Volcano Plot for Statistical Significance — Makie.jl

A volcano plot displays statistical significance (-log10 p-value) on the y-axis versus effect size (log2 fold change) on the x-axis. Points are typically color-coded to highlight features that are both statistically significant and have large effect sizes. This visualization is essential for quickly identifying the most important changes in differential expression, proteomics, and genomics studies.

Volcano Plot for Statistical Significance rendered with Makie.jl

Renders

Julia source (Makie.jl)

# anyplot.ai
# volcano-basic: Volcano Plot for Statistical Significance
# Library: makie 0.21.9 | Julia 1.11.9
# Quality: 91/100 | Created: 2026-09-09

using CairoMakie
using Colors
using Random

Random.seed!(42)

# --- Theme tokens -------------------------------------------------------
const THEME       = get(ENV, "ANYPLOT_THEME", "light")
const PAGE_BG     = THEME == "light" ? colorant"#FAF8F1" : colorant"#1A1A17"
const ELEVATED_BG = THEME == "light" ? colorant"#FFFDF6" : colorant"#242420"
const INK         = THEME == "light" ? colorant"#1A1A17" : colorant"#F0EFE8"
const INK_SOFT    = THEME == "light" ? colorant"#4A4A44" : colorant"#B8B7B0"
const MUTED       = THEME == "light" ? colorant"#6B6A63" : colorant"#A8A79F"

# Volcano plots follow a domain-standard convention (Imprint semantic
# exception): non-significant -> muted, up-regulated -> matte red,
# down-regulated -> blue.
const COLOR_NONSIG = MUTED
const COLOR_UP     = colorant"#AE3030"
const COLOR_DOWN   = colorant"#4467A3"

# --- Data: simulated differential gene expression (RNA-seq) -------------
n_genes = 2200
gene_names = "Gene" .* string.(1:n_genes)
log2_fold_change = randn(n_genes) .* 1.3
# Independent additive noise dominates over the fold-change-linked term so the
# cloud scatters realistically around the thresholds instead of forming a
# clean deterministic "V" (borderline points land on either side by chance,
# as in real differential-expression data).
neg_log10_pvalue = abs.(log2_fold_change .* (1.1 .+ 0.55 .* randn(n_genes))) .+
                    abs.(randn(n_genes) .* 1.3)

fc_threshold = 1.0
p_threshold = -log10(0.05)

is_up = (log2_fold_change .>= fc_threshold) .& (neg_log10_pvalue .>= p_threshold)
is_down = (log2_fold_change .<= -fc_threshold) .& (neg_log10_pvalue .>= p_threshold)
is_nonsig = .!(is_up .| is_down)

# --- Plot -----------------------------------------------------------------
fig = Figure(resolution = (1600, 900), fontsize = 14, backgroundcolor = PAGE_BG)

ax = Axis(
    fig[1, 1];
    title = "volcano-basic · julia · makie · anyplot.ai",
    titlesize = 20,
    titlecolor = INK,
    xlabel = "log2(Fold Change)",
    ylabel = "-log10(p-value)",
    xlabelsize = 14,
    ylabelsize = 14,
    xlabelcolor = INK,
    ylabelcolor = INK,
    xticklabelsize = 12,
    yticklabelsize = 12,
    xticklabelcolor = INK_SOFT,
    yticklabelcolor = INK_SOFT,
    backgroundcolor = PAGE_BG,
    topspinevisible = false,
    rightspinevisible = false,
    leftspinecolor = INK_SOFT,
    bottomspinecolor = INK_SOFT,
    xgridcolor = RGBAf(INK.r, INK.g, INK.b, 0.12),
    ygridcolor = RGBAf(INK.r, INK.g, INK.b, 0.12),
    xminorgridvisible = false,
    yminorgridvisible = false,
)

scatter!(ax, log2_fold_change[is_nonsig], neg_log10_pvalue[is_nonsig];
    color = (COLOR_NONSIG, 0.45), markersize = 7, strokewidth = 0,
    label = "Non-significant")
scatter!(ax, log2_fold_change[is_down], neg_log10_pvalue[is_down];
    color = (COLOR_DOWN, 0.75), markersize = 8, strokewidth = 0,
    label = "Down-regulated")
scatter!(ax, log2_fold_change[is_up], neg_log10_pvalue[is_up];
    color = (COLOR_UP, 0.75), markersize = 8, strokewidth = 0,
    label = "Up-regulated")

hlines!(ax, [p_threshold]; color = INK_SOFT, linestyle = :dash, linewidth = 1.5)
vlines!(ax, [-fc_threshold, fc_threshold]; color = INK_SOFT, linestyle = :dash,
    linewidth = 1.5)

# Label the top few most-significant up/down genes by name, per the spec's
# optional annotation suggestion — a distinctive use of Makie's text! recipe.
n_label = 3
top_up = findall(is_up)[sortperm(neg_log10_pvalue[is_up]; rev = true)[1:min(n_label, count(is_up))]]
top_down = findall(is_down)[sortperm(neg_log10_pvalue[is_down]; rev = true)[1:min(n_label, count(is_down))]]

for i in top_up
    text!(ax, log2_fold_change[i] + 0.08, neg_log10_pvalue[i];
        text = gene_names[i], color = INK, fontsize = 11, align = (:left, :center))
end
for i in top_down
    text!(ax, log2_fold_change[i] - 0.08, neg_log10_pvalue[i];
        text = gene_names[i], color = INK, fontsize = 11, align = (:right, :center))
end

axislegend(ax; position = :rt, backgroundcolor = ELEVATED_BG,
    framecolor = INK_SOFT, labelcolor = INK)

# --- Save -------------------------------------------------------------------
save("plot-$(THEME).png", fig; px_per_unit = 2)

Retrieve this implementation

Runnable source as JSON, for any HTTP client: https://api.anyplot.ai/specs/volcano-basic/makie/code. Any spec id and library id listed in llms-full.txt fit the same URL shape; every URL below is complete and callable.

{
  "spec_id": "volcano-basic",
  "language": "julia",
  "library": "makie",
  "page": "https://anyplot.ai/volcano-basic/julia/makie",
  "hub": "https://anyplot.ai/volcano-basic",
  "code_json": "https://api.anyplot.ai/specs/volcano-basic/makie/code",
  "spec_json": "https://api.anyplot.ai/specs/volcano-basic",
  "render_light_png": "https://storage.googleapis.com/anyplot-images/plots/volcano-basic/julia/makie/plot-light.png",
  "render_dark_png": "https://storage.googleapis.com/anyplot-images/plots/volcano-basic/julia/makie/plot-dark.png",
  "quality_score": 91.0,
  "license": "MIT",
  "guide": "https://anyplot.ai/llms.txt"
}

Part of Volcano Plot for Statistical Significance on anyplot.ai.

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