Volcano Plot Maker
Paste gene, log2 fold change and p-value to get a labeled volcano plot.
Paste three columns: gene, log2 fold change and p-value or adjusted p-value, for example from DESeq2, edgeR or limma. Set the fold change and p cutoffs and the tool colors genes as up, down or not significant, labels the most significant genes and counts each group. Download the plot as SVG or PNG and copy the up and down gene lists.
Free, runs in your browser. Nothing you enter is uploaded.
What you get
- Volcano plot with cutoff lines
- Up, down and not significant counts
- Labels for the top N genes
- Copyable up and down gene lists
- SVG and PNG download
Questions
What is a volcano plot?
A scatter plot of log2 fold change on the x axis against minus log10 p-value on the y axis. Genes that change a lot and are highly significant sit in the upper left and upper right corners.
What cutoffs should I use for a volcano plot?
A common choice is an absolute log2 fold change of at least 1, which is a twofold change, and an adjusted p-value below 0.05. Stricter studies use 0.01. Report the cutoffs in the figure legend.
Should I use p-value or adjusted p-value?
Use the adjusted p-value, such as the Benjamini-Hochberg padj from DESeq2, to decide significance. Raw p-values do not account for testing thousands of genes and give many false positives.
How do I make a volcano plot from DESeq2 output?
Export the results table and keep three columns in this order: gene name, log2FoldChange and padj. Paste them here. Rows with NA values are skipped and counted.
Why are some p-values plotted at the top edge?
A p-value reported as exactly 0 has an infinite minus log10 value. Those genes are plotted at the smallest nonzero p-value in your data so they stay visible.
More Data Visualization
All free tools · By Dr. Zubair Khalid, DVM, MS, PhD.