Compute specific and intersection elements with R

This is my first posts about R language, my first english post and my first R package: venn.compute, which use case in bioinformatics is compare list of genes.

This R package is intended to compute specific elements in intersections of Venn diagram instead of plot.

• Custom reader of files to create list of character arrays (such requiered for this package and VennDiagram).
• Compute specific elements in intersections of Venn diagram in memory or write to files.
• Plot with VennDiagram.

Example

Use 3 files in tests directory with names primes.txt, even.txt y fibo.txt whose content are primes, even and Fibonacci numbers until 20.

Install

You can install from GitHub as:

devtools::install_github("cosmoscalibur/venn.compute")

Downloading GitHub repo cosmoscalibur/venn.compute@master

formatR (1.6 -> 1.7) [CRAN]


Installing 1 packages: formatR
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done


✔  checking for file ‘/tmp/RtmpT7UVx3/remotes61d65fec5ae1/cosmoscalibur-venn.compute-6f4fb43/DESCRIPTION’ ...
─  preparing ‘venn.compute’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘venn.compute_1.1.0.tar.gz’

If an error about TAR executable is showed (common in Linux with Anaconda, sh: 1: /bin/gtar: not found), you need to setup your TAR path.

Sys.setenv(TAR = "/bin/tar")

How to use

First, load the package.

library(venn.compute)

Lectura de archivos

Read files

This is a custom reader to include multiple files and associate its custom names, returned a named list of character arrays (each element is an element line of the file).

sets <- read.lists_from_files(c(file.path("tests", "primes.txt"),
                                file.path("tests", "even.txt"),
                                file.path("tests", "fibo.txt")),
                              c("primes", "even", "fibo"))
print(sets)

$primes
[1] "1"  "2"  "3"  "5"  "7"  "11" "13" "17"

$even
 [1] "0"  "2"  "4"  "6"  "8"  "10" "12" "14" "16" "18"

$fibo
[1] "1"  "2"  "3"  "5"  "8"  "13"

Compute intersections and specific elements

Now you can compute specific elements of Venn diagram intersections.

venn.compute_specific(sets)

$primes_even_fibo

'2'

$primes_even

$primes_fibo

1. '1'
2. '3'
3. '5'
4. '13'

$even_fibo

'8'

$primes

1. '7'
2. '11'
3. '17'

$even

1. '0'
2. '4'
3. '6'
4. '10'
5. '12'
6. '14'
7. '16'
8. '18'

$fibo

If you need to write sets in files, add an output path. Files are written using convention of join sets name with underscore.

venn.compute_specific(sets, output_dir = file.path("tests", "output"))

We can verify written files.

dir(file.path("tests", "output"))

1. 'even_fibo.txt'
2. 'even.txt'
3. 'fibo.txt'
4. 'primes_even_fibo.txt'
5. 'primes_even.txt'
6. 'primes_fibo.txt'
7. 'primes.txt'

Plot Venn diagram

Finally, if you want to save plot, invoke this function with the same arguments as before (internally using VennDiagram)

venn.compute_plot(sets, output_dir = file.path("tests", "output"))

Now, we have a primes_even_fibo.png file.