使用venn.diagram包的面积比例维恩图

Question

I read in another thread closed to comment that it is possible to create an area proportional venn diagram using the package venn.diagram in R.

I adapted the code to my data (gene lists), but the area of the circles does not correlate with the length of the data vectors.

Any suggestions to solve this problem?

Thanks! code and output below.

CODE SAMPLE

venn.diagram(x = list(G015_All, G08_Female, G015_Male),
                 na = "remove",
                 category.names = c("G015_All", "G08_Female", "G015_Male"),
                 fill = c('lightyellow', 'paleturquoise', 'lightgreen'),
                 alpha = c(0.5, 0.5, 0.5),
                 cex = 2,
                 cat.fontface = 4,
                 lty =2,
                 fontfamily =3,
                 filename = "VennPlot.png",
                 imagetype = "png",
                 output = T)

OUTPUT

Answer 1

There are several R packages to do that, each with different approaches. My own attempt, nVennR draws proportional circles that are enclosed by the lines in the diagram. You can read the vignette for examples on how to use it. There is also a web server for up to six sets. I have attempted to reproduce the diagram you show as an example. I had to enter the set sizes by hand, but the diagram can also be produced from the lists as in your example (as shown in the vignette):

> library(nVennR)
> myV <- createVennObj(nSets = 3, sNames = c("G015_All", "G08_Female", "G015_Male"), sSizes = c(0, 7, 5212, 35, 1, 0, 2, 37))
> myV <- plotVenn(nVennObj = myV, setColors=c('yellow', 'turquoise', 'green')) 

And the result:

Just a couple of things. First, I changed the colors. nVennR uses opacity to mix colors, and therefore you get fainter colors by default. Second, the shape of the small sets is not perfect. This has to do with the algorithm to pack the circles, and should only happen in rare cases, like extreme imbalances in group sizes.