An MA plot (M-versus-A plot) visualizes the relationship between log fold change (M) and mean average expression (A) when comparing two experimental conditions. Each point represents a gene or feature, with significantly differentially expressed genes highlighted. This plot is a standard diagnostic tool in RNA-seq and microarray analysis for assessing differential expression results and detecting systematic expression-dependent bias.
// anyplot.ai
// ma-differential-expression: MA Plot for Differential Expression
// Library: highcharts 12.6.0 | JavaScript 22.22.3
// Quality: 86/100 | Created: 2026-06-21
const t = window.ANYPLOT_TOKENS;
// Muted color for non-significant genes (theme-adaptive)
const MUTED = window.ANYPLOT_THEME === "light" ? "#6B6A63" : "#A8A79F";
// Deterministic LCG — no seeded Math.random in browser
let seed = 42;
function lcg() {
seed = (seed * 1664525 + 1013904223) >>> 0;
return seed / 0x100000000;
}
function normal() {
let u;
do { u = lcg(); } while (u === 0);
return Math.sqrt(-2 * Math.log(u)) * Math.cos(2 * Math.PI * lcg());
}
// Generate RNA-seq MA plot data (~12 000 genes, typical whole-transcriptome)
const N = 12000;
const genes = [];
for (let i = 0; i < N; i++) {
// Mean expression A: skewed so more genes land at moderate values
const A = +(1 + Math.pow(lcg(), 0.55) * 13).toFixed(3);
// Variance (fan shape): higher at low expression, tighter at high
const sigma = Math.max(0.18, 1.7 / Math.sqrt(A + 0.5));
// Slight systematic upward bias at low expression (realistic normalisation artefact)
const bias = A < 4 ? 0.12 * (4 - A) / 4 : 0;
const M = +(normal() * sigma + bias).toFixed(3);
// Significance: genes with large |M| and sufficient coverage
const absM = Math.abs(M);
const sigScore = A > 2 ? (absM - 0.95) * 0.28 : 0;
const significant = sigScore > 0 && lcg() < sigScore;
genes.push({ A, M, significant });
}
// Partition into three series
const nonSig = genes.filter(g => !g.significant).map(g => [g.A, g.M]);
const upReg = genes.filter(g => g.significant && g.M > 0).map(g => [g.A, g.M]);
const downReg = genes.filter(g => g.significant && g.M < 0).map(g => [g.A, g.M]);
// LOESS-like smoothed trend: sliding window average over sorted genes
const sorted = [...genes].sort((a, b) => a.A - b.A);
const WIN = 700;
const STEP = 70;
const loess = [];
for (let i = 0; i + WIN <= sorted.length; i += STEP) {
const chunk = sorted.slice(i, i + WIN);
const avgA = +(chunk.reduce((s, g) => s + g.A, 0) / WIN).toFixed(3);
const avgM = +(chunk.reduce((s, g) => s + g.M, 0) / WIN).toFixed(3);
loess.push([avgA, avgM]);
}
Highcharts.chart("container", {
chart: {
type: "scatter",
backgroundColor: "transparent",
animation: false,
style: { fontFamily: "inherit" },
marginRight: 30,
},
credits: { enabled: false },
colors: t.palette,
title: {
text: "ma-differential-expression · javascript · highcharts · anyplot.ai",
style: { color: t.ink, fontSize: "22px", fontWeight: "600" },
},
xAxis: {
title: {
text: "A — Mean Average Expression (log₂)",
style: { color: t.inkSoft, fontSize: "16px" },
},
lineColor: t.inkSoft,
tickColor: t.inkSoft,
gridLineColor: t.grid,
gridLineWidth: 1,
labels: { style: { color: t.inkSoft, fontSize: "14px" } },
},
yAxis: {
title: {
text: "M — Log₂ Fold Change",
style: { color: t.inkSoft, fontSize: "16px" },
},
lineColor: t.inkSoft,
tickColor: t.inkSoft,
gridLineColor: t.grid,
gridLineWidth: 1,
labels: { style: { color: t.inkSoft, fontSize: "14px" } },
plotLines: [
{
value: 0,
color: t.inkSoft,
width: 1.5,
dashStyle: "Solid",
zIndex: 4,
},
{
value: 1,
color: t.inkSoft,
width: 1,
dashStyle: "ShortDash",
zIndex: 4,
label: {
text: "+1 (2× up)",
align: "right",
style: { color: t.inkSoft, fontSize: "12px" },
},
},
{
value: -1,
color: t.inkSoft,
width: 1,
dashStyle: "ShortDash",
zIndex: 4,
label: {
text: "−1 (2× down)",
align: "right",
style: { color: t.inkSoft, fontSize: "12px" },
},
},
],
},
legend: {
enabled: true,
align: "right",
verticalAlign: "top",
itemStyle: { color: t.inkSoft, fontSize: "15px" },
itemHoverStyle: { color: t.ink },
backgroundColor: t.elevatedBg,
borderColor: t.grid,
borderWidth: 1,
borderRadius: 4,
padding: 12,
},
tooltip: { enabled: false },
plotOptions: {
series: { animation: false },
},
series: [
{
name: "Not significant",
type: "scatter",
data: nonSig,
color: MUTED,
opacity: 0.40,
marker: { radius: 2, symbol: "circle" },
enableMouseTracking: false,
},
{
// Triangle-up + brand green: color AND shape encode upregulation (CVD-safe)
name: "Upregulated (padj < 0.05)",
type: "scatter",
data: upReg,
color: t.palette[0],
opacity: 0.85,
marker: { radius: 4, symbol: "triangle" },
enableMouseTracking: false,
},
{
// Triangle-down + matte red: color AND shape encode downregulation (CVD-safe)
name: "Downregulated (padj < 0.05)",
type: "scatter",
data: downReg,
color: t.palette[4],
opacity: 0.85,
marker: { radius: 4, symbol: "triangle-down" },
enableMouseTracking: false,
},
{
name: "LOESS bias trend",
type: "spline",
data: loess,
color: t.amber,
lineWidth: 2.5,
marker: { enabled: false },
enableMouseTracking: false,
},
],
});
Part of MA Plot for Differential Expression on anyplot.ai.