multi_volcano: Multiple volcano plots

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

Multiple volcano plots

Description

Multiple volcano plots, where one or more comparisons are inferred from columns of tab e.g. AvsB.logFC, and each comparison is plotted with ezvolcano.

Usage

multi_volcano(
  tab,
  lab.col = "Gene.Symbol",
  ntop.sig = 0,
  ntop.lfc = 0,
  alpha = 0.4,
  name = "volcanoes",
  ann.rnames = NULL,
  up.ann.color = "black",
  down.ann.color = "black",
  same.scale = FALSE,
  type.sig = c("p", "FDR"),
  cut.color = "black",
  cut.lfc = 1,
  cut.sig = 0.05,
  lines.sig = ifelse(type.sig[1] == "p", yes = 0.05, no = NA),
  raster = FALSE,
  sep = ".",
  na.lab = c("---", ""),
  seed = 0,
  plot = TRUE
)

Arguments

tab	Table of output from ezlimma.
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.
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).
same.scale	Logical, should axes' scales be the same for the different plots?
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

Uses colnames(tab) that have suffix logFC to infer comparisons.

Value

Invisibly, a list of ggplot objects from ezvolcano.

See Also

ezvolcano

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