The goal of ggvolcano is to provide a flexible and customizable solution for generating publication-ready volcano plots in R. It simplifies the process of visualizing differential expression results from analyses like RNA-seq, making it easier to communicate key findings.
You can install the development version of ggvolcano from GitHub using the following commands:
# Install devtools if you haven't already
install.packages("devtools")This is a basic example showing how to create a volcano plot using the ggvolcano package:
# Load the package
library(ggvolcano)
# Load example data
data <- read.csv(system.file("extdata", "example.csv", package = "ggvolcano"))
# Create a volcano plot
ggvolcano(data,
logFC_col = "log2FoldChange", # Column containing log2 fold changes
pval_col = "pvalue", # Column containing p-values
pval_cutoff = 10e-4, # Cutoff for significance in p-values
logFC_cutoff = 1.5, # Cutoff for significance in fold change
x_limits = c(-5.5, 5.5), # X-axis limits
y_limits = c(0, -log10(10e-12)), # Y-axis limits
title = "Example Volcano plot", # Title of the plot
caption = "FC cutoff, 1.5; p-value cutoff, 10e-4", # Caption of the plot
legend_aes = list(position = "right"), # Position legend on the right
gridlines = list(major = TRUE, minor = TRUE), # Show major and minor gridlines
horizontal_line = 10e-8, # Draw a horizontal line at this p-value cutoff
horizontal_line_aes = list(type = "dashed", color = "red", width = 0.5) # Aesthetics for horizontal line
)