Tom Wenseleers - 6 months ago 36

R Question

In a paper I recently came across a nice 5 sets Venn diagram:

I was wondering what software might have been used to draw this? Can this be done in R perhaps?

Most of the packages I looked at seem to produce the less clear version

Any thoughts?

EDIT: seems the Nature article used this web tool:

http://bioinformatics.psb.ugent.be/webtools/Venn/

might still be nice to port it to some R package, especially the asymmetric Venns, which are currently not available in any package that I know of

EDIT2: Just discovered one can go up to 8 and even 11 sets: http://www.emis.de/journals/EJC/Surveys/ds5/VennSymmExamples.html - Tufte will be pleased!

Answer

I also used the online Venn diagram generator at the University of Ghent Bioinformatics site and wanted my own function. The idea of course is to have each intersection region reasonably sized so that the text for the counts can all be the same size. Here is my attempt:

```
fiveCellVenn <- function(colorList=col2rgb(rainbow(5)),
cellCounts=seq(1,31,1),
cellLabels=c("one","two","three","four","five"),
saturation=.25){
rotateVec <-function(vec,amount){
return(c(vec[(amount+1):length(vec)], vec[1:amount]))
}
n=70
xhull <- c()
yhull <- c()
for (i in 1:n){
xhull <- c(xhull, cos((i*2*pi)/n))
yhull <- c(yhull, sin((i*2*pi)/n))
}
## The Venn cells begin as a 70-sided regular polygon
## plot(xhull, yhull)
## polygon(xhull, yhull)
## Multiply each unit vector in the hull by a scalar, arrived at by
## iterative adjustment.
adjust <-c(10,10.35,10.6,10.5,10.4,10.3,10.1,9.6,9,8.5,
8,7.625,7.25,7.125,7,6.875,6.75,6.875,7,7.125,
7.25,7.625,8.1,9.125,10.25,11.375,12.5,13.15,13.8,14.3,
14.6,14.725,14.7,14.7,14.7,14.4,14.1,13.8,13.5,12.8,
12.1,11.15,10.2,9.6,8.95,8.3,7.7,7,6.25,5.6,
5,4.75,4.5,4.25,4,3.8,3.6,3.45,3.45,3.45,
3.5,3.625,3.75,3.825,4,4.25,4.5,5.75,7.25,8.5)
newxhull <- xhull*adjust
newyhull <- yhull*adjust
## Text location was also done by hand:
textLocationX <- c(-13,-3,8,9,-4,-7.5,7.5,-9,-8,4,6.5,-2,9,-4,1.4,4,-7.5,-3.5,7.5,-6,-6.5,6,1.5,4,-0.5,4.5,0,-5,-3.5,3.5,0)
textLocationY <- c(1,12,8,-8,-12,6.5,4.5,1,-4,8.5,-6,8.5,-1.5,-8,-9,5,3.5,6,1.5,-6,-1.5,-2,8,-7,-6.5,2,5.5,2,-3.5,-4,0)
textLocationMatrix <- matrix(cbind(textLocationX,textLocationY),nrow=31,ncol=2)
plot(newxhull, newyhull, pch=".", xlim=c(-16,16), ylim=c(-16,16),
axes=FALSE,xlab="",ylab="")
newAdjust<-adjust
for (i in 1:5){
newxhull <- xhull*newAdjust
newyhull <- yhull*newAdjust
polygon(newxhull, newyhull,
border=rgb(colorList[1,i]/255, colorList[2,i]/255, colorList[3,i]/255, 1),
lwd=2,
col=rgb(colorList[1,i]/255, colorList[2,i]/255, colorList[3,i]/255,saturation))
newAdjust <- rotateVec(newAdjust,14)
}
text(textLocationMatrix[,1], textLocationMatrix[,2],labels=as.character(cellCounts))
text(textLocationMatrix[c(17,2,3,24,14),1]*c(2,1.25,1.5,2,2),
textLocationMatrix[c(17,2,3,24,14),2]*c(2,1.35,1.5,2,2),
labels=cellLabels)
## uncomment and run to get points and grid for adjusting text location
## points(textLocationMatrix[,1], textLocationMatrix[,2])
## for (i in -16:16){
## if (i%%5==0){
## color="black"
## }else{
## color="lightblue"
## }
## abline(v=i,col=color)
## abline(h=i, col=color)
## }
}
```

Then

```
fiveCellVenn()
```

yields a Venn similar to your first one. I don't have the rep to post an image yet. You'll probably want to subdue the colors and move the cell names around.