Venn Diagram with R or RStudio: A Million Ways

Create a demo data

set.seed(20190708)
genes <- paste("gene",1:1000,sep="")
x <- list(
  A = sample(genes,300), 
  B = sample(genes,525), 
  C = sample(genes,440),
  D = sample(genes,350)
  )

Using the ggvenn R package

This package is a ggplot2 extension. A color can be assigned to each set.

Installation:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("yanlinlin82/ggvenn")

Usage:

library(ggvenn)
ggvenn(
  x, 
  fill_color = c("#0073C2FF", "#EFC000FF", "#868686FF", "#CD534CFF"),
  stroke_size = 0.5, set_name_size = 4
  )

Read more: Beautiful GGPlot Venn Diagram with R

Using the ggVennDiagram R package

This package is a ggplot2 extension. The ggVennDiagram package maps the fill color of each region to quantity, allowing us to visually observe the differences between different parts.

Installation:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("gaospecial/ggVennDiagram")

Usage:

library("ggVennDiagram")
ggVennDiagram(x, label_alpha = 0)

Read more: Beautiful GGPlot Venn Diagram with R

Using the VennDiagram R package

Installation:

install.packages("VennDiagram")`

Usage:

Create a Venn diagram and save it into a file. The function venn.diagram() takes a list and creates a file containing a publication-quality Venn Diagram.

library(VennDiagram)
venn.diagram(x, filename = "venn-4-dimensions.png")

Display the plot directly in R:

# Helper function to display Venn diagram
display_venn <- function(x, ...){
  library(VennDiagram)
  grid.newpage()
  venn_object <- venn.diagram(x, filename = NULL, ...)
  grid.draw(venn_object)
}

# Four dimension Venn plot
display_venn(x)

# Three dimension Venn plot
display_venn(x[1:3])

# Change category names
# Change fill color
display_venn(
  x,
  category.names = c("Set 1" , "Set 2 " , "Set 3", "Set 4"),
  fill = c("#999999", "#E69F00", "#56B4E9", "#009E73")
  )

# Further customization
display_venn(
        x,
        category.names = c("Set 1" , "Set 2 " , "Set 3", "Set 4"),
        # Circles
        lwd = 2,
        lty = 'blank',
        fill = c("#999999", "#E69F00", "#56B4E9", "#009E73"),
        # Numbers
        cex = .9,
        fontface = "italic",
        # Set names
        cat.cex = 1,
        cat.fontface = "bold",
        cat.default.pos = "outer",
        cat.dist = c(0.055, 0.055, 0.1, 0.1)
)

Using the gplots R package

Installation:

install.package("gplots")`

Usage:

library(gplots)
v.table <- venn(x)

Access to the intersection data:

print(v.table)

