Enhanced volcano plot (deprecated wrapper)

custom_enhanced_volcano() is retained for existing scripts. It forwards the commonly used arguments to volcano_plot(), and ignores the rest with a warning. New code should call volcano_plot() directly.

Usage

custom_enhanced_volcano(
  toptable,
  lab = rownames(toptable),
  x = "logFC",
  y = "FDR",
  selectLab = NULL,
  xlim = NULL,
  ylim = NULL,
  title = "Volcano plot",
  subtitle = NULL,
  caption = NULL,
  pCutoff = 0.05,
  FCcutoff = 0.25,
  pointSize = 3,
  labSize = 3.5,
  col = c("grey30", "forestgreen", "royalblue", "red2"),
  colCustom = NULL,
  colAlpha = 0.2,
  legendPosition = "top",
  ...
)

Arguments

toptable

Data frame with x and y columns.

lab

Point labels (defaults to the row names).

x, y

Names of the fold-change and adjusted p-value columns.

selectLab

Genes to label (all points passing both cutoffs if NULL).

xlim, ylim

Axis limits.

title, subtitle, caption

Plot annotations.

pCutoff, FCcutoff

Adjusted p-value and absolute log fold change cutoffs.

pointSize, labSize

Point and label sizes.

col

Four group colours (NS, FC, P, FC + P).

colCustom

Per-point colours (see colour_volcano_points()).

colAlpha

Point transparency.

legendPosition

Legend position.

...

Other EnhancedVolcano-style arguments, which are ignored.

Value

A ggplot object.

See also

volcano_plot()