Venn diagram

• 2014 Paper eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses which includes an overview of several tools. The paper is linked from the website https://upset.app.
• eulerr package
• Visualization biological data using proportional venn diagrams
• VENN DIAGRAM WITH R OR RSTUDIO: A MILLION WAYS
• limma http://www.ats.ucla.edu/stat/r/faq/venn.htm - only black and white only?

• gplots package (black and white?)

  gplots::venn(list(A = 1:150, B = 121:170, C=141:200))
  

• VennDiagram - input has to be the numbers instead of the original vector?
  • Example from the help

    grid.newpage()
    grid.draw(venn.diagram(list(A = 1:150, B = 121:170), NULL) )
    grid.newpage()
    grid.draw(venn.diagram(list(A = 1:150, B = 121:170, C=141:200), NULL, 
                            category.names = c("Set 1" , "Set 2 ", "Set 3"), 
                            fill = c("#0073C2FF", "#CD534CFF", "#EFC000FF")) ) # weird
    

  • VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. scaling is one option.
  • https://www.r-graph-gallery.com/venn-diagram.html
  • And a trick to make scaling works.
• ggvenn package (best so far)

  library(ggvenn)
  ggvenn(list(A = 1:150, B = 121:170, C=141:200), 
           fill_color = c("#0073C2FF", "#CD534CFF", "#EFC000FF")) # looks normal

• Vennerable package https://github.com/js229/Vennerable
  • Make Venn Diagram in R with Correctly Weighted Areas
  • Venn Diagrams with R

    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install("graph")
    BiocManager::install("RBGL") # fail on Rstudio cloud
    install.packages("Vennerable", repos="http://R-Forge.R-project.org")
    

• venn package

• http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Venn-Diagrams and the R code or the Bioc package systemPipeR

  # systemPipeR package method
  library(systemPipeR)
  setlist <- list(A=sample(letters, 18), B=sample(letters, 16), C=sample(letters, 20), D=sample(letters, 22), E=sample(letters, 18)) 
  OLlist <- overLapper(setlist[1:3], type="vennsets")
  vennPlot(list(OLlist))                             
  
  # R script source method
  source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/overLapper.R") 
  setlist <- list(A=sample(letters, 18), B=sample(letters, 16), C=sample(letters, 20), D=sample(letters, 22), E=sample(letters, 18)) 
  # or (obtained by dput(setlist))
  setlist <- structure(list(A = c("o", "h", "u", "p", "i", "s", "a", "w", 
  "b", "z", "n", "c", "k", "j", "y", "m", "t", "q"), B = c("h", 
  "r", "x", "y", "b", "t", "d", "o", "m", "q", "g", "v", "c", "u", 
  "f", "z"), C = c("b", "e", "t", "u", "s", "j", "o", "k", "d", 
  "l", "g", "i", "w", "n", "p", "a", "y", "x", "m", "z"), D = c("f", 
  "g", "b", "k", "j", "m", "e", "q", "i", "d", "o", "l", "c", "t", 
  "x", "r", "s", "u", "w", "a", "z", "n"), E = c("u", "w", "o", 
  "k", "n", "h", "p", "z", "l", "m", "r", "d", "q", "s", "x", "b", 
  "v", "t"), F = c("o", "j", "r", "c", "l", "l", "u", "b", "f", 
  "d", "u", "m", "y", "t", "y", "s", "a", "g", "t", "m", "x", "m"
  )), .Names = c("A", "B", "C", "D", "E", "F"))
  
  OLlist <- overLapper(setlist[1:3], type="vennsets")
  counts <- list(sapply(OLlist$Venn_List, length))  
  vennPlot(counts=counts)                           
  

  File:Vennplot.png

UpSet plot

• https://upset.app/
• UpSetR
• ComplexUpset: Create Complex UpSet Plots Using 'ggplot2' Components
• Chapter 8 UpSet plot