##      num A B C D
## 0000   0 0 0 0 0
## 0001  58 0 0 0 1
## 0010 111 0 0 1 0
## 0011  37 0 0 1 1
## 0100 144 0 1 0 0
## 0101  66 0 1 0 1
## 0110 108 0 1 1 0
## 0111  56 0 1 1 1
## 1000  50 1 0 0 0
## 1001  35 1 0 0 1
## 1010  31 1 0 1 0
## 1011  33 1 0 1 1
## 1100  46 1 1 0 0
## 1101  41 1 1 0 1
## 1110  40 1 1 1 0
## 1111  24 1 1 1 1
## attr(,"intersections")
## attr(,"intersections")$A
##  [1] "gene835" "gene910" "gene866" "gene785" "gene532" "gene385" "gene201" "gene74"  "gene941" "gene401" "gene642"
## [12] "gene299" "gene819" "gene245" "gene834" "gene700" "gene422" "gene176" "gene643" "gene852" "gene584" "gene560"
## [23] "gene638" "gene164" "gene122" "gene419" "gene521" "gene363" "gene724" "gene160" "gene988" "gene328" "gene452"
## [34] "gene236" "gene707" "gene865" "gene342" "gene165" "gene572" "gene565" "gene206" "gene663" "gene107" "gene620"
## [45] "gene917" "gene298" "gene402" "gene840" "gene992" "gene225"
## 
## attr(,"intersections")$B
##   [1] "gene129" "gene150" "gene307" "gene73"  "gene651" "gene40"  "gene722" "gene374" "gene779" "gene772"
##  [11] "gene574" "gene355" "gene970" "gene429" "gene979" "gene656" "gene208" "gene274" "gene252" "gene585"
##  [21] "gene662" "gene535" "gene709" "gene589" "gene964" "gene569" "gene113" "gene851" "gene111" "gene308"
##  [31] "gene18"  "gene309" "gene977" "gene530" "gene929" "gene720" "gene83"  "gene256" "gene217" "gene287"
##  [41] "gene596" "gene776" "gene573" "gene99"  "gene470" "gene689" "gene44"  "gene473" "gene380" "gene246"
##  [51] "gene774" "gene799" "gene621" "gene134" "gene659" "gene947" "gene322" "gene397" "gene664" "gene266"
##  [61] "gene556" "gene210" "gene272" "gene389" "gene84"  "gene771" "gene55"  "gene349" "gene51"  "gene137"
##  [71] "gene462" "gene106" "gene353" "gene801" "gene943" "gene297" "gene678" "gene546" "gene617" "gene289"
##  [81] "gene480" "gene361" "gene913" "gene875" "gene948" "gene777" "gene788" "gene743" "gene199" "gene879"
##  [91] "gene229" "gene951" "gene447" "gene175" "gene715" "gene942" "gene668" "gene698" "gene559" "gene812"
## [101] "gene52"  "gene337" "gene413" "gene757" "gene472" "gene526" "gene876" "gene567" "gene813" "gene147"
## [111] "gene685" "gene114" "gene614" "gene427" "gene508" "gene247" "gene540" "gene986" "gene241" "gene731"
## [121] "gene591" "gene279" "gene120" "gene346" "gene403" "gene333" "gene922" "gene135" "gene200" "gene603"
## [131] "gene914" "gene820" "gene492" "gene19"  "gene978" "gene804" "gene655" "gene332" "gene958" "gene903"
## [141] "gene564" "gene989" "gene386" "gene151"
## 
## attr(,"intersections")$C
##   [1] "gene169" "gene390" "gene265" "gene581" "gene250" "gene634" "gene188" "gene319" "gene994" "gene366"
##  [11] "gene213" "gene610" "gene661" "gene654" "gene453" "gene935" "gene193" "gene251" "gene243" "gene545"
##  [21] "gene178" "gene411" "gene737" "gene953" "gene902" "gene557" "gene691" "gene221" "gene920" "gene495"
##  [31] "gene474" "gene543" "gene695" "gene100" "gene686" "gene383" "gene125" "gene608" "gene278" "gene59" 
##  [41] "gene895" "gene828" "gene288" "gene611" "gene441" "gene396" "gene93"  "gene448" "gene428" "gene367"
##  [51] "gene438" "gene459" "gene579" "gene395" "gene248" "gene867" "gene45"  "gene29"  "gene437" "gene77" 
##  [61] "gene70"  "gene484" "gene633" "gene85"  "gene854" "gene490" "gene177" "gene426" "gene887" "gene550"
##  [71] "gene923" "gene792" "gene412" "gene212" "gene590" "gene292" "gene795" "gene30"  "gene159" "gene304"
##  [81] "gene471" "gene62"  "gene790" "gene28"  "gene770" "gene533" "gene575" "gene173" "gene832" "gene860"
##  [91] "gene683" "gene878" "gene818" "gene944" "gene789" "gene357" "gene391" "gene888" "gene919" "gene796"
## [101] "gene631" "gene82"  "gene733" "gene732" "gene197" "gene368" "gene909" "gene816" "gene843" "gene765"
## [111] "gene898"
## 
## attr(,"intersections")$D
##  [1] "gene738" "gene321" "gene149" "gene938" "gene487" "gene145" "gene783" "gene15"  "gene871" "gene475" "gene528"
## [12] "gene706" "gene130" "gene570" "gene43"  "gene489" "gene640" "gene161" "gene293" "gene966" "gene171" "gene498"
## [23] "gene926" "gene701" "gene632" "gene649" "gene853" "gene702" "gene869" "gene831" "gene392" "gene694" "gene271"
## [34] "gene650" "gene880" "gene906" "gene541" "gene538" "gene420" "gene140" "gene677" "gene124" "gene644" "gene233"
## [45] "gene868" "gene152" "gene800" "gene12"  "gene496" "gene39"  "gene726" "gene674" "gene226" "gene379" "gene916"
## [56] "gene602" "gene857" "gene523"
## 
## attr(,"intersections")$`A:B`
##  [1] "gene168" "gene301" "gene86"  "gene133" "gene786" "gene235" "gene209" "gene205" "gene451" "gene372" "gene794"
## [12] "gene889" "gene838" "gene604" "gene280" "gene848" "gene249" "gene965" "gene877" "gene599" "gene263" "gene607"
## [23] "gene998" "gene17"  "gene561" "gene592" "gene123" "gene186" "gene270" "gene872" "gene96"  "gene170" "gene645"
## [34] "gene817" "gene239" "gene957" "gene993" "gene222" "gene154" "gene510" "gene983" "gene476" "gene658" "gene253"
## [45] "gene773" "gene973"
## 
## attr(,"intersections")$`A:C`
##  [1] "gene393" "gene20"  "gene71"  "gene479" "gene343" "gene826" "gene56"  "gene87"  "gene8"   "gene50"  "gene115"
## [12] "gene464" "gene981" "gene760" "gene485" "gene54"  "gene255" "gene822" "gene892" "gene359" "gene325" "gene117"
## [23] "gene769" "gene805" "gene497" "gene516" "gene855" "gene488" "gene553" "gene763" "gene862"
## 
## attr(,"intersections")$`A:D`
##  [1] "gene982" "gene46"  "gene901" "gene697" "gene782" "gene635" "gene563" "gene692" "gene269" "gene657" "gene132"
## [12] "gene25"  "gene261" "gene211" "gene486" "gene710" "gene991" "gene126" "gene870" "gene121" "gene404" "gene499"
## [23] "gene945" "gene833" "gene172" "gene219" "gene830" "gene406" "gene345" "gene797" "gene444" "gene3"   "gene64" 
## [34] "gene544" "gene10" 
## 
## attr(,"intersections")$`B:C`
##   [1] "gene703"  "gene874"  "gene27"   "gene627"  "gene182"  "gene254"  "gene41"   "gene163"  "gene967" 
##  [10] "gene257"  "gene975"  "gene899"  "gene962"  "gene494"  "gene845"  "gene189"  "gene47"   "gene326" 
##  [19] "gene109"  "gene940"  "gene514"  "gene334"  "gene588"  "gene897"  "gene780"  "gene264"  "gene158" 
##  [28] "gene424"  "gene600"  "gene750"  "gene587"  "gene858"  "gene766"  "gene511"  "gene524"  "gene500" 
##  [37] "gene856"  "gene515"  "gene861"  "gene320"  "gene240"  "gene338"  "gene939"  "gene849"  "gene810" 
##  [46] "gene423"  "gene775"  "gene69"   "gene752"  "gene622"  "gene502"  "gene713"  "gene542"  "gene755" 
##  [55] "gene431"  "gene153"  "gene905"  "gene598"  "gene667"  "gene439"  "gene192"  "gene88"   "gene764" 
##  [64] "gene194"  "gene408"  "gene282"  "gene884"  "gene626"  "gene162"  "gene90"   "gene335"  "gene995" 
##  [73] "gene823"  "gene273"  "gene295"  "gene183"  "gene468"  "gene315"  "gene1000" "gene507"  "gene348" 
##  [82] "gene259"  "gene803"  "gene911"  "gene577"  "gene1"    "gene728"  "gene873"  "gene223"  "gene101" 
##  [91] "gene63"   "gene781"  "gene446"  "gene864"  "gene81"   "gene196"  "gene195"  "gene615"  "gene354" 
## [100] "gene719"  "gene954"  "gene549"  "gene23"   "gene376"  "gene613"  "gene809"  "gene606"  "gene26"  
## 
## attr(,"intersections")$`B:D`
