2f:Tc6a,Plot.plot({ marks: [ Plot.dot(normal, { x: "logFC", y: "negLogP", fill: color, opacity: 0.2, symbol: "circle", r: 5, render: (index, scales, values, dimensions, context, next) => { const g = next(index, scales, values, dimensions, context, next); const children = d3.select(g).selectChildren(); children .on('mousemove', function(event, i) { // Bring hovered point to front this.parentNode.appendChild(this); // Add outline and emphasize d3.select(this) .attr("stroke", "black") .attr("stroke-width", 2) .attr("opacity", 1); // Tooltip toolTip .style("left", event.pageX + 18 + "px") .style("top", event.pageY + 18 + "px") .style("display", "block") .html(` Analyte ${data[i].gene} elevated in X for Study SINUS-52 and modality Microarray `); d3.select(event.target).style("cursor", "pointer"); }) .on('mouseout', function(event, d) { // Reset style d3.select(this) .attr("stroke", "transparent") .attr("stroke-width", 0) .attr("opacity", 0.2); toolTip.style("display", "none"); d3.select(event.target).style("cursor", "default"); }); return g; } }), Plot.dot(highlighted, { x: "logFC", y: "negLogP", fill: "white", stroke: color, symbol: targetPath, r: 7, render: (index, scales, values, dimensions, context, next) => { const g = next(index, scales, values, dimensions, context, next); const children = d3.select(g).selectChildren(); children .on('mousemove', function(event, i) { // Bring hovered point to front this.parentNode.appendChild(this); // Change stroke to black temporarily d3.select(this) .attr("stroke-width", 2) .attr("opacity", 1); // Tooltip toolTip .style("left", event.pageX + 18 + "px") .style("top", event.pageY + 18 + "px") .style("display", "block") .html(` Analyte ${data[i].gene} elevated in X for Study SINUS-52 and modality Microarray `); d3.select(event.target).style("cursor", "pointer"); }) .on('mouseout', function(event, i) { // Restore original stroke using your color function const origColor = color(highlighted[i]); d3.select(this) .attr("stroke", origColor) .attr("stroke-width", 1) .attr("opacity", 1); toolTip.style("display", "none"); d3.select(event.target).style("cursor", "default"); }); return g; } }), Plot.ruleY([negLogPThreshold], {stroke: "black", strokeWidth: 1, strokeDasharray: "4,4"}), Plot.ruleX([-logFCThreshold, logFCThreshold], {stroke: "black", strokeWidth: 1, strokeDasharray: "4,4"}) ], x: {label: "log2 Fold Change"}, y: {label: "-log10(p-value)"}, width: width - 100, height: 700, style: { fontFamily: "Roboto, serif", fontSize: 12, } });30:Tf33,data = [ {gene: "Gene1", logFC: 1.23, pvalue: 0.045, negLogP: 1.35}, {gene: "Gene2", logFC: -2.01, pvalue: 0.001, negLogP: 3.0}, {gene: "Gene3", logFC: 0.87, pvalue: 0.12, negLogP: 0.92}, {gene: "Gene4", logFC: -1.45, pvalue: 0.03, negLogP: 1.52}, {gene: "Gene5", logFC: 2.05, pvalue: 0.0005, negLogP: 3.3}, {gene: "Gene6", logFC: -0.56, pvalue: 0.21, negLogP: 0.68}, {gene: "Gene7", logFC: 1.78, pvalue: 0.005, negLogP: 2.3}, {gene: "Gene8", logFC: -2.22, pvalue: 0.0001, negLogP: 4.0}, {gene: "Gene9", logFC: 0.45, pvalue: 0.33, negLogP: 0.48}, {gene: "Gene10", logFC: -1.12, pvalue: 0.02, negLogP: 1.7}, {gene: "Gene11", logFC: 0.99, pvalue: 0.07, negLogP: 1.15}, {gene: "Gene12", logFC: -0.87, pvalue: 0.15, negLogP: 0.82}, {gene: "Gene13", logFC: 1.5, pvalue: 0.008, negLogP: 2.1}, {gene: "Gene14", logFC: -1.75, pvalue: 0.002, negLogP: 2.7}, {gene: "Gene15", logFC: 0.33, pvalue: 0.45, negLogP: 0.35}, {gene: "Gene16", logFC: -0.65, pvalue: 0.18, negLogP: 0.74}, {gene: "Gene17", logFC: 2.1, pvalue: 0.0008, negLogP: 3.1}, {gene: "Gene18", logFC: -1.98, pvalue: 0.004, negLogP: 2.4}, {gene: "Gene19", logFC: 0.55, pvalue: 0.27, negLogP: 0.57}, {gene: "Gene20", logFC: -1.22, pvalue: 0.01, negLogP: 2.0}, {gene: "Gene21", logFC: 1.11, pvalue: 0.06, negLogP: 1.22}, {gene: "Gene22", logFC: -0.98, pvalue: 0.09, negLogP: 1.04}, {gene: "Gene23", logFC: 1.45, pvalue: 0.003, negLogP: 2.52}, {gene: "Gene24", logFC: -1.6, pvalue: 0.0015, negLogP: 2.82}, {gene: "Gene25", logFC: 0.25, pvalue: 0.51, negLogP: 0.29}, {gene: "Gene26", logFC: -0.78, pvalue: 0.12, negLogP: 0.92}, {gene: "Gene27", logFC: 2.3, pvalue: 0.0006, negLogP: 3.22}, {gene: "Gene28", logFC: -2.05, pvalue: 0.0009, negLogP: 3.05}, {gene: "Gene29", logFC: 0.62, pvalue: 0.23, negLogP: 0.64}, {gene: "Gene30", logFC: -1.35, pvalue: 0.008, negLogP: 2.1}, {gene: "Gene31", logFC: 0.89, pvalue: 0.11, negLogP: 0.96}, {gene: "Gene32", logFC: -0.44, pvalue: 0.33, negLogP: 0.48}, {gene: "Gene33", logFC: 1.66, pvalue: 0.002, negLogP: 2.7}, {gene: "Gene34", logFC: -1.81, pvalue: 0.001, negLogP: 3.0}, {gene: "Gene35", logFC: 0.38, pvalue: 0.41, negLogP: 0.39}, {gene: "Gene36", logFC: -0.71, pvalue: 0.17, negLogP: 0.77}, {gene: "Gene37", logFC: 2.05, pvalue: 0.0004, negLogP: 3.4}, {gene: "Gene38", logFC: -1.95, pvalue: 0.002, negLogP: 2.7}, {gene: "Gene39", logFC: 0.58, pvalue: 0.26, negLogP: 0.58}, {gene: "Gene40", logFC: -1.15, pvalue: 0.01, negLogP: 2.0}, {gene: "Gene41", logFC: 1.02, pvalue: 0.05, negLogP: 1.3}, {gene: "Gene42", logFC: -0.88, pvalue: 0.09, negLogP: 1.04}, {gene: "Gene43", logFC: 1.55, pvalue: 0.004, negLogP: 2.4}, {gene: "Gene44", logFC: -1.67, pvalue: 0.0018, negLogP: 2.74}, {gene: "Gene45", logFC: 0.31, pvalue: 0.44, negLogP: 0.36}, {gene: "Gene46", logFC: -0.69, pvalue: 0.19, negLogP: 0.72}, {gene: "Gene47", logFC: 2.12, pvalue: 0.0007, negLogP: 3.15}, {gene: "Gene48", logFC: -1.99, pvalue: 0.003, negLogP: 2.52}, {gene: "Gene49", logFC: 0.63, pvalue: 0.21, negLogP: 0.68}, {gene: "Gene50", logFC: -1.27, pvalue: 0.007, negLogP: 2.15}, {gene: "Gene51", logFC: 1.19, pvalue: 0.06, negLogP: 1.22}, {gene: "Gene52", logFC: -0.93, pvalue: 0.1, negLogP: 1.0}, {gene: "Gene53", logFC: 1.48, pvalue: 0.0035, negLogP: 2.46}, {gene: "Gene54", logFC: -1.72, pvalue: 0.0012, negLogP: 2.92}, {gene: "Gene55", logFC: 0.29, pvalue: 0.46, negLogP: 0.34}, {gene: "Gene56", logFC: -0.75, pvalue: 0.14, negLogP: 0.85}, {gene: "Gene57", logFC: 2.08, pvalue: 0.0005, negLogP: 3.3}, {gene: "Gene58", logFC: -2.03, pvalue: 0.0011, negLogP: 2.96}, {gene: "Gene59", logFC: 0.54, pvalue: 0.28, negLogP: 0.55}, {gene: "Gene60", logFC: -1.18, pvalue: 0.009, negLogP: 2.05}, {gene: "Gene61", logFC: 1.08, pvalue: 0.05, negLogP: 1.3}, {gene: "Gene62", logFC: -0.84, pvalue: 0.11, negLogP: 0.96} ] 31:Tdb4,targetPath = ({ draw: (context, size) => { context.lineJoin = "round"; context.lineCap = "round"; context.lineWidth = Math.max(1, Math.sqrt(size) * 0.06); // scale factor to normalize 0-500 SVG coordinates to Plot size const scale = Math.sqrt(size) / 500; // helper to scale const x = (v) => v * scale; const y = (v) => v * scale; // keep track of current point for relative commands let cx = 437; let cy = 204; // Move to start context.moveTo(x(cx), y(cy)); // M437 204 c108,9 193,97 200,205 context.bezierCurveTo( x(cx + 108), y(cy + 9), x(cx + 193), y(cy + 97), x(cx + 200), y(cy + 205) ); cx += 200; cy += 205; // l103 0 cx += 103; context.lineTo(x(cx), y(cy)); // c11,0 20,9 20,20 context.bezierCurveTo( x(cx + 11), y(cy + 0), x(cx + 20), y(cy + 9), x(cx + 20), y(cy + 20) ); cx += 20; cy += 20; // l0 0 (no-op) context.lineTo(x(cx), y(cy)); // c0,11 -9,20 -20,20 context.bezierCurveTo( x(cx + 0), y(cy + 11), x(cx - 9), y(cy + 20), x(cx - 20), y(cy + 20) ); cx -= 20; cy += 20; // l-104 0 cx -= 104; context.lineTo(x(cx), y(cy)); // c-13,103 -96,184 -199,193 context.bezierCurveTo( x(cx - 13), y(cy + 103), x(cx - 96), y(cy + 184), x(cx - 199), y(cy + 193) ); cx -= 199; cy += 193; // l0 86 cy += 86; context.lineTo(x(cx), y(cy)); // c0,11 -9,20 -20,20 context.bezierCurveTo( x(cx + 0), y(cy + 11), x(cx - 9), y(cy + 20), x(cx - 20), y(cy + 20) ); cx -= 20; cy += 20; // l0 0 (no-op) context.lineTo(x(cx), y(cy)); // c-11,0 -20,-9 -20,-20 context.bezierCurveTo( x(cx - 11), y(cy + 0), x(cx - 20), y(cy - 9), x(cx - 20), y(cy - 20) ); cx -= 20; cy -= 20; // l0 -86 cy -= 86; context.lineTo(x(cx), y(cy)); // c-103,-9 -186,-90 -199,-193 context.bezierCurveTo( x(cx - 103), y(cy - 9), x(cx - 186), y(cy - 90), x(cx - 199), y(cy - 193) ); cx -= 199; cy -= 193; // l-91 0 cx -= 91; context.lineTo(x(cx), y(cy)); // c-11,0 -20,-9 -20,-20 context.bezierCurveTo( x(cx - 11), y(cy + 0), x(cx - 20), y(cy - 9), x(cx - 20), y(cy - 20) ); cx -= 20; cy -= 20; // l0 0 (no-op) context.lineTo(x(cx), y(cy)); // c0,-11 9,-20 20,-20 context.bezierCurveTo( x(cx + 0), y(cy - 11), x(cx + 9), y(cy - 20), x(cx + 20), y(cy - 20) ); cx += 20; cy -= 20; // l90 0 cx += 90; context.lineTo(x(cx), y(cy)); // c7,-108 92,-196 200,-205 context.bezierCurveTo( x(cx + 7), y(cy - 108), x(cx + 92), y(cy - 196), x(cx + 200), y(cy - 205) ); cx += 200; cy -= 205; // l0 -85 cy -= 85; context.lineTo(x(cx), y(cy)); // c0,-11 9,-20 20,-20 context.bezierCurveTo( x(cx + 0), y(cy - 11), x(cx + 9), y(cy - 20), x(cx + 20), y(cy - 20) ); cx += 20; cy -= 20; // l0 0 (no-op) context.lineTo(x(cx), y(cy)); // c11,0 20,9 20,20 context.bezierCurveTo( x(cx + 11), y(cy + 0), x(cx + 20), y(cy + 9), x(cx + 20), y(cy + 20) ); cx += 20; cy += 20; // l0 85 cy += 85; context.lineTo(x(cx), y(cy)); cx += 125; if (typeof context.stroke === "function") context.stroke(); } }); 32:[] 2d:{"title":"Volcano","cells":[{"id":0,"value":"# Volcano","pinned":false,"hidden":false,"mode":"md"},{"id":260,"value":"highlighted = data.filter(d => highlightGenes.includes(d.gene));","pinned":true,"hidden":false,"mode":"ojs"},{"id":262,"value":"normal = data.filter(d => !highlightGenes.includes(d.gene));","pinned":true,"hidden":false,"mode":"ojs"},{"id":6,"value":"$2f","pinned":true,"hidden":false,"mode":"ojs"},{"id":159,"value":"toolTip = d3.select(\"body\").append(\"div\").attr(\"class\", \"toolTip\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":289,"value":"html``\n","pinned":true,"hidden":false,"mode":"ojs"},{"id":118,"value":"","pinned":true,"hidden":false,"mode":"html"},{"id":95,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":30,"value":"color = d => {\n if (d.pvalue < pvalThreshold && d.logFC > logFCThreshold) return \"red\"; // positive significant\n if (d.pvalue < pvalThreshold && d.logFC < -logFCThreshold) return \"blue\"; // negative significant\n return \"gray\"; // not significant\n};","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"pvalThreshold = 0.05;","pinned":false,"hidden":false,"mode":"ojs"},{"id":17,"value":"logFCThreshold = 1;","pinned":true,"hidden":false,"mode":"ojs"},{"id":19,"value":"negLogPThreshold = -Math.log10(pvalThreshold);","pinned":true,"hidden":false,"mode":"ojs"},{"id":35,"value":"highlightGenes = [\"Gene24\",\"Gene4\",\"Gene27\", \"Gene2\", \"Gene55\", \"Gene25\", \"Gene 23\", \"Gene 52\"];","pinned":true,"hidden":false,"mode":"ojs"},{"id":37,"value":"$31","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}