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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
)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.