##  [1] "gene456" "gene747" "gene839" "gene699" "gene759" "gene364" "gene230" "gene327" "gene886" "gene268" "gene14" 
## [12] "gene527" "gene260" "gene112" "gene985" "gene204" "gene681" "gene595" "gene36"  "gene128" "gene824" "gene180"
## [23] "gene352" "gene351" "gene971" "gene660" "gene7"   "gene224" "gene744" "gene609" "gene793" "gene666" "gene97" 
## [34] "gene136" "gene506" "gene285" "gene156" "gene946" "gene725" "gene102" "gene883" "gene33"  "gene387" "gene605"
## [45] "gene740" "gene339" "gene329" "gene139" "gene568" "gene432" "gene980" "gene504" "gene505" "gene517" "gene460"
## [56] "gene687" "gene629" "gene218" "gene671" "gene734" "gene375" "gene932" "gene167" "gene639" "gene407" "gene416"
## 
## attr(,"intersections")$`C:D`
##  [1] "gene399" "gene960" "gene531" "gene708" "gene323" "gene837" "gene704" "gene381" "gene95"  "gene458" "gene503"
## [12] "gene493" "gene443" "gene915" "gene281" "gene891" "gene716" "gene636" "gene220" "gene762" "gene179" "gene696"
## [23] "gene844" "gene42"  "gene314" "gene184" "gene394" "gene937" "gene896" "gene672" "gene918" "gene103" "gene324"
## [34] "gene721" "gene286" "gene141" "gene928"
## 
## attr(,"intersections")$`A:B:C`
##  [1] "gene882" "gene157" "gene49"  "gene119" "gene384" "gene5"   "gene166" "gene807" "gene586" "gene296" "gene969"
## [12] "gene231" "gene108" "gene317" "gene227" "gene934" "gene554" "gene421" "gene316" "gene418" "gene16"  "gene330"
## [23] "gene481" "gene714" "gene53"  "gene340" "gene730" "gene347" "gene283" "gene181" "gene727" "gene571" "gene836"
## [34] "gene679" "gene445" "gene501" "gene933" "gene410" "gene529" "gene94" 
## 
## attr(,"intersections")$`A:B:D`
##  [1] "gene904" "gene79"  "gene207" "gene382" "gene331" "gene753" "gene924" "gene356" "gene142" "gene463" "gene341"
## [12] "gene537" "gene829" "gene144" "gene21"  "gene815" "gene4"   "gene729" "gene646" "gene931" "gene997" "gene312"
## [23] "gene859" "gene594" "gene465" "gene684" "gene949" "gene539" "gene440" "gene398" "gene425" "gene174" "gene597"
## [34] "gene405" "gene653" "gene612" "gene75"  "gene927" "gene378" "gene370" "gene908"
## 
## attr(,"intersections")$`A:C:D`
##  [1] "gene449" "gene369" "gene78"  "gene414" "gene358" "gene749" "gene984" "gene893" "gene37"  "gene32"  "gene148"
## [12] "gene718" "gene907" "gene138" "gene739" "gene723" "gene578" "gene930" "gene336" "gene680" "gene234" "gene455"
## [23] "gene547" "gene756" "gene388" "gene688" "gene717" "gene754" "gene758" "gene61"  "gene552" "gene518" "gene202"
## 
## attr(,"intersections")$`B:C:D`
##  [1] "gene558" "gene131" "gene238" "gene65"  "gene536" "gene955" "gene630" "gene6"   "gene641" "gene682" "gene802"
## [12] "gene576" "gene900" "gene827" "gene814" "gene433" "gene624" "gene601" "gene127" "gene228" "gene310" "gene652"
## [23] "gene670" "gene841" "gene894" "gene936" "gene365" "gene711" "gene616" "gene974" "gene566" "gene216" "gene921"
## [34] "gene466" "gene2"   "gene302" "gene311" "gene806" "gene520" "gene811" "gene191" "gene277" "gene360" "gene990"
## [45] "gene232" "gene469" "gene400" "gene214" "gene665" "gene72"  "gene846" "gene31"  "gene92"  "gene583" "gene242"
## [56] "gene483"
## 
## attr(,"intersections")$`A:B:C:D`
##  [1] "gene371" "gene735" "gene787" "gene38"  "gene66"  "gene415" "gene284" "gene477" "gene768" "gene454" "gene522"
## [12] "gene784" "gene582" "gene34"  "gene618" "gene741" "gene850" "gene373" "gene742" "gene912" "gene748" "gene291"
## [23] "gene863" "gene143"
## 
## attr(,"class")
## [1] "venn"

Conclusion

This article describes multiple solutions to create Venn diagrams in R.