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Templates / Volcano Plot

Volcano Plot Template

Publication-quality volcano plot template for differential expression analysis. Supports RNA-seq (DESeq2, edgeR), proteomics, and ATAC-seq data. Includes FDR threshold line, fold-change cutoffs, gene labels, and color coding — ready for Nature, Cell, and Science.

Use this template →

Template specifications

Chart type

Volcano (scatter)

X-axis

Log₂ fold change

Y-axis

−log₁₀(adjusted p-value)

FDR threshold

0.05 (configurable)

Fold-change cutoff

|L2FC| > 1 (configurable)

Color coding

Up (red), Down (blue), NS (gray)

Gene labels

Top hits by −log₁₀(p) via ggrepel

Export

TIFF 300–1200 DPI / PDF

Journal width

89 mm (Nature) / 85 mm (Cell)

How to use the volcano plot template

  1. 01

    Prepare your data

    Export your DESeq2, edgeR, or limma results as CSV. You need columns for: gene name, log₂ fold change, and adjusted p-value (FDR).

  2. 02

    Paste into FigureGuild

    Open the Graph Builder and select "Volcano Plot". Paste or upload your CSV. Map the gene, L2FC, and padj columns.

  3. 03

    Set thresholds

    Adjust FDR cutoff (default: 0.05) and fold-change cutoff (default: |L2FC| > 1). The plot updates instantly.

  4. 04

    Label key genes

    Select genes to label. FigureGuild positions labels without overlap automatically.

  5. 05

    Select journal and export

    Choose your target journal (Nature, Cell, etc.) and export as TIFF at 1200 DPI or PDF.

FAQ

What input data format does the volcano plot template accept?

CSV or TSV with columns for feature identifier (gene/protein), log₂ fold change, and adjusted p-value. DESeq2, edgeR, and limma output can be pasted directly.

Should I use nominal or adjusted p-value?

Always use adjusted p-value (FDR/q-value) on the y-axis. Using nominal p-values overstates the number of significant hits. FigureGuild defaults to adjusted p-value and labels the axis accordingly.

Can I change the color palette?

Yes. The default palette (coral for upregulated, blue for downregulated, gray for NS) can be customized to match your paper's color scheme.

Read the full guide: How to create a volcano plot for publication

Build your volcano plot

Paste your differential expression data and export in 2 minutes.

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