Introduction

Creating a Venn Diagram in R to Visualize Data

In this article, we will explore how to create a Venn diagram in R using the nVennR package. A Venn diagram is a useful tool for visualizing data with overlapping sets. In this case, we are interested in creating a Venn diagram that shows whether certain tests on different machines are performed by all participants.

Background

A Venn diagram consists of multiple overlapping circles, each representing a set. The intersection of two or more circles represents the overlap between those sets. In our case, we have three machines and multiple tests for each machine. We want to visualize the number of tests that are common to all three machines, as well as the number of tests that are unique to each machine.

Data Preparation

To create a Venn diagram, we first need to prepare our data. This involves converting the data into a format that can be used by the nVennR package. We will use the nVennR function to convert each row of the data into a binary representation that can be used to calculate the overlap between sets.

library(nVennR)
dat <- data.frame(id=1:30,
                  machine1 = sample(0:7, 30, replace=T),
                  machine2 = sample(0:3, 30, replace=T),
                  machine3 = sample(0:6, 30, replace=T))

Converting Data to Binary Representation

To convert the data into a binary representation, we will use an auxiliary function called toBin. This function takes a vector of values and converts them into a binary representation.

toBin <- function(l){
  result <- 0
  bit <- 0
  for (v in rev(l)){
    if (v > 0){
      bpos <- bitwShiftL(1, bit)
      result <- result + bpos
    }
    bit <- bit + 1
  }
  return(result + 1)
}

nReg <- bitwShiftL(1, ncol(dat) - 1)
sets <- as.list(rep(0, nReg))
for (r in rownames(dat)){
  set <- toBin(dat[r, 2:ncol(dat)])
  sets[[set]] <- sets[[set]] + sum(dat[r, 2:ncol(dat)])
}

Creating the Venn Diagram

With the data converted into a binary representation, we can now create the Venn diagram using the createVennObj function from the nVennR package.

myV <- createVennObj(nSets = ncol(dat) - 1, sNames = colnames(dat[,2:ncol(dat)]), sSizes = sets)

Plotting the Venn Diagram

Finally, we can plot the Venn diagram using the plotVenn function from the nVennR package.

myV <- plotVenn(nVennObj = myV)

Results and Discussion

The resulting Venn diagram shows the number of tests that are common to all three machines, as well as the number of tests that are unique to each machine. The nVennR package is a powerful tool for creating Venn diagrams in R, and it can be used to visualize a wide range of data sets.

Conclusion

In this article, we explored how to create a Venn diagram in R using the nVennR package. We covered the basics of preparing the data, converting the data into a binary representation, and creating the Venn diagram. With practice and experience, you can use the nVennR package to create complex Venn diagrams that help to visualize your data.

Code Blocks

The following code blocks are used in this article:

# Load necessary libraries
library(nVennR)

# Create a sample dataset
dat <- data.frame(id=1:30,
                  machine1 = sample(0:7, 30, replace=T),
                  machine2 = sample(0:3, 30, replace=T),
                  machine3 = sample(0:6, 30, replace=T))

# Convert the data into a binary representation
toBin <- function(l){
  result <- 0
  bit <- 0
  for (v in rev(l)){
    if (v > 0){
      bpos <- bitwShiftL(1, bit)
      result <- result + bpos
    }
    bit <- bit + 1
  }
  return(result + 1)
}

nReg <- bitwShiftL(1, ncol(dat) - 1)
sets <- as.list(rep(0, nReg))
for (r in rownames(dat)){
  set <- toBin(dat[r, 2:ncol(dat)])
  sets[[set]] <- sets[[set]] + sum(dat[r, 2:ncol(dat)])
}

# Create the Venn diagram
myV <- createVennObj(nSets = ncol(dat) - 1, sNames = colnames(dat[,2:ncol(dat)]), sSizes = sets)

# Plot the Venn diagram
myV <- plotVenn(nVennObj = myV)

This code can be used to generate a Venn diagram for any dataset. Simply replace the sample data with your own data and adjust the parameters as needed.

References

nVennR Package Documentation
How to Create a Venn Diagram in R
[Making a Venn diagram from a count table](https://seananderson.net posts/making-a-venn-diagram-from-count-tables/)

Last modified on 2023-08-26