volcanoPlot: Create a volcano plot

In henna: A Versatile Visualization Suite

Create a volcano plot

Description

This function creates a volcano plot for a data frame with a log column and a p-value column. The gene names must be provided as row names.

Usage

volcanoPlot(
  df,
  title = NULL,
  logCol = "avg_log2FC",
  pvalCol = "p_val_adj",
  xLab = expression(log[2] ~ fold ~ change),
  yLab = expression(-log[10] ~ `p-value`),
  legendTitle = "Significance",
  legendLabs = c("Not significant", expression(log[2] ~ FC), "p-value",
    expression(`p-value` ~ and ~ log[2] ~ FC)),
  legendPos = c("right", "top", "left", "bottom"),
  logFCThr = 1,
  pvalThr = 1e-05,
  labeledGenes = NULL,
  labelOutside = FALSE,
  labLogFCThr = 1.8,
  labPvalThr = 1e-12,
  labelType = c("boxed", "free"),
  labelSize = 2.2,
  labelColor = "black",
  labelRepulsion = 1,
  labelPull = 0,
  maxOverlaps = 100,
  boxPadding = 0.2,
  labelPadding = 0.1,
  labelSegWidth = 0.4,
  pointSize = 0.8,
  alpha = 0.6,
  palette = c("gray31", "goldenrod2", "orchid3", "red2"),
  legendTextSize = 10,
  legendTitleSize = 10,
  axisTextSize = 12,
  axisTitleSize = 12,
  theme = c("minimal", "bw", "classic", "linedraw"),
  ...
)

Arguments

df	A data frame with rownames as genes, a log column and a p-value column.
title	Plot title.
logCol	Log column.
pvalCol	P-value column.
xLab	x axis label.
yLab	y axis label.
legendTitle	Legend title.
legendLabs	Legend labels.
legendPos	Legend position.
logFCThr	Threshold used to separate significant log values.
pvalThr	Threshold used to separate significant p-values.
labeledGenes	Gene labels to be displayed on the plot. Default is NULL, entailing that gene labels will be displayed on the basis of labLogFCThr and labPvalThr, if at least one of them is not NULL.
labelOutside	Display labels for points specified by labeledGenes even if they fall outside the boundaries imposed by labLogFCThr and labPvalThr. Ignored if labeledGenes is NULL or both labLogFCThr and labPvalThr are NULL.
labLogFCThr	Threshold used to plot gene labels based on log values. Ignored if labeledGenes is not NULL.
labPvalThr	Threshold used to plot gene labels based on p-values. Ignored if labeledGenes is not NULL.
labelType	Whether to draw a box around labels (option 'boxed') or not (option 'free'). Default is 'free'.
labelSize	Label size.
labelColor	Label color.
labelRepulsion	Repulsion strength between labels.
labelPull	Attraction strength between a text label and its data point.
maxOverlaps	Maximum number of allowed overlaps.
boxPadding	Amount of padding around box.
labelPadding	Amount of padding around label.
labelSegWidth	Thickness of segment connecting label to point.
pointSize	Point size.
alpha	Opaqueness level of point color.
palette	Color palette.
legendTextSize	Legend text size.
legendTitleSize	Legend title size.
axisTextSize	Axis text size.
axisTitleSize	Axis title size.
theme	Plot theme. Choose between 'bw', 'classic', 'linedraw' and 'minimal'. Default is 'minimal'.
...	Additional arguments passed to EnhancedVolcano::EnhancedVolcano.

Details

Users can input labeled genes in two ways:

1) By using p-value and log fold-change thresholds (the default option).

2) By inputting a list of labels.

Value

An object of class gg.

Examples

if (requireNamespace("EnhancedVolcano", quietly=TRUE)){
filePath <- system.file('extdata', 'volcanoPlot.qs2', package='henna')
df <- qs2::qs_read(filePath)
p <- volcanoPlot(df, title='Volcano plot - beta cells', pvalThr=1e-10,
logFCThr=1,
labPvalThr=1e-150,
labLogFCThr=5.3)
}

henna documentation built on Feb. 17, 2026, 9:08 a.m.