Venn diagram
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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)
UpSet plot
- https://upset.app/
- UpSetR
- ComplexUpset: Create Complex UpSet Plots Using 'ggplot2' Components
- Chapter 8 UpSet plot
venn
- venn package (best so far)
- 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.
Cons: there is no way to have multiple colors for different sets.
VennDiagram
- VennDiagram. As good as the "venn" package. Many reverse imports and suggests.
- Venn Diagram with R or RStudio: A Million Ways
- 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
ggvenn package
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