Intro
Venn diagrams – named after the English logician and philosopher John Venn – “illustrate the logical relationships between two or more sets of items” with overlapping circles.
In this tutorial, I'll show how to plot a three set venn diagram using R and the ggplot2 package.
Packages and Data
For the R code to run, we need to install and load three R packages. Unlike tidyverse and ggforce, the limma package must be installed from Bioconductor rather than from CRAN.
Moreover, we create a random data frame using the rbinom() function.
source("http://www.bioconductor.org/biocLite.R")
biocLite("limma")
library(limma)
library(tidyverse)
library(ggforce)
set.seed((123))
mydata <- data.frame(A = rbinom(100, 1, 0.8),
B = rbinom(100, 1, 0.7),
C = rbinom(100, 1, 0.6)) %>%
mutate_all(., as.logical)
Drawing the Circles
Next, we create a data frame defining the x and y coordinates for the three circles we want to draw and a variable defining the labels. For plotting the circles – the basic structure of our venn diagram – we need the geom_circle() function of the ggforce package. We employ the geom_circle()-function of the ggforce package to actually draw the circles. With the parameter r (= 1.5), we define the radius of the circles.
df.venn <- data.frame(x = c(0, 0.866, -0.866),
y = c(1, -0.5, -0.5),
labels = c('A', 'B', 'C'))
ggplot(df.venn, aes(x0 = x, y0 = y, r = 1.5, fill = labels)) +
geom_circle(alpha = .3, size = 1, colour = 'grey') +
coord_fixed() +
theme_void()
Furthermore, we need a data frame with the values we want the plot and the coordinates for plotting these values. The values can be obtained using the vennCounts() function of the limma package. Since ggplot2 requires data frames we need to first transform the vdc object (class VennCounts) into a matrix and then into a data frame. In addition, we need to add the x and y coordinates for plotting the values.
vdc <- vennCounts(mydata)
class(vdc) <- 'matrix'
df.vdc <- as.data.frame(vdc)[-1,] %>%
mutate(x = c(0, 1.2, 0.8, -1.2, -0.8, 0, 0),
y = c(1.2, -0.6, 0.5, -0.6, 0.5, -1, 0))
The final Plot
Finally, we'll customize the look of our venn diagram and plot the values.
ggplot(df.venn) +
geom_circle(aes(x0 = x, y0 = y, r = 1.5, fill = labels), alpha = .3, size = 1, colour = 'grey') +
coord_fixed() +
theme_void() +
theme(legend.position = 'bottom') +
scale_fill_manual(values = c('cornflowerblue', 'firebrick', 'gold')) +
scale_colour_manual(values = c('cornflowerblue', 'firebrick', 'gold'), guide = FALSE) +
labs(fill = NULL) +
annotate("text", x = df.vdc$x, y = df.vdc$y, label = df.vdc$Counts, size = 5)
