---
title: "Using ggvolcano for Publication-Ready Volcano Plots"
author: "Yaoxiang Li"
date: "2017-01-05"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Using ggvolcano for Publication-Ready Volcano Plots}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(ggplot2)
library(grid)
library(ggvolcano)
```
# Introduction
This vignette demonstrates various ways to create and customize volcano plots using the `ggvolcano` function. Each example below highlights different aspects of customization—from basic plotting to modifying point aesthetics, labels, gridlines, and legends—to produce publication-ready plots.
## Example 1: Basic Volcano Plot
Load the example data and create a basic volcano plot with default aesthetics and thresholds.
```{r example-1, fig.width=7.2, fig.height=5}
data <- read.csv(system.file("extdata", "example.csv", package = "ggvolcano"))
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-6,
logFC_cutoff = 1.0,
title = "Basic Volcano Plot",
caption = paste("Total variables:", nrow(data)))
```
## Example 2: Volcano Plot with Custom Point Aesthetics
Customize point shapes, colors, and sizes for a distinct visual style.
```{r example-2, fig.width=7.2, fig.height=5}
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-4,
logFC_cutoff = 1.5,
title = "Custom Points Volcano Plot",
caption = "Customized point shapes and colors",
point_aes = list(
size = 2,
shape = c(16, 17, 18, 19), # Different shapes for NS, FC, P, and FC_P
color = c("lightgrey", "blue", "green", "red"),
alpha = 0.8
))
```
## Example 3: Volcano Plot with Color Gradient
Apply a color gradient to the points to represent the range of p-values.
```{r example-3, fig.width=7.2, fig.height=5}
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-6,
logFC_cutoff = 1.0,
title = "Volcano Plot with Color Gradient",
caption = "Color gradient represents the range of p-values",
point_aes = list(
size = 2,
shape = c(16, 17, 18, 19),
alpha = 0.85,
# Activate the color gradient by specifying two colors and associated options:
color_gradient = c("yellow", "red"),
color_gradient_limits = c(min(data$pvalue, na.rm = TRUE), max(data$pvalue, na.rm = TRUE)),
color_gradient_breaks = seq(min(data$pvalue, na.rm = TRUE), max(data$pvalue, na.rm = TRUE), length.out = 5),
color_gradient_labels = round(seq(min(data$pvalue, na.rm = TRUE), max(data$pvalue, na.rm = TRUE), length.out = 5), 3)
))
```
## Example 4: Volcano Plot with Custom Labels and Connectors
Add custom labels (using column X) and connectors to highlight selected points.
```{r example-4, fig.width=7.2, fig.height=5}
ggvolcano(data,
labels = data$X, # Use the column 'X' for labels
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-6,
logFC_cutoff = 2.0,
xlab = "Log2 Fold Change", # Custom x-axis label
ylab = "-Log10(p-value)", # Custom y-axis label
title = "Enhanced Volcano Plot with Labels and Connectors",
subtitle = "Differential Expression Analysis",
caption = "p-value gradient: yellow (low) to red (high)",
point_aes = list(
size = 1.5,
shape = c(16, 17, 18, 19),
alpha = 0.9,
color_gradient = c("blue", "red"),
color_gradient_limits = c(min(data$pvalue, na.rm = TRUE),
max(data$pvalue, na.rm = TRUE)),
color_gradient_breaks = seq(min(data$pvalue, na.rm = TRUE),
max(data$pvalue, na.rm = TRUE),
length.out = 5),
color_gradient_labels = round(seq(min(data$pvalue, na.rm = TRUE),
max(data$pvalue, na.rm = TRUE),
length.out = 5), 3)
))
```
## Example 5: Volcano Plot with Custom Gridlines and Full Border
Customize the gridlines and add a full border to the plot.
```{r example-5, fig.width=7.2, fig.height=5}
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-4,
logFC_cutoff = 1.5,
title = "Volcano Plot with Custom Gridlines & Border",
caption = "Major gridlines only; full border in blue",
gridlines = list(major = TRUE, minor = FALSE),
plot_border = "full",
border_width = 1.0,
border_color = "blue")
```
## Example 6: Volcano Plot with an Additional Horizontal Line
Add an extra horizontal reference line at a custom p-value threshold.
```{r example-6, fig.width=7.2, fig.height=5}
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 0.05,
logFC_cutoff = 1.0,
title = "Volcano Plot with Reference Line",
caption = "Extra horizontal line",
horizontal_line = 1e-9,
horizontal_line_aes = list(type = "dotted", color = "purple", width = 1))
```
## Example 7: Volcano Plot with Custom Axis Labels and Subtitle
Customize the axis labels and add a subtitle for additional context.
```{r example-7, fig.width=7.2, fig.height=5}
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-6,
logFC_cutoff = 1.0,
xlab = "Log2 Fold Change",
ylab = "-Log10(p-value)",
title = "Volcano Plot with Custom Axes",
subtitle = "Differential Expression Analysis",
caption = "Customized axis labels and subtitle")
```
## Example 8: Volcano Plot with a Custom Legend
Modify the legend labels and position for clarity.
```{r example-8, fig.width=7.2, fig.height=6}
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 1e-4,
logFC_cutoff = 1.5,
title = "Volcano Plot with Custom Legend",
caption = "Legend labels and position modified",
legend_aes = list(
labels = c("Non-sig", "FC Sig", "P-value Sig", "Both Sig"),
position = "bottom",
label_size = 12,
icon_size = 6
))
```