; label: string }> {\n\t\tconst dtUsage = structuredClone(this.state.config.settings.dtUsage)\n\n\t\tif (dtUsage[dtsnvindel]) {\n\t\t\tdtUsage[dtsnvindel].checked = this.dom.snvindelCheckbox.property('checked')\n\t\t}\n\t\tif (dtUsage[dtcnv]) {\n\t\t\tdtUsage[dtcnv].checked = this.dom.cnvCheckbox.property('checked')\n\t\t}\n\t\tif (dtUsage[dtfusionrna]) {\n\t\t\tdtUsage[dtfusionrna].checked = this.dom.fusionCheckbox.property('checked')\n\t\t}\n\t\tif (dtUsage[dtsv]) {\n\t\t\tdtUsage[dtsv].checked = this.dom.svCheckbox.property('checked')\n\t\t}\n\n\t\treturn dtUsage\n\t}\n\n\tprivate getSelectedConsequences(): string[] {\n\t\tconst consequences: string[] = []\n\n\t\tObject.entries(this.dom.consequenceCheckboxes).forEach(([classKey, checkbox]) => {\n\t\t\tif (checkbox.property('checked')) {\n\t\t\t\tconsequences.push(classKey)\n\t\t\t}\n\t\t})\n\n\t\treturn consequences\n\t}\n\n\tprivate updateRunButtonFromCheckboxes() {\n\t\tconst dtUsage = this.getDtUsageFromCheckboxes()\n\t\tthis.updateRunButtonState(dtUsage)\n\t}\n\tprivate async runAnalysis() {\n\t\tthis.dom.controls.style('pointer-events', 'none').style('opacity', '0.5')\n\t\ttry {\n\t\t\t// Get checkbox states\n\t\t\tconst dtUsage = this.getDtUsageFromCheckboxes()\n\n\t\t\tthis.dom.runButton.property('disabled', true).text('Running GRIN2...')\n\n\t\t\t// Clear previous results\n\t\t\tthis.dom.div.selectAll('*').remove()\n\n\t\t\t// Get configuration and make request using the dtUsage we just read\n\t\t\tconst configValues = this.getConfigValues(dtUsage)\n\t\t\tconst requestData = {\n\t\t\t\tfilter: getNormalRoot(this.state.termfilter.filter),\n\t\t\t\tfilter0: this.state.termfilter.filter0,\n\t\t\t\twidth: this.state.config.settings.manhattan?.plotWidth,\n\t\t\t\theight: this.state.config.settings.manhattan?.plotHeight,\n\t\t\t\tpngDotRadius: this.state.config.settings.manhattan?.pngDotRadius,\n\t\t\t\tdevicePixelRatio: window.devicePixelRatio,\n\t\t\t\tmaxGenesToShow: this.state.config.settings?.manhattan?.maxGenesToShow,\n\t\t\t\tlesionTypeColors: this.state.config.settings?.manhattan?.lesionTypeColors,\n\t\t\t\tqValueThreshold: this.state.config.settings?.manhattan?.qValueThreshold,\n\t\t\t\tmaxCappedPoints: this.state.config.settings?.manhattan?.maxCappedPoints,\n\t\t\t\thardCap: this.state.config.settings?.manhattan?.hardCap,\n\t\t\t\tbinSize: this.state.config.settings?.manhattan?.binSize,\n\t\t\t\t...configValues\n\t\t\t}\n\n\t\t\tconst response = await this.app.vocabApi.getGrin2Data(requestData, this.api!.getAbortSignal())\n\n\t\t\tif (response.status === 'error') throw `GRIN2 analysis failed: ${response.error}`\n\n\t\t\tthis.renderResults(response)\n\n\t\t\t// After the analysis completes successfully, dispatch with the updated config to save state\n\t\t\tconst updatedConfig = {\n\t\t\t\t...this.state.config,\n\t\t\t\tsettings: {\n\t\t\t\t\t...this.state.config.settings,\n\t\t\t\t\t...configValues,\n\t\t\t\t\tdtUsage: dtUsage,\n\t\t\t\t\trunAnalysis: true\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig: updatedConfig\n\t\t\t})\n\t\t} catch (error) {\n\t\t\tif (this.dom.div) {\n\t\t\t\tsayerror(this.dom.div, `Error running GRIN2: ${error instanceof Error ? error.message : error}`)\n\t\t\t} else {\n\t\t\t\t// while request running and sandbox deleted by user, it reaches here but dom.