ComplexHeatmap: Create Complex Heatmaps in R

Renesh Bedre    2 minute read

Heatmap is a statistical visualization method for visualizing complex data sets in matrix form and quickly gaining insights from large datasets.

Heatmaps are widely used in bioinformatics for analyzing and visualizing large gene expression datasets obtained from different samples and conditions.

This tutorial explains how to use the Heatmap() function from the ComplexHeatmap R Bioconductor package for visualizing complex heatmaps.

Install ComplexHeatmap

You can install the ComplexHeatmap R package (from Bioconductor) as below:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ComplexHeatmap")

Getting the dataset

We will use the sample RNA-seq gene expression dataset for creating heatmaps using the ComplexHeatmap package.

# load dataset
df = read.csv("https://reneshbedre.github.io/assets/posts/heatmap/hm_data.csv", row.names="Gene")
# convert to matrix
df_mat = data.matrix(df)
# view first few rows of data 
head(df, 5)
# output
             A         B         C        D        E         F
B-CHI1 4.505700  3.260360 -1.249400  8.89807  8.05955 -0.842803
CTL2-1 3.508560  1.660790 -1.856680 -2.57336 -1.37370  1.196000
B-CHI2 2.160030  3.146520  0.982809  9.02430  6.05832 -2.967420
CTL2-2 1.884750  2.295690  0.408891 -3.91404 -2.28049  1.628820
CHIV1  0.255193 -0.761204 -1.022350  3.65059  2.46525 -1.188140

Basic heatmaps

Create and visualize a single heatmap with the default settings,

# load package
library(ComplexHeatmap)

# visualize heatmap
Heatmap(df_mat)

default heatmap with ComplexHeatmap

Change color of the heatmap

You can change the color of the heatmap using the col argument

# create color scale
library(circlize)
col_fun = colorRamp2(seq(min(df_mat), max(df_mat), length = 3),  
                     c("green", "black", "red"))

# visualize heatmap
Heatmap(df_mat, col = col_fun)

change heatmap color with ComplexHeatmap

Change borders of the heatmap

You can change the individual cell borders of the heatmap using the rect_gp argument

Heatmap(df_mat, rect_gp = gpar(col = "white", lwd = 2))

Change borders of heatmap with ComplexHeatmap

Add titles to the heatmap

You can add row and column titles to the heatmap using the column_title and row_title arguments

Heatmap(df_mat, column_title = "Conditions", row_title = "Genes", 
        column_title_side = "bottom")

add titles to heatmap with ComplexHeatmap

Clustering

The row and column clustering is plotted by default in ComplexHeatmap.

You can turn off row and column clustering using cluster_rows and show_column_dend arguments

# turn off row clustering
Heatmap(df_mat, cluster_rows = FALSE)

# turn off column clustering
Heatmap(df_mat, show_column_dend = FALSE)

ComplexHeatmap with no row clustering ComplexHeatmap with no column clustering

Color the clusters

You can also color the individual row clusters,

# install.packages("dendextend")
library(dendextend)
row_dend = as.dendrogram(hclust(dist(df_mat)))

# color row clustering
Heatmap(df_mat, cluster_rows = color_branches(row_dend, k = 5))

ComplexHeatmap with color for row clustering

Split the heatmaps

You can also split the heatmap by rows and columns to better understand the clustering of the data. It uses k-means clustering to split the clusters.

# split row clusters
Heatmap(df_mat, name = "scale", row_km = 5)

# split column clusters
Heatmap(df_mat, name = "scale", column_km = 2)

split heatmap by row in ComplexHeatmap split heatmap by column in ComplexHeatmap

Split by both rows and columns simultaneously,

# split row and column clusters at same time
Heatmap(df_mat, name = "scale", row_km = 5, column_km = 2)

split heatmap by row and column in ComplexHeatmap

Change legend position

You can change the legend position in the ComplexHeatmap as below,

draw(Heatmap(df_mat), heatmap_legend_side = "left")

change legend position in ComplexHeatmap

Similarly, you can use the bottom and top positions to adjust the legend position.

Related: pheatmap: create annotated heatmaps in R

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