ggVennBed()

Adrià Mitjavila Ventura

Source: vignettes/13-ggVennBed.Rmd

Last updated: 2023-01-04

Load plotmics 

# load plotmics
library(plotmics)

Run ggVennBed()

ggVennBed() draws an Venn diagram plot with the intersections of two BED files (A and B). It counts the number of unique regions in A and B, as well as the regions from A intersecting with B and viceversa. It uses the function ggvenn() from the ggvenn package, and the function bt.intersect() from the bedtoolsr package.

Look at the ggvenn package documentation.

Look at the bedtoolsr package documentation.

Required input

As input, ggVennBed() takes two data frames in BED format or the paths to two BED-like files.

# Example input. 
regionsX_path = "../testdata/regionsX.bed"
regionsY_path = "../testdata/regionsY.bed"

regionsX = read.delim(regionsX_path, header = F)
regionsY = read.delim(regionsY_path, header = F)

head(regionsX)
##     V1       V2       V3      V4   V5 V6
## 1 chr1  4598409  4598766  peak_2  358  +
## 2 chr1  7498822  7499889  peak_5 1068  +
## 3 chr1  9780318  9780582  peak_8  265  +
## 4 chr1  9943458  9944059  peak_9  602  +
## 5 chr1 24107692 24108215 peak_18  524  +
## 6 chr1 37300732 37300976 peak_20  245  +

Default run

You can run ggVennBed using the paths to two BED files:

ggVennBed(a = regionsX_path,  b = regionsY_path)

Or use two different data frames in BED-like format:

ggVennBed(a = regionsX,  b = regionsY)

Specify strandedness

By default, ggVennBed() intersects the regions with the same strandedness (bedtools intersect -s -u -a regionA -b regionB). To change this behaviour, change stranded to FALSE or NULL.

ggVennBed(a = regionsX,  b = regionsY, stranded = TRUE) + ggtitle("Intersection with the same strandednes") +
ggVennBed(a = regionsX,  b = regionsY, stranded = FALSE) + ggtitle("Intersection regardless the strand")

Customize plot 

ggVennBed(a = regionsX,  b = regionsY, title = "This is a title", title_size = 15, title_face = "bold")

ggVennBed(a = regionsX,  b = regionsY, title = "This is a title", subtitle = "This is a subtitle")

ggVennBed(a = regionsX,  b = regionsY, title = "This is a title", subtitle = "This is a subtitle", subtitle_size = 15, subtitle_face = "bold")

ggVennBed(a = regionsX,  b = regionsY, color = c("red", "green"))

ggVennBed(a = regionsX,  b = regionsY, color = c("red", "green"), alpha = 0.2)

ggVennBed(a = regionsX,  b = regionsY, labsize = 10)

ggVennBed(a = regionsX,  b = regionsY, setnames = c("RegionX", "RegionsY"))

ggVennBed(a = regionsX,  b = regionsY, setnames = c("RegionX", "RegionsY"), namesize = 10)

Further costumization

Since ggVennBed() outputs a ggvenn-based Venn diagram and ggvenn is based in ggplot2, it can be further customized with scales, theme, etc…