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: chartjs 4.4.7 | JavaScript 22.22.3
// Quality: 86/100 | Created: 2026-06-21
//# anyplot-orientation: landscape
const t = window.ANYPLOT_TOKENS;
// Seeded LCG pseudo-random number generator (deterministic, no Math.random)
function lcg(seed) {
let s = seed >>> 0;
return () => {
s = (Math.imul(s, 1664525) + 1013904223) >>> 0;
return s / 4294967296;
};
}
// Box-Muller transform: uniform -> standard normal
function randn(rng) {
const u = rng() + 1e-10;
const v = rng();
return Math.sqrt(-2 * Math.log(u)) * Math.cos(2 * Math.PI * v);
}
// --- Data ------------------------------------------------------------------
const rng = lcg(42);
const genes = [];
// 4000 background genes: noise increases at low expression levels
for (let i = 0; i < 4000; i++) {
const a = 0.5 + Math.pow(rng(), 0.65) * 13.5;
const sigma = 0.12 + 0.55 * Math.exp(-a / 4.5);
const bias = -0.28 * Math.exp(-a / 2.8);
const m = randn(rng) * sigma + bias;
genes.push({ a, m });
}
// 500 true differentially expressed genes (medium-high expression)
const rng2 = lcg(7919);
for (let i = 0; i < 500; i++) {
const a = 2.5 + rng2() * 10;
const up = rng2() > 0.45;
const m = (up ? 1 : -1) * (1.8 + rng2() * 2.5) + randn(rng2) * 0.35;
genes.push({ a, m });
}
// Classify by |M| > 1.5 significance threshold
const notSig = [], sigUp = [], sigDown = [];
genes.forEach(({ a, m }) => {
if (m > 1.5) sigUp.push({ x: a, y: m });
else if (m < -1.5) sigDown.push({ x: a, y: m });
else notSig.push({ x: a, y: m });
});
// --- LOESS smooth (tricube kernel, bandwidth = 2.5 A-units) ----------------
const smooth = Array.from({ length: 51 }, (_, i) => {
const ax = 0.5 + (14.0 / 50) * i;
let ws = 0, wt = 0;
genes.forEach(({ a, m }) => {
const d = Math.abs(a - ax) / 2.5;
if (d < 1) {
const w = Math.pow(1 - d * d * d, 3);
ws += w * m;
wt += w;
}
});
return wt > 2 ? { x: ax, y: ws / wt } : null;
}).filter(Boolean);
// --- Reference lines -------------------------------------------------------
const refZero = [{ x: 0.2, y: 0 }, { x: 14.8, y: 0 }];
const refPos1 = [{ x: 0.2, y: 1 }, { x: 14.8, y: 1 }];
const refNeg1 = [{ x: 0.2, y: -1 }, { x: 14.8, y: -1 }];
// --- Mount -----------------------------------------------------------------
const canvas = document.createElement("canvas");
document.getElementById("container").appendChild(canvas);
// --- Chart -----------------------------------------------------------------
const TITLE = "ma-differential-expression · javascript · chartjs · anyplot.ai";
new Chart(canvas, {
type: "scatter",
data: {
datasets: [
{
label: "Not significant (" + notSig.length + ")",
data: notSig,
backgroundColor: t.inkSoft + "2E",
borderWidth: 0,
pointRadius: 1.5,
pointHoverRadius: 2.5,
},
{
label: "Up-regulated (" + sigUp.length + ")",
data: sigUp,
backgroundColor: t.palette[0] + "CC",
borderWidth: 0,
pointRadius: 3.5,
pointHoverRadius: 5,
},
{
label: "Down-regulated (" + sigDown.length + ")",
data: sigDown,
backgroundColor: "#AE3030CC",
borderWidth: 0,
pointRadius: 3.5,
pointHoverRadius: 5,
},
{
label: "M = 0",
type: "line",
data: refZero,
borderColor: t.ink + "99",
borderWidth: 1.5,
pointRadius: 0,
fill: false,
},
{
label: "±1 fold change",
type: "line",
data: refPos1,
borderColor: t.inkSoft + "77",
borderWidth: 1.5,
borderDash: [8, 5],
pointRadius: 0,
fill: false,
},
{
label: "",
type: "line",
data: refNeg1,
borderColor: t.inkSoft + "77",
borderWidth: 1.5,
borderDash: [8, 5],
pointRadius: 0,
fill: false,
},
{
label: "LOESS trend",
type: "line",
data: smooth,
borderColor: t.palette[2],
borderWidth: 4,
pointRadius: 0,
fill: false,
tension: 0.3,
spanGaps: false,
},
],
},
options: {
responsive: true,
maintainAspectRatio: false,
animation: false,
plugins: {
title: {
display: true,
text: TITLE,
color: t.ink,
font: { size: 22, weight: "500" },
padding: { top: 10, bottom: 14 },
},
legend: {
position: "top",
labels: {
color: t.ink,
font: { size: 14 },
usePointStyle: true,
filter: (item) => item.text !== "",
padding: 20,
},
},
},
scales: {
x: {
type: "linear",
min: 0,
max: 15,
title: {
display: true,
text: "A: Mean Average Expression (log₂)",
color: t.ink,
font: { size: 16 },
padding: { top: 8 },
},
ticks: { color: t.inkSoft, font: { size: 13 } },
grid: { display: false },
border: { display: false },
},
y: {
type: "linear",
min: -7,
max: 7,
title: {
display: true,
text: "M: Log₂ Fold Change",
color: t.ink,
font: { size: 16 },
padding: { bottom: 8 },
},
ticks: { color: t.inkSoft, font: { size: 13 } },
grid: { color: t.grid },
border: { display: false },
},
},
},
});
Part of MA Plot for Differential Expression on anyplot.ai.