How to Make a Volcano Plot (and Read One)
A volcano plot shows thousands of genes, proteins or metabolites at once. Each point is one feature: the x-axis is the size of the change and the y-axis is how significant it is.
The axes
- x-axis: log2 fold change. 0 means no change, +1 means doubled, −1 means halved.
- y-axis: −log10 p-value (or adjusted p-value). Higher means more significant; p = 0.05 sits at about 1.3, p = 0.001 at 3.
Data you need
A table with one row per feature and at least three columns: name, log2 fold change and p-value (ideally the adjusted p-value / FDR from your differential-expression tool, such as DESeq2 or limma).
Choosing cut-offs
Common choices are |log2 FC| > 1 and adjusted p < 0.05. Draw them as dashed lines, colour the significant up- and down-regulated points, and leave the rest grey. State the cut-offs in the legend and report how many features pass each one.
Making it readable
- Use colour-blind safe colours (for example orange for up, blue for down).
- Label only the top few features, and keep labels from overlapping.
- Use small points with no outline so dense areas do not turn into a blob.
Upload your CSV to the Volcano Plot Generator and describe the cut-offs; you get a journal-style plot plus the Python code that made it.
Make your figure nowDescribe it or upload a sketch. Free to start.
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