vennplot: Venn diagram with VennDiagram

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

Venn diagram with VennDiagram

Description

Venn diagram with VennDiagram

Usage

vennplot(
  input.ls,
  palette.vc = RColorBrewer::brewer.pal(9, "Set1")[1:5],
  title.c = NA,
  sub.c = "",
  cat_pos.vi = NA,
  label_col.c = "black",
  lwd.i = 2,
  inverted.l = FALSE,
  figure.c = "none"
)

Arguments

input.ls	Named list of vectors to be compared
palette.vc	Character vector: Color palette
title.c	Character: Plot title
sub.c	Character: Plot subtitle
cat_pos.vi	Integer vector giving the position (in degrees) of each category name along the circle, with 0 at 12 o'clock; if NA, (-50, 50), (-40, 40, 180), (-15, 15, 0, 0), and (0, 287.5, 215, 145, 70) values are used
label_col.c	Character: Label color
lwd.i	Integer: Width of the circle's circumference
inverted.l	Logical: Should the Venn diagram be flipped along its vertical axis (pairwise venn only)
figure.c	Character: Filename for image output (with either .tiff, .png, or .svg extensions); if 'none' (default) the grid object is displayed interactively

Value

invisible grid object

Examples

sacurine.eset <- phenomis::reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
sacurine.eset <- phenomis::correcting(sacurine.eset, figure.c = 'none')
sacurine.eset <- sacurine.eset[, Biobase::pData(sacurine.eset)[, "sampleType"] != "pool"]
sacurine.eset <- phenomis::transforming(sacurine.eset)
sacurine.eset <- sacurine.eset[, Biobase::sampleNames(sacurine.eset) != "HU_neg_096_b2"]
# Student's T test
sacurine.eset <- phenomis::hypotesting(sacurine.eset, "ttest", "gender")
# Wilcoxon T test
sacurine.eset <- phenomis::hypotesting(sacurine.eset, "wilcoxon", "gender")
signif.ls <- list(ttest = which(Biobase::fData(sacurine.eset)[, "ttest_gender_Female.Male_signif"] > 0),
wilcoxon =  which(Biobase::fData(sacurine.eset)[, "wilcoxon_gender_Female.Male_signif"] > 0))
vennplot(signif.ls, label_col.c = "black", title.c = "Signif. features\nwith Student or Wilcoxon tests")

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.