## ----echo=FALSE, out.width="20%", fig.align="center"--------------------------
knitr::include_graphics("figures/20250827_hex_gVenn_v1.png")

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)
suppressWarnings(library(GenomicRanges))

## ----echo=FALSE, out.width="100%", fig.align="center"-------------------------
knitr::include_graphics("figures/20250827_graphical_abstract_v2.png")

## ----setup--------------------------------------------------------------------
library(gVenn)

## ----load_chip_dataset--------------------------------------------------------
# Load the example A549 ChIP-seq peaks (subset on chr7 for demo)
data(a549_chipseq_peaks)

## ----compute_overlaps---------------------------------------------------------
genomic_overlaps <- computeOverlaps(a549_chipseq_peaks)

## ----plot_venn, fig.width=5, fig.height=3, fig.align='center'-----------------
plotVenn(genomic_overlaps)

## ----plot_upset, fig.width=5, fig.height=3, fig.align='center'----------------
plotUpSet(genomic_overlaps)

## ----save_plot, eval=FALSE----------------------------------------------------
# venn <- plotVenn(genomic_overlaps)
# saveViz(venn,
#         output_dir = ".",
#         output_file = "figure_gVenn",
#         format = "pdf")

## ----save_plot2, eval=FALSE---------------------------------------------------
# saveViz(venn,
#         output_dir = ".",
#         output_file = "figure_gVenn",
#         format = "png")
# 
# saveViz(venn,
#         output_dir = ".",
#         output_file = "figure_gVenn",
#         format = "svg")

## ----extractOverlaps_example1-------------------------------------------------
groups <- extractOverlaps(genomic_overlaps)

## ----extractOverlaps_example2-------------------------------------------------
# Display the number of genomic regions per overlap group
sapply(groups, length)

## ----extractOverlaps_example3-------------------------------------------------
# Extract elements in group_111 (present in A, B, and C)
peaks_in_all_sets <- groups[["group_111"]]

# Display the elements
peaks_in_all_sets

## ----exportOverlaps, eval=FALSE-----------------------------------------------
# # export overlpas
# exportOverlaps(genomic_overlaps,
#                output_dir = ".",
#                output_file = "overlap_groups")

## ----session-info-------------------------------------------------------------
sessionInfo()