ezvolcano: Volcano plot

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Volcano plot

Description

Volcano plot in ggplot2 using output from ezlimma package, e.g. limma_contrasts. The logFC and significance columns are supplied by the user, or inferred from the supplied comparison, e.g. if comparison="AvsB", ezvolcano expects column names AvsB.logFC and, depending on type.sig, AvsB.p or AvsB.FDR.

Usage

ezvolcano(
  tab,
  lfc.col = NA,
  sig.col = NA,
  lab.col = "Gene.Symbol",
  ntop.sig = 0,
  ntop.lfc = 0,
  comparison = NULL,
  alpha = 0.4,
  name = "volcano",
  ann.rnames = NULL,
  up.ann.color = "black",
  down.ann.color = "black",
  shape = 19,
  x.bound = NULL,
  y.bound = NULL,
  type.sig = c("p", "FDR"),
  cut.color = "black",
  cut.lfc = 1,
  cut.sig = 0.05,
  lines.sig = NA,
  raster = FALSE,
  sep = ".",
  na.lab = c("---", ""),
  seed = 0,
  plot = TRUE
)

Arguments

tab	Table of output from ezlimma.
lfc.col	Column name or index of tab with logFC. Some features should be > 0 and others < 0.
sig.col	Column name or index of tab with p-values or FDRs.
lab.col	Column name or index of tab with labels, such as gene symbol, annotating features. If NULL, no points are annotated.
ntop.sig	Number of top significant features to annotate.
ntop.lfc	Number of top logFC features to annotate.
comparison	Name of contrast to plot. If given, it's assumed that lfc.col=paste0(comparison, '.logFC') and sig.col=paste0(comparison, '.p') or paste0(comparison, '.FDR'), and these are over-ridden.
alpha	Transparency for non-annotated points, passed to geom_point.
name	Name of file to create. Set to NA to plot to screen instead of to file.
ann.rnames	Character vector of additional rownames of tab to annotate; elements must be in rownames(tab).
up.ann.color	Color for annotated points that are upregulated (logFC>0).
down.ann.color	Color for annotated points that are downregulated (logFC<0).
shape	Shape of non-annotated dots. Set to 1 for empty dots.
x.bound	x-axis limits are set to c(-x.bound, x.bound). If NULL, x.bound=max(abs(tab[,lfc.col])).
y.bound	y-axis limits are set to c(0, y.bound). If NULL, y.bound=max(tab[,'nlg10sig']).
type.sig	Type of significance y-axis should use, either "p" or "FDR".
cut.color	Color of points that meet both cut.lfc and cut.sig but are not labeled.
cut.lfc	Points need to have |logFC| >= cut.lfc to have cut.color.
cut.sig	Points need to have significance tab[,sig.col] <= cut.sig to have cut.color.
lines.sig	Numeric vector of values of sig.type at which to draw lines. For example, if type.sig="p", you may want to set lines.sig = 0.05, which will draw a line at y = -log10(0.05).
raster	Rasterize points using ggrastr so plot is lighter.
sep	Separator string between contrast names and suffix such as logFC.
na.lab	Character vector of labels in lab.col to treat as missing, in addition to NA.
seed	Numeric seed for reproducibility since ggrepel uses a random algorithm.
plot	Logical; should plot be generated?

Details

If ntop.sig>0 or ntop.lfc>0, then lab.col must be in colnames(tab). For annotated points, up.ann.color & down.ann.color dominate cut.color.

Value

Invisibly, a ggplot object.

See Also

multi_volcano

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.