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How do I plot fold change against significance?

Make a volcano plot

Turning a differential expression table into a labelled figure.

A volcano plot puts log2 fold change on the x-axis and −log10 of the adjusted p-value on the y. The statistics come from your differential expression analysis; the plot is only presentation, so the tool that draws it does not need to be the tool that computed it.

Choose thresholds before you look at the plot and state them in the legend. Label the genes that matter to the argument rather than everything that clears the cut-off.

What to use

If you script

Command-line and library options. No page here — they need an environment rather than a browser.

Drafted from the literature and not yet reviewed by a specialist. Treat it as a starting point, and tell us if something here is wrong. Last touched .

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