* are undefined and should not crash\n\t\t\t}\n\t\t} finally {\n\t\t\tthis.dom.controls?.style('pointer-events', 'auto').style('opacity', '1')\n\t\t\tthis.dom.runButton?.property('disabled', false).text('Run GRIN2')\n\t\t}\n\t}\n\n\tasync init() {\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.massControls.style('display', 'inline-block'),\n\t\t\tinputs: []\n\t\t})\n\n\t\t/** Removing the burger and download btn for now. Will implement later.*/\n\t\tconst burgerMenu = this.dom.massControls.select('div > svg.bi.bi-copy')\n\t\tif (burgerMenu) burgerMenu.remove()\n\t\tconst downloadBtn = this.dom.massControls.select('div > svg.bi.bi-download')\n\t\tif (downloadBtn) downloadBtn.remove()\n\n\t\tthis.components.controls.on('helpClick.grin2', () => {\n\t\t\twindow.open('https://github.com/stjude/proteinpaint/wiki/Grin2')\n\t\t})\n\t}\n\n\tasync main() {\n\t\t// Initialize the table with the different data types and options\n\t\tconst config = structuredClone(this.state.config)\n\t\tif (config.childType != this.type && config.chartType != this.type) return\n\n\t\tif (!this.dom.runButton) {\n\t\t\tthis.createConfigTable()\n\t\t}\n\t}\n\n\tprivate renderResults(result: any) {\n\t\t// Display Manhattan plot\n\t\tif (result.pngImg) {\n\t\t\tconst plotData = result\n\t\t\tconst plotDiv = this.dom.div\n\t\t\tconst manhattanSettings = this.state.config.settings.manhattan\n\t\t\tplotManhattan(plotDiv, plotData, manhattanSettings, this.app)\n\t\t}\n\n\t\t// Display top genes table\n\t\tif (result.topGeneTable) {\n\t\t\tconst tableContainer = this.dom.div.append('div').style('margin', this.sectionMargin)\n\n\t\t\t// Create header with title\n\t\t\tconst headerDiv = tableContainer\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('margin', this.btnMargin)\n\n\t\t\theaderDiv\n\t\t\t\t.append('h3')\n\t\t\t\t.style('margin', this.headerMargin)\n\t\t\t\t.style('font-size', `${this.headerFontSize}px`)\n\t\t\t\t.text(`Top Genes (showing ${result.stats.lst[0].rows[1][1]} of ${result.stats.lst[0].rows[0][1]})`)\n\n\t\t\tconst tableDiv = tableContainer.append('div')\n\n\t\t\t// Define lesion type colors and q-value threshold\n\t\t\tconst lesionTypeColors = this.state.config.settings.manhattan.lesionTypeColors\n\t\t\tconst qValueThreshold = this.state.config.settings.manhattan.qValueThreshold\n\n\t\t\t// Find column indices for q-values\n\t\t\tconst columns = result.topGeneTable.columns\n\n\t\t\t// Map dt types to their column labels and lesion types\n\t\t\tconst dtMapping = {}\n\t\t\tObject.entries(dt2lesion).forEach(([dt, config]) => {\n\t\t\t\tdtMapping[dt] = config.lesionTypes.map(lt => ({\n\t\t\t\t\tcol: `Q-value (${lt.name})`,\n\t\t\t\t\ttype: lt.lesionType\n\t\t\t\t}))\n\t\t\t})\n\n\t\t\t// Build qValue entries for enabled data types\n\t\t\tconst qValueEntries: Array<{ colIndex: number; type: string }> = []\n\t\t\tObject.entries(this.state.config.settings.dtUsage).forEach(([key, isChecked]) => {\n\t\t\t\tif (isChecked && dtMapping[key]) {\n\t\t\t\t\tdtMapping[key].forEach(({ col, type }) => {\n\t\t\t\t\t\tconst colIndex = columns.findIndex(c => c.label === col)\n\t\t\t\t\t\tif (colIndex !