multi_venn: Multiple Venn diagrams

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

Multiple Venn diagrams

Description

Plot multiple Venn diagrams using output from ezlimma package. Each is a page in a PDF, and a single table with all results is invisibly returned.

Usage

multi_venn(
  tab,
  prefix.lst,
  p.cutoff = NULL,
  fdr.cutoff = NULL,
  logfc.cutoff = NULL,
  circle.names.lst = prefix.lst,
  main.v = "",
  name = "multi",
  cex = c(1, 1, 1)
)

Arguments

tab	Table of output from ezlimma.
prefix.lst	A list of prefix.v vectors passed to ezvenn.
p.cutoff	p-value cutoff to threshold features in tab. p-values < p.cutoff are significant.
fdr.cutoff	FDR cutoff to threshold features in tab. FDRs < fdr.cutoff are significant.
logfc.cutoff	log fold-change cutoff to threshold features in tab, when tab came from limma_contrasts.
circle.names.lst	List of length length(prefix.lst), where each element is a circle.names vector. Passed to ezvenn.
main.v	Vector of names of length length(prefix.lst).
name	Name of file to create. Set to NA to plot to screen instead of to file.
cex	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. See par.

Details

One of fdr.cutoff or p.cutoff must be given. If both are given, only fdr.cutoff is used. logfc.cutoff if given is used in addition to these.

"_venn.pdf" is appended to name.

If main.v=="" and names(prefix.lst) is not NULL, main.v is assigned names(prefix.lst).

Value

Invisibly, a matrix with elements -1, 0, 1 indicating which features (rows) of tab were significant with specified cutoffs. 0 indicates no significant change; -1 indicates down; and 1 indicates up if corresponding logFC columns are found, otherwise 1 indicates significance.

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