Drawing Nested Venn Diagrams

Question

I have data that contains binary indicators for two groups and for more groups that are nested in one of the first two groups.

For instance:

set.seed(1) df <- data.frame(a=rep(0,10),b=rep(0,10),b.1=rep(0,10),b.2=rep(0,10)) df$a[sample(10,5,replace=F)] <- 1 df$b[sample(10,5,replace=F)] <- 1 df$b.1[sample(which(df$b==1),3,replace=F)] <- 1 df$b.2[sample(which(df$b==1),3,replace=F)] <- 1 df <- df[which(rowSums(df)==0),] 

a and b are two groups, and b.1 and b.2 nested in group b .

What I would like to do is draw a single venn diagram of all the groups. This means that b.1 and b.2 will be described inside b that cross a .

Is there any way to achieve this? Using a ggplot solution would be great.

R VennDiagram 's attempt only for groups b, b.1 and b.2 does not even work for me:

 library(VennDiagram) draw.triple.venn(area1=sum(df$b),area2=sum(df$b.1),area3=sum(df$b.2), n12=sum(df$b*df$b.1),n23=sum(df$b.1*df$b.2),n13=sum(df$b*df$b.2),n123=sum(df$b*df$b.1*df$b.2), category=c("b","b1","b2")) 

With the Vennerable package Vennerable I only approach drawing groups "b":

 library(Vennerable) plot(Venn(Sets=list(b=which(df$b==1),b.1=which(df$b.1==1),b.2=which(df$b.2==1))),doEuler=T,doWeight=T) 

But when I add the group a , it gets messed up:

Because I really need one circle for group a with an intersecting area with group b , and inside the circle of group b are circles of groups b.1 and b.2 .

Answer 1

The basic idea is to draw a triple Venn with a , b1 and b2 , and then manually apply an ellipse to b .

 library(VennDiagram) library(gridExtra) polygons <- draw.triple.venn( area1=sum(df$a), area2=sum(df$b.1), area3=sum(df$b.2), n12=sum(df$a*df$b.1), n23=sum(df$b.1*df$b.2), n13=sum(df$a*df$b.2), n123=sum(df$a*df$b.1*df$b.2), category=c("a","b1","b2"), margin=.1) 

Now we will draw an ellipse and add a label. This requires a fair bit of trial and error to get the right location, angle, and size. Be that as it may, it is not perfect, but it is almost there.

 b <- ellipseGrob( x=unit(0.562,"npc"), y=unit(0.515,"npc"), angle=(1.996*pi)/3, size=65.5, ar=2, gp=gpar(lwd=2.2)) grid.draw(b) grid.text("b", x=unit(.9,"npc"), y=unit(.9,"npc"), gp=gpar(fontfamily="serif")) 

Answer 2

There are several options for arranging circles in your assumption. I think it would be better to make your function() .

Here is my example (edited, change the default value of vp):

 nest_venn <- function(data_list, fill = c(2, 4, 5, 6), alpha = 0.15, vp = viewport(height=unit(1 ,"snpc"), width=unit(1,"snpc"))) { counts <- get.venn.partitions(data_list)$..count.. # calculation of each area value if(any(counts[c(3, 4, 7, 8, 11, 12)]==!0)) warning("data_list[[3]] and/or data_list[[4]] isn't nested") grobs <- grobTree( circleGrob(x = 0.33, y = 0.5, r = 0.3, gp = gpar(fill = alpha(fill[1], alpha), col=8, lwd = 2)), # a circle circleGrob(x = 0.67, y = 0.5, r = 0.3, gp = gpar(fill = alpha(fill[2], alpha), col=8, lwd = 2)), # b circle circleGrob(x = 0.67, y = 0.6, r = 0.16, gp = gpar(fill = alpha(fill[3], alpha), col=8, lwd = 2)), # b.1 circle circleGrob(x = 0.67, y = 0.4, r = 0.16, gp = gpar(fill = alpha(fill[4], alpha), col=8, lwd = 2)), # b.2 circle textGrob(names(data_list)[1], x = 0.33, y = 0.82, gp = gpar(cex = 1, fontface = 4)), # a label textGrob(names(data_list)[2], x = 0.67, y = 0.82, gp = gpar(cex = 1, fontface = 4)), # b label textGrob(names(data_list)[3], x = 0.83, y = 0.7, gp = gpar(cex = 1, fontface = 4)), # b.1 label textGrob(names(data_list)[4], x = 0.83, y = 0.3, gp = gpar(cex = 1, fontface = 4)), # b.2 label textGrob(counts[15], x = 0.28, y = 0.5, gp = gpar(cex = 1.2)), # a textGrob(counts[14], x = 0.9, y = 0.5, gp = gpar(cex = 1.2)), # b textGrob(counts[13], x = 0.47, y = 0.5, gp = gpar(cex = 1.2)), # a & b textGrob(counts[10], x = 0.68, y = 0.65, gp = gpar(cex = 1.2)), # b & b.1 textGrob(counts[6], x = 0.68, y = 0.35, gp = gpar(cex = 1.2)), # b & b.2 textGrob(counts[9], x = 0.57, y = 0.6, gp = gpar(cex = 1.2)), # a & b & b.1 textGrob(counts[5], x = 0.57, y = 0.4, gp = gpar(cex = 1.2)), # a & b & b.2 textGrob(counts[2], x = 0.69, y = 0.5, gp = gpar(cex = 1.2)), # b & b.1 & b.2 textGrob(counts[1], x = 0.6, y = 0.5, gp = gpar(cex = 1.2)), # a & b & b.1 & b.2 vp = vp) return(grobs) } 

data list preparation:

 set.seed(1) df <- data.frame(a=rep(0,10),b=rep(0,10),b.1=rep(0,10),b.2=rep(0,10)) df$a[sample(10,5,replace=F)] <- 1 df$b[sample(10,5,replace=F)] <- 1 df$b.1[sample(which(df$b==1),3,replace=F)] <- 1 df$b.2[sample(which(df$b==1),3,replace=F)] <- 1 df <- df[-which(rowSums(df)==0),] # the same as OP example data data_list <- list() for(i in colnames(df)) data_list[[i]] <- which(df[,i]==1) # > data_list[1] # $a # [1] 2 3 4 5 7 

use the function above and draw the output:

 library(VennDiagram); library(grid); library(ggplot2) nestvenn.obj <- nest_venn(data_list) grid.newpage() grid.draw(nestvenn.obj) # [ edited ] # If you want a fixed size etc, please give an argument, vp. vp1 <- viewport(height=unit(150 ,"mm"), width=unit(150, "mm")) # example nestvenn.obj <- nest_venn(data_list, vp = vp1) grid.newpage() 

 # an example with ggplot library(gtable); library(dplyr) grid.newpage() ggplot(data.frame(x=1, y=1), aes(x, y)) %>% ggplotGrob() %>% gtable_filter("panel") %>% gList(nestvenn.obj) %>% grid.draw()