load library

library(rtracklayer)
library(tidyverse)
library(ChIPpeakAnno)
library(ggsci)

load peak files

From “The ChIPpeakAnno user’s guide”

bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno")
gr1 <- toGRanges(bed, format="BED", header=FALSE)

gff <- system.file("extdata", "GFF_peaks.gff", package="ChIPpeakAnno")
gr2 <- toGRanges(gff, format="GFF", header=FALSE, skip=3)

## If you are importing files downloaded from ensembl, 
##           it will be better to import the files into a TxDb object,
##           and then convert to GRanges by toGRanges. Here is the sample code:
##           library(GenomicFeatures)
##           txdb <- makeTxDbFromGFF('/config/binaries/R/4.2.0/R_libraries/ChIPpeakAnno/extdata/GFF_peaks.gff')
##           anno <- toGRanges(txdb, format='gene')

ol <- findOverlapsOfPeaks(gr1, gr2)

## duplicated or NA names found. 
##                 Rename all the names by numbers.

make venn diagram

col_npg5 <- c(ggsci::pal_npg()(10)[c(3,4,9,1,2)])

# don't write log file for VennDiagram
futile.logger::flog.threshold(futile.logger::ERROR, name = "VennDiagramLogger")

makeVennDiagram(ol,
                fill=col_npg5[1:2], # circle fill color
                col=col_npg5[1:2], #circle border color
                #connectedPeaks = "merge", connectedPeaks = "keepAll", min keepFirstListConsistent
                cat.col=col_npg5[1:2], connectedPeaks = "merge", scaled=T, by = "region", main = "venn", NameOfPeaks = c("control","treatment_1"), cat.cex = 1.5, cat.pos = c(0, 0))