== -1) qValueEntries.push({ colIndex, type })\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\n\t\t\t// Add significance column to the beginning\n\t\t\tconst modifiedColumns = [{ label: '', width: '20px' }, ...result.topGeneTable.columns]\n\n\t\t\t// Cache the circles HTML\n\t\t\tconst lesionTypeCircleCache = new Map(\n\t\t\t\tObject.entries(lesionTypeColors).map(([type, color]) => [\n\t\t\t\t\ttype,\n\t\t\t\t\t`<span style=\"display:inline-block;width:8px;height:8px;border-radius:50%;background-color:${color};margin-right:3px;\"></span>`\n\t\t\t\t])\n\t\t\t)\n\n\t\t\t// Process rows to add significance indicators\n\t\t\tconst processedRows = result.topGeneTable.rows.map(row => {\n\t\t\t\tconst circles = qValueEntries\n\t\t\t\t\t.filter(({ colIndex }) => {\n\t\t\t\t\t\tconst qValue = row[colIndex]?.value\n\t\t\t\t\t\treturn typeof qValue === 'number' && qValue < qValueThreshold\n\t\t\t\t\t})\n\t\t\t\t\t.map(({ type }) => lesionTypeCircleCache.get(type)!)\n\n\t\t\t\treturn [{ value: '', html: circles.join('') }, ...row]\n\t\t\t})\n\n\t\t\t// Use showResultsTable for consistent table rendering\n\t\t\tshowResultsTable({\n\t\t\t\ttableDiv,\n\t\t\t\tapp: this.app,\n\t\t\t\tcolumns: modifiedColumns,\n\t\t\t\trows: processedRows,\n\t\t\t\tdataItems: result.topGeneTable.rows,\n\t\t\t\tgetGene: (row: any) => row[0]?.value,\n\t\t\t\tmatrixButtonFormat: 'Matrix ({n} genes selected)',\n\t\t\t\tmaxHeight: '400px',\n\t\t\t\tmaxWidth: '100%',\n\t\t\t\tdataTestId: 'sjpp-grin2-top-genes-table',\n\t\t\t\tresize: 'both',\n\t\t\t\tselectAll: false,\n\t\t\t\tallowRestoreRowOrder: true,\n\t\t\t\trestoreButtonInFooter: true,\n\t\t\t\tdownload: {\n\t\t\t\t\tfileName: `grin2_top_genes_${new Date().toISOString().replace(/[:.]/g, '-').slice(0, -5)}.tsv`\n\t\t\t\t},\n\t\t\t\theader: {\n\t\t\t\t\tallowSort: true,\n\t\t\t\t\tstyle: {\n\t\t\t\t\t\t'font-weight': this.statsTableFontWeight,\n\t\t\t\t\t\t'background-color': this.backgroundColor\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\t// Display run stats information\n\t\tif (result.stats?.lst) {\n\t\t\tconst tablesContainer = this.dom.div.append('div').style('margin-top', '50px')\n\n\t\t\t// Skip first section (contains Total Genes and Showing Top used in header)\n\t\t\tfor (const section of result.stats.lst.slice(1)) {\n\t\t\t\ttablesContainer\n\t\t\t\t\t.append('h4')\n\t\t\t\t\t.style('margin', this.headerMargin)\n\t\t\t\t\t.style('margin-top', '15px')\n\t\t\t\t\t.style('font-size', `${this.headerFontSize - 2}px`)\n\t\t\t\t\t.text(section.name)\n\n\t\t\t\tconst table = table2col({ holder: tablesContainer.append('div'), margin: '2px 8px' })\n\t\t\t\tfor (const [k, v] of section.rows) {\n\t\t\t\t\ttable.addRow(k, v)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport const grin2Init = getCompInit(GRIN2)\nexport const componentInit = grin2Init\n\nexport function getDefaultSettings(opts) {\n\tconst defaults = {\n\t\tmanhattan: {\n\t\t\t// Core plot dimensions\n\t\t\tplotWidth: 1000,\n\t\t\tplotHeight: 400,\n\t\t\tpngDotRadius: 2,\n\n\t\t\t// Layout spacing\n\t\t\tyAxisX: 70,\n\t\t\tyAxisY: 40,\n\t\t\tyAxisSpace: 20,\n\t\t\txAxisLabelPad: 30,\n\t\t\tyAxisPad: 5,\n\t\t\taxisColor: '#545454',\n\t\t\tshowYAxisLine: