How to Use pheatmap() in R to Create Heatmaps

You can use the pheatmap() function from the pheatmap package in R to create highly customized heatmaps.

The following examples show how to use this function in practice with the following fake dataset:

#make this example reproducible
set.seed(1)

#create matrix with fake data values
data = matrix(rnorm(100), 20, 5)
data [1:10, seq(1, 5, 1)] = data [1:10, seq(1, 5, 1)] + 3
data [11:20, seq(2, 5, 1)] = data [11:20, seq(2, 5, 1)] + 2
data [15:20, seq(2, 5, 1)] = data [15:20, seq(2, 5, 1)] + 4

#add column names and row names
colnames(data) = paste("T", 1:5, sep = "")
rownames(data) = paste("Gene", 1:20, sep = "")

#view matrx
data

                T1       T2        T3       T4       T5
Gene1   2.37354619 3.918977 2.8354764 5.401618 2.431331
Gene2   3.18364332 3.782136 2.7466383 2.960760 2.864821
Gene3   2.16437139 3.074565 3.6969634 3.689739 4.178087
Gene4   4.59528080 1.010648 3.5566632 3.028002 1.476433
Gene5   3.32950777 3.619826 2.3112443 2.256727 3.593946
Gene6   2.17953162 2.943871 2.2925048 3.188792 3.332950
Gene7   3.48742905 2.844204 3.3645820 1.195041 4.063100
Gene8   3.73832471 1.529248 3.7685329 4.465555 2.695816
Gene9   3.57578135 2.521850 2.8876538 3.153253 3.370019
Gene10  2.69461161 3.417942 3.8811077 5.172612 3.267099
Gene11  1.51178117 3.358680 2.3981059 2.475510 1.457480
Gene12  0.38984324 1.897212 1.3879736 1.290054 3.207868
Gene13 -0.62124058 2.387672 2.3411197 2.610726 3.160403
Gene14 -2.21469989 1.946195 0.8706369 1.065902 2.700214
Gene15  1.12493092 4.622940 7.4330237 4.746367 7.586833
Gene16 -0.04493361 5.585005 7.9803999 6.291446 6.558486
Gene17 -0.01619026 5.605710 5.6327785 5.556708 4.723408
Gene18  0.94383621 5.940687 4.9558654 6.001105 5.426735
Gene19  0.82122120 7.100025 6.5697196 6.074341 4.775387
Gene20  0.59390132 6.763176 5.8649454 5.410479 5.526599

Example 1: Create Basic Heatmap

We can create a heatmap with the default settings in pheatmap to visualize all of the values in the matrix:

library(pheatmap)

#create basic heatmap
pheatmap(data)

Example 2: Create Heatmap with Cell Labels

We can create use the arguments display_numbers and fontsize_number to display the numerical values in each cell of the heatmap with a specific font size:

library(pheatmap)

#create heatmap with numerical labels in cells
pheatmap(data, display_numbers=TRUE, fontsize_number=12)

Note: The default value for fontsize_number is 8.

Example 3: Create Heatmap with Custom Colors

We can create use the colorRampPalette argument to specify the colors to use for the low, medium and high values in the heatmap as well:

library(pheatmap)

#create heatmap with custom colors
pheatmap(data, color=colorRampPalette(c("blue", "white", "red"))(20))

The low values are now shown in blue, the middle values are shown in white, and the high values are shown in red.

Feel free to specify whichever colors you would like to create your own color scale for your heatmap.

Additional Resources

The following tutorials explain how to perform other common tasks in R:

How to Create a Correlation Heatmap in R
How to Create a Heatmap in R Using ggplot2
How to Plot Categorical Data in R