Creating a Volcano Plot

Introduction

Here we will create a volcano plot from differential expression results.

A volcano plot is a type of scatter plot commonly used in RNA-Seq analysis to examine genes that may demonstrate biological significance. Log-fold change in expression is plotted on the x-axis and statistical significance is plotted on the y-axis. Learn more about Volcano plots here.

Note: In the following plot, labels are Ensembl IDs. For a more useful figure, consider adding an annotation step.

Create a Volcano Plot from DESeq2 differential expression results

Load the libraries

library(EnhancedVolcano)

Warning: package 'EnhancedVolcano' was built under R version 4.5.2

Loading required package: ggplot2

Warning: package 'ggplot2' was built under R version 4.5.2

Loading required package: ggrepel

library(dplyr)

Warning: package 'dplyr' was built under R version 4.5.2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Load the data from command line arguments

The data were filtered to remove adjusted p-values that were NA; these were genes excluded by DESeq2 as a part of independent filtering.

data<-read.csv("deseq2_DEGs.csv",row.names=1) %>% filter(!is.na(padj))

Plot

Create label subsets for plotting.

labs<-head(row.names(data),5)

Figure 1 allows us to identify which genes are statistically significant with large fold changes.

EnhancedVolcano(data,
                title = "Enhanced Volcano with Airways",
                lab = rownames(data),
                selectLab=labs,
                labSize=3,
                drawConnectors = TRUE,
                x = 'log2FoldChange',
                y = 'padj')   

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the EnhancedVolcano package.
  Please report the issue to the authors.

Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the EnhancedVolcano package.
  Please report the issue to the authors.