8 Heatmap

In this chapter, we introduce the heatmap in ggplot2, pheatmap and ComplexHeatmap styles.

Install related packages

install.packages(c("ggplot2","pheatmap","ComplexHeatmap"))

Load packages and create dummy data

library(ggplot2)
library(pheatmap)
library(ComplexHeatmap)
library(paintingr) # for generation of color palettes

# Dummy data
x <- LETTERS[1:20]
y <- paste0("var", seq(1,20))
dum.data <- expand.grid(X=x, Y=y)
dum.data$Z <- seq(1,20)+runif(400, 0, 5)

head(dum.data)

##   X    Y        Z
## 1 A var1 5.449923
## 2 B var1 5.902715
## 3 C var1 7.513017
## 4 D var1 5.348068
## 5 E var1 8.868486
## 6 F var1 9.888554

8.1 ggplot2

Basic heatmap in ggplot2 style (geom_tile)

# Heatmap 
pal <- paint_palette("Autumn", n=100, type="continuous")
ggplot(dum.data, aes(X, Y, fill= Z)) + 
  geom_tile() + 
  scale_fill_gradientn(colours = pal) + 
  scale_x_discrete(expand = c(0, 0)) +
  scale_y_discrete(expand = c(0, 0)) + 
  coord_equal() 

8.2 pheatmap

Both pheatmap and ComplexHeatmap require matrix like input

# Dummy data
set.seed(123)
dum.mat <- matrix(rnorm(1000), ncol=10)

head(dum.mat)

##             [,1]        [,2]       [,3]       [,4]        [,5]        [,6]
## [1,] -0.56047565 -0.71040656  2.1988103 -0.7152422 -0.07355602 -0.60189285
## [2,] -0.23017749  0.25688371  1.3124130 -0.7526890 -1.16865142 -0.99369859
## [3,]  1.55870831 -0.24669188 -0.2651451 -0.9385387 -0.63474826  1.02678506
## [4,]  0.07050839 -0.34754260  0.5431941 -1.0525133 -0.02884155  0.75106130
## [5,]  0.12928774 -0.95161857 -0.4143399 -0.4371595  0.67069597 -1.50916654
## [6,]  1.71506499 -0.04502772 -0.4762469  0.3311792 -1.65054654 -0.09514745
##             [,7]       [,8]       [,9]      [,10]
## [1,]  1.07401226 -0.7282191  0.3562833 -1.0141142
## [2,] -0.02734697 -1.5404424 -0.6580102 -0.7913139
## [3,] -0.03333034 -0.6930946  0.8552022  0.2995937
## [4,] -1.51606762  0.1188494  1.1529362  1.6390519
## [5,]  0.79038534 -1.3647095  0.2762746  1.0846170
## [6,] -0.21073418  0.5899827  0.1441047 -0.6245675

Create basic pheatmap

pheatmap::pheatmap(dum.mat)

8.2.1 Control color

pal2 <- paint_palette("Twilight", 100, "continuous")
pheatmap::pheatmap(dum.mat, color = pal2, border_color = NA)

8.3 ComplexHeatmap

Create basic ComplexHeatmap

ComplexHeatmap::Heatmap(dum.mat, name="mat")

8.3.1 Control color

Pass vector of colors to change the color

ComplexHeatmap::Heatmap(dum.mat, name="mat", col=paint_palette("Vesuvius"))

Color of ComplexHeatmap can also be modified with a color mapping function.

# generate color mapping function
col_fun <- circlize::colorRamp2(breaks