# Installing necessary packages
if (!requireNamespace("ComplexHeatmap", quietly = TRUE)) {
BiocManager::install("ComplexHeatmap")
}
if (!requireNamespace("ggplot2", quietly = TRUE)) {
install.packages("ggplot2")
}
if (!requireNamespace("dplyr", quietly = TRUE)) {
install.packages("dplyr")
}
if (!requireNamespace("tidyr", quietly = TRUE)) {
install.packages("tidyr")
}
if (!requireNamespace("circlize", quietly = TRUE)) {
install.packages("circlize")
}
# Load packages
library(ComplexHeatmap)
library(ggplot2)
library(dplyr)
library(tidyr)
library(circlize)ATAC-seq Accessibility Heatmap
Chromatin-accessibility experiments (ATAC-seq, DNase-seq) are reported as aggregate heatmaps over genomic regions: rows are peaks, columns are binned signal per condition, sorted so induced and unresponsive regions separate [1]. This tutorial draws that layout on simulated bigWig-style binned matrices โ the plotting half of the deeptools workflow (align โ MACS2 โ multiBigwigSummary โ this figure), with the locus-level difference view the reference paper highlights.
Example
Setup
System Requirements: Cross-platform (Linux/MacOS/Windows)
Programming Language: R
Dependent packages:
ComplexHeatmap;ggplot2;dplyr;tidyr;circlize
sessioninfo::session_info("attached")โ Session info โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
setting value
version R version 4.6.2 (2026-10-29)
os Ubuntu 26.04.1 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz UTC
date 2026-11-05
pandoc 3.7.0.2 @ /usr/bin/ (via rmarkdown)
quarto 1.11.9 @ /usr/local/bin/quarto
โ Packages โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
! package * version date (UTC) lib source
P circlize * 0.4.18 2026-04-04 [?] RSPM
P ComplexHeatmap * 2.28.0 2026-04-28 [?] Bioconductor 3.23 (R 4.6.2)
P dplyr * 1.2.1 2026-04-03 [?] RSPM
P ggplot2 * 4.0.3.9000 2026-11-03 [?] Github (tidyverse/ggplot2@b638d65)
P tidyr * 1.3.2 2025-12-19 [?] RSPM
[1] /home/runner/.cache/R/renv/library/Bizard-5140bdc6/linux-ubuntu-resolute/R-4.6/x86_64-pc-linux-gnu
[2] /home/runner/work/_temp/Library
[3] /opt/R/4.6.2/lib/R/library
* โโ Packages attached to the search path.
P โโ Loaded and on-disk path mismatch.
โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโData Preparation
In practice the input is the matrix multiBigwigSummary BED-file writes (one column per bigWig, one row per peak). We simulate 120 peaks measured in four conditions โ WT and KO macrophages, each with and without LXR agonist treatment โ with a treatment-responsive block and an unresponsive block.
set.seed(701)
n_induced <- 50; n_flat <- 70
n_bin <- 30
conditions <- c("WT", "WT_treated", "KO", "KO_treated")
## binned ChIP/ATAC signal: rows = peaks, columns = 30 bins x 4 conditions
shape_vals <- dnorm(seq(-3, 3, length.out = n_bin)) # peaked profile
mk_profile <- function(peak_effect, n) {
do.call(cbind, lapply(conditions, function(cn) {
eff <- peak_effect *
ifelse(cn == "WT_treated", 1, ifelse(cn == "KO_treated", 0.25, 0))
do.call(cbind, lapply(seq_len(n_bin), function(b)
0.6 + eff * shape_vals[b] + rnorm(n, sd = 0.12))) # n peaks x 1 bin
}))
}
peaks_induced <- mk_profile(2.2, n_induced)
peaks_flat <- mk_profile(0.0, n_flat)
colnames(peaks_induced) <- colnames(peaks_flat) <-
paste0(rep(conditions, each = n_bin), "_b", rep(seq_len(n_bin), times = 4))
peak_mat <- rbind(peaks_induced, peaks_flat)
rownames(peak_mat) <- c(paste0("Induced_peak_", seq_len(n_induced)),
paste0("Flat_peak_", seq_len(n_flat)))
peak_group <- factor(c(rep("GW3965-induced", n_induced), rep("Unresponsive", n_flat)),
levels = c("GW3965-induced", "Unresponsive"))
dim(peak_mat)[1] 120 120Visualization
1. Group-Mean Accessibility Profiles
prof <- as.data.frame(peak_mat) |>
mutate(group = peak_group) |>
group_by(group) |>
summarise(across(where(is.numeric), mean), .groups = "drop") |>
pivot_longer(-group, names_to = "key", values_to = "signal") |>
mutate(condition = sub("_b[0-9]+$", "", key),
bin = as.integer(sub(".*_b", "", key)))
ggplot(prof, aes(bin, signal, colour = condition, fill = condition)) +
stat_summary(geom = "line", linewidth = 0.9) +
facet_wrap(~group, nrow = 1) +
scale_colour_manual(values = c(WT = "#2874C5", WT_treated = "#2874C5",
KO = "#B2182B", KO_treated = "#B2182B"),
labels = c(WT = "WT", WT_treated = "WT + GW3965",
KO = "KO", KO_treated = "KO + GW3965"),
name = NULL) +
scale_fill_manual(values = c(WT = "#2874C5", WT_treated = "#2874C5",
KO = "#B2182B", KO_treated = "#B2182B")) +
labs(x = "Position over peak (binned)", y = "Mean accessibility") +
guides(fill = "none") +
theme_classic(base_size = 11) +
theme(legend.position = "top", legend.key.size = unit(3, "mm"))
The WT + GW3965 curve separates from KO + GW3965 in the induced set but not in the unresponsive set โ the treatment effect the reference figure reports.
2. Accessibility-Difference Heatmap
col_fun <- circlize::colorRamp2(c(0, 1.2, 2.8), c("#F7F7F7", "#FDAE61", "#B2182B"))
row_ord <- order(peak_group, # group first
rowMeans(peak_mat[, grep("KO_treated_b", colnames(peak_mat))] -
peak_mat[, grep("KO_b", colnames(peak_mat))]),
decreasing = TRUE)
mat_sorted <- peak_mat[row_ord, ]
grp_sorted <- peak_group[row_ord]
col_names <- rep(seq_len(n_bin), times = 4)
ha_top <- HeatmapAnnotation(
Condition = rep(conditions, each = n_bin),
col = list(Condition = c(WT = "#BDD7E7", WT_treated = "#2171B5",
KO = "#FCAE91", KO_treated = "#B2182B")),
show_legend = FALSE)
Heatmap(mat_sorted, name = "Accessibility",
top_annotation = ha_top,
col = col_fun,
cluster_rows = FALSE, cluster_columns = FALSE,
row_split = grp_sorted, column_split = factor(rep(conditions, each = n_bin), conditions),
column_gap = unit(1, "mm"),
show_column_names = FALSE, show_row_names = FALSE,
border = TRUE)
Tip
Practice tips
- Sort rows by the biological contrast (here KO-treated minus KO) inside each group โ clustering would scramble the induced/unresponsive split the figure exists to show.
-
column_split+column_gapkeeps the four condition blocks visually separate; the top annotation maps each block to its condition colour. - Upstream, the real matrices come from
multiBigwigSummary BED-file; normalise samples first (deeptoolsbigwigCompareor RPGC), or the condition colours will reflect depth, not accessibility.
Application
Aggregate accessibility heatmaps are the standard figure for reporting condition-specific chromatin opening (drug treatment, knockout, lineage transitions). The same layout serves ChIP-seq signal over peak sets.
Reference
[1] Ramรญrez F, Dรผndar F, Diehl S, Grรผning BA, Manke T. deepTools: a flexible web platform for exploring high-throughput sequencing data. Nucleic Acids Res. 2014;42(W1):W187-191. doi:10.1093/nar/gku365
[2] Xiaofan Lu, et al.ย FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency. iMetaMed. 2025. doi:10.1002/imm3.70005