Venn diagram

Misc

• 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.
• Visualization biological data using proportional venn diagrams
• VENN DIAGRAM WITH R OR RSTUDIO: A MILLION WAYS

• 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

Online tools

• https://molbiotools.com/listcompare.php
• https://www.interactivenn.net/
• https://www.deepvenn.com/.
  • Proportional Circles
  • Labels (eg "Set A") can be moved outside manually if we click "Draw as SVG"
  • It has a 4 built-in examples (near the bottom)

UpSet plot

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

VennDiagram*

• VennDiagram. As good as the "venn" package. Many reverse imports and suggests.
• Venn Diagram with R or RStudio: A Million Ways. Question: why the sets orders are changed?
• Example from the help

  grid.newpage()
  grid.draw(venn.diagram(list(A = 1:150, B = 121:170), NULL) ) # no colors (BW), circle size proportional to size
  
  list1 <- paste0("A", 1:30)
  list2 <- c(paste0("A", 15:35), paste0("B", 1:10))
  list3 <- c(paste0("A", 10:20), paste0("B", 5:15), paste0("C", 1:10))
  grid.newpage()
  grid.draw(venn.diagram(list(A = list1, B = list2, C=list3), NULL, 
                          category.names = c("Set 1" , "Set 2 ", "Set 3"), 
                          fill = c("#0073C2FF", "#CD534CFF", "#EFC000FF"),
                         alpha = .8, 
                         col = "transparent"  # no border
             ) )  # 3 circles same size

• 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.

venn

• venn package (best so far)
  • polygon() function call.
• Introduction to the venn Package in R (6 Examples) | How to Draw Up to 7 Sets

library(venn)
set.seed(12345)
x <- list(First = 1:40, Second = 15:60, Third = sample(25:50, 25), 
          Fourth=sample(15:65, 35))
venn(x, ilabels = "counts", zcolor = "style", ilcs = 1.2, sncs = 1)

In this example, ilcs and sncs will control the font size of the intersection labels and set names, respectively.

ggVennDiagram

https://cloud.r-project.org/web/packages/ggVennDiagram/index.html, github.

# Install if needed
install.packages("ggVennDiagram")
library(ggVennDiagram)
library(ggplot2)

# Define your sets
genes <- list(
  GroupA = c("gene1", "gene2", "gene3", "gene4", "gene5"),
  GroupB = c("gene3", "gene4", "gene6", "gene7"),
  GroupC = c("gene4", "gene5", "gene7", "gene8", "gene9")
)

# Basic plot
ggVennDiagram(genes) +
  scale_fill_gradient(low = "#F4FAFE", high = "#08519C") +
  theme(legend.position = "none")

# Save publication-ready figure
ggsave("venn_diagram.pdf", width = 6, height = 5, dpi = 300)
ggsave("venn_diagram.png", width = 6, height = 5, dpi = 300)

ggvenn

• ggvenn package
• RNA-seq Analysis in R

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

Cons: The generated plot looks good. But the locations of set labels are weird and not adjustable.

gplots

black and white?

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

Vennerable

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")
  

limma

• https://rdrr.io/bioc/limma/man/venn.html
• User guide. Only black and white.

eulerr

• eulerr package
• The circle sizes are proportional to the list sizes. However, the diagram can look very weird sometimes.
• For some reason, if I use png() to save the plot, it works in the interactive mode, but not when I try to render a Rmd file.