true,\n\n\t\t\t// Typography\n\t\t\tfontSize: 12,\n\n\t\t\t// Legend settings\n\t\t\tshowLegend: true,\n\t\t\tlegendItemWidth: 80,\n\t\t\tlegendDotRadius: 3,\n\t\t\tlegendRightOffset: 15,\n\t\t\tlegendTextOffset: 12,\n\t\t\tlegendVerticalOffset: 4,\n\t\t\tlegendFontSize: 12,\n\n\t\t\t// Interactive dots\n\t\t\tshowInteractiveDots: true,\n\t\t\tinteractiveDotRadius: 2,\n\t\t\tinteractiveDotStrokeWidth: 1,\n\n\t\t\t// Download options\n\t\t\tshowDownload: true,\n\n\t\t\t// Max genes to show in table, interactive dots cap, and tooltip genes\n\t\t\tmaxGenesToShow: 500,\n\t\t\tinteractiveDotsCap: 5000,\n\t\t\tmaxTooltipGenes: 5,\n\n\t\t\t// Q-value threshold for significance indicators in the table, tooltips, and for determining which dots become interactive\n\t\t\tqValueThreshold: 0.05,\n\n\t\t\t// Colors for lesion types (currently used for table significance indicators. Long term will also be used for the rust code colors)\n\t\t\tlesionTypeColors: {\n\t\t\t\tmutation: '#44AA44', // green\n\t\t\t\tloss: '#4444FF', // blue\n\t\t\t\tgain: '#FF4444', // red\n\t\t\t\tfusion: '#FFA500', // orange\n\t\t\t\tsv: '#9932CC' // purple\n\t\t\t},\n\n\t\t\t// Threshold for the rust code when determining if we need to raise the cap value from the default\n\t\t\tmaxCappedPoints: 5,\n\n\t\t\t// Bin size for cap calculations\n\t\t\tbinSize: 10,\n\n\t\t\t// Hard cap regardless of data distribution\n\t\t\thardCap: 200\n\t\t}\n\t}\n\n\treturn Object.assign(defaults, opts?.overrides)\n}\n\nexport async function getPlotConfig(opts: GRIN2Opts, app: MassAppApi) {\n\tconst queries = app.vocabApi.termdbConfig.queries\n\tconst defaultSettings = getDefaultSettings(opts)\n\n\tconst dtUsage: any = {}\n\n\t// Dynamically add data type options based on availability\n\tif (queries?.snvindel) {\n\t\tdtUsage[dtsnvindel] = { checked: true, label: dt2lesion[dtsnvindel].uilabel }\n\t}\n\n\tif (queries?.cnv) {\n\t\tdtUsage[dtcnv] = { checked: true, label: dt2lesion[dtcnv].uilabel }\n\t}\n\n\tif (queries?.svfusion) {\n\t\tif (queries.svfusion.dtLst.includes(dtfusionrna)) {\n\t\t\tdtUsage[dtfusionrna] = { checked: false, label: dt2lesion[dtfusionrna].uilabel }\n\t\t}\n\t\tif (queries.svfusion.dtLst.includes(dtsv)) {\n\t\t\tdtUsage[dtsv] = { checked: false, label: dt2lesion[dtsv].uilabel }\n\t\t}\n\t}\n\n\tconst config = {\n\t\tchartType: 'grin2',\n\t\tsettings: {\n\t\t\tcontrols: {},\n\t\t\tdtUsage: dtUsage,\n\t\t\trunAnalysis: false,\n\t\t\tmanhattan: {\n\t\t\t\t...defaultSettings.manhattan,\n\t\t\t\t...opts?.manhattan\n\t\t\t},\n\t\t\tsnvindelOptions: queries?.snvindel\n\t\t\t\t? {\n\t\t\t\t\t\t// minTotalDepth: 10,\n\t\t\t\t\t\t// minAltAlleleCount: 2,\n\t\t\t\t\t\tconsequences: [],\n\t\t\t\t\t\thyperMutator: 1000\n\t\t\t\t  }\n\t\t\t\t: undefined,\n\t\t\tcnvOptions: queries?.cnv\n\t\t\t\t? {\n\t\t\t\t\t\tlossThreshold: -0.4,\n\t\t\t\t\t\tgainThreshold: 0.3,\n\t\t\t\t\t\tmaxSegLength: 0,\n\t\t\t\t\t\thyperMutator: 500\n\t\t\t\t  }\n\t\t\t\t: undefined,\n\t\t\tfusionOptions: queries?.svfusion?.dtLst?.includes(dtfusionrna) ? {} : undefined,\n\t\t\tsvOptions: queries?.svfusion?.dtLst?.includes(dtsv) ? {} : undefined\n\t\t}\n\t}\n\n\treturn copyMerge(config, opts)\n}\n"],
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