23.2 Volcano plots with EnhancedVolcano package

Volcano plots are a type of scatter plot used to visualize significant changes in large datasets: in our use case, we can use volcano plots to highlight top differentially expressed genes.

A Volcano plots shows:

• Fold Changes on the x-axis
• P-values on the y-axis (in -log10 scale)

if (!requireNamespace('BiocManager', quietly = TRUE))
  install.packages('BiocManager')

BiocManager::install('EnhancedVolcano')

Load package:

library(EnhancedVolcano)

Use default parameters:

EnhancedVolcano(geneexp,
    lab = geneexp$GeneSymbol,
    x = 'log2FoldChange',
    y = 'padj')

Change default cutoffs:

EnhancedVolcano(geneexp,
    lab = geneexp$GeneSymbol,
    x = 'log2FoldChange',
    y = 'padj',
    pCutoff=0.1,
    FCcutoff=0.5)