ggvolcano {ggvolcano} | R Documentation |
Creates a volcano plot to visualize differential expression results. This function is highly configurable to suit publication standards.
ggvolcano(
data,
labels = "",
logFC_col,
pval_col,
x_limits = c(min(data[[logFC_col]], na.rm = TRUE) - 1.5, max(data[[logFC_col]], na.rm =
TRUE) + 1.5),
y_limits = c(0, max(-log10(data[[pval_col]]), na.rm = TRUE) + 5),
xlab = bquote(~Log[2] ~ "fold change"),
ylab = bquote(~-Log[10] ~ italic(P)),
title = "Volcano plot",
subtitle = "",
caption = paste0("total = ", nrow(data), " variables"),
pval_cutoff = 1e-06,
logFC_cutoff = 1,
cutoff_line = list(type = "longdash", color = "black", width = 0.4),
point_aes = list(size = 1.5, shape = c(19, 19, 19, 19), color = c("grey30", "#00CD6C",
"#009ADE", "#FF1F5B"), alpha = 0.9),
label_aes = list(size = 2.5, color = "black", face = "plain", parse = FALSE),
legend_aes = list(labels = c("NS", expression(Log[2] ~ FC), "p-value", expression(p -
value ~ and ~ log[2] ~ FC)), position = "right", label_size = 14, icon_size = 5),
shade_options = NULL,
connector_aes = list(line_width = 0.5, arrow_type = "closed", arrow_ends = "first",
arrow_length = unit(0.01, "npc"), line_color = "grey10", direction = "both",
draw_arrowheads = TRUE),
gridlines = list(major = TRUE, minor = TRUE),
plot_border = "partial",
border_width = 0.8,
border_color = "black",
horizontal_line = NULL,
horizontal_line_aes = list(type = "longdash", color = "black", width = 0.4)
)
data |
A data frame containing test statistics. Requires at least columns for variable names, log2 fold changes, and p-values. |
labels |
Column name or row names for variable names. |
logFC_col |
Column name for log2 fold changes. |
pval_col |
Column name for nominal or adjusted p-values. |
x_limits |
Limits of the x-axis (default auto-calculated). |
y_limits |
Limits of the y-axis (default auto-calculated). |
xlab |
X-axis label. |
ylab |
Y-axis label. |
title |
Plot title. |
subtitle |
Plot subtitle. |
caption |
Plot caption. |
pval_cutoff |
P-value cutoff for significance. |
logFC_cutoff |
Log2 fold-change cutoff for significance. |
cutoff_line |
List of options for cutoff lines ('type', 'color', 'width'). |
point_aes |
List of aesthetic options for points ('size', 'shape', 'color', 'alpha'). |
label_aes |
List of aesthetic options for labels ('size', 'color', 'face', 'parse'). |
legend_aes |
List of aesthetic options for legend ('labels', 'position', 'label_size', 'icon_size'). |
shade_options |
List of options for shading regions in the plot. |
connector_aes |
List of aesthetic options for connectors ('line_width', 'arrow_type', 'arrow_ends', 'arrow_length', 'line_color', 'direction', 'draw_arrowheads'). |
gridlines |
List with logical values indicating whether to draw gridlines ('major', 'minor'). |
plot_border |
Add a border for plot axes ('"partial"' or '"full"'). |
border_width |
Width of the border. |
border_color |
Color of the border. |
horizontal_line |
Numeric value(s) for drawing horizontal line(s). |
horizontal_line_aes |
List of aesthetic options for the horizontal line(s) ('type', 'color', 'width'). |
A ggplot2
object representing the volcano plot.
data <- read.csv(system.file("extdata", "example.csv", package = "ggvolcano"))
ggvolcano(data,
logFC_col = "log2FoldChange",
pval_col = "pvalue",
pval_cutoff = 10e-4,
logFC_cutoff = 1.5,
x_limits = c(-5.5, 5.5),
y_limits = c(0, -log10(10e-12)),
title = "Example Volcano plot",
caption = "FC cutoff, 1.5; p-value cutoff, 10e-4",
gridlines = list(major = TRUE, minor = TRUE),
horizontal_line = 10e-8, # Draw horizontal line for p-value cutoff
horizontal_line_aes = list(type = "dashed", color = "red", width = 0.5)
)