CODEWITHSUNDEEP
rvenn-diagram
TheFoxx
TheFoxx

Reputation: 1693

How to make venn diagrams in R?

Hi I'm new to R and I must use it to make a venn diagram. I've been googling it for a while and all the examples I could find deal with binary variables. However I have 2 lists (well actually 2 csv files). The items in the list are just strings, like PSF113_xxxx. I must compare them to see what is unique to each and what is shared. How would I make a venn diagram out of this in R?

Also the files don't have the same number of things in them, one has slightly more then the other, which means the cbind function returns an error.

I've come up with this so far, but this just gets me an image with a circle named group 1 with a 1 inside and a 0 outside.

matLis <- list(matrix(A), matrix(B))

n <- max(sapply(matLis, nrow))
do.call(cbind, lapply(matLis, function (x)
     rbind(x, matrix(, n-nrow(x), ncol(x))))) 

x = vennCounts(n)
vennDiagram(x)

This is an example of the data

2 PSF113_0018
3 PSF113_0079
4 PSF113_0079a
5 PSF113_0079b

The numbering on the left isn't anything I've done, it added that when I imported the files into R from excel

head(A)
> head(A)
            V1
1 PSF113_0016a
2  PSF113_0018
3  PSF113_0079
4 PSF113_0079a
5 PSF113_0079b
6 PSF113_0079c

> head(b,10)
             V1
1  PSF113_0016a
2   PSF113_0021
3   PSF113_0048
4   PSF113_0079
5  PSF113_0079a
6  PSF113_0079b
7  PSF113_0079c
8   PSF113_0295
9  PSF113_0324a
10 PSF113_0324b

Upvotes: 2

Views: 5609

Answers (1)

Tyler Rinker
Tyler Rinker

Reputation: 110004

Your code still isn't quite reproducible because you haven't defined A or B. Here's a guide for a venn diagram in the package venneuler as I found it more flexible.

List1 <- c("apple", "apple", "orange", "kiwi", "cherry", "peach")
List2 <- c("apple", "orange", "cherry", "tomatoe", "pear", "plum", "plum")
Lists <- list(List1, List2)  #put the word vectors into a list to supply lapply
items <- sort(unique(unlist(Lists)))   #put in alphabetical order
MAT <- matrix(rep(0, length(items)*length(Lists)), ncol=2)  #make a matrix of 0's
colnames(MAT) <- paste0("List", 1:2)
rownames(MAT) <- items
lapply(seq_along(Lists), function(i) {   #fill the matrix
    MAT[items %in% Lists[[i]], i] <<- table(Lists[[i]])
})

MAT   #look at the results
library(venneuler)
v <- venneuler(MAT)
plot(v)

Edit: The head is very helpful in that it gives us something to work with. Try this approach:

#For reproducibility (skip this and read in the csv files)
A <- structure(list(V1 = structure(1:6, .Label = c("PSF113_0016a", 
    "PSF113_0018", "PSF113_0079", "PSF113_0079a", "PSF113_0079b", 
    "PSF113_0079c"), class = "factor")), .Names = "V1", 
    class = "data.frame", row.names = c("1", 
    "2", "3", "4", "5", "6"))

B <- structure(list(V1 = structure(1:10, .Label = c("PSF113_0016a", 
    "PSF113_0021", "PSF113_0048", "PSF113_0079", "PSF113_0079a", 
    "PSF113_0079b", "PSF113_0079c", "PSF113_0295", "PSF113_0324a", 
    "PSF113_0324b"), class = "factor")), .Names = "V1", 
    class = "data.frame", row.names = c("1", 
    "2", "3", "4", "5", "6", "7", "8", "9", "10"))

run code from here:

#after reading in the csv files start here
Lists <- list(A, B)  #put the word vectors into a list to supply lapply
Lists <- lapply(Lists, function(x) as.character(unlist(x)))
items <- sort(unique(unlist(Lists)))   #put in alphabetical order
MAT <- matrix(rep(0, length(items)*length(Lists)), ncol=2)  #make a matrix of 0's
colnames(MAT) <- paste0("List", 1:2)
rownames(MAT) <- items
lapply(seq_along(Lists), function(i) {   #fill the matrix
    MAT[items %in% Lists[[i]], i] <<- table(Lists[[i]])
})

MAT   #look at the results
library(venneuler)
v <- venneuler(MAT)
plot(v)

The difference in this approach was that I unlisted the two data frames (if they're dataframes) and then turned them to character vectors. I think this should work.

Upvotes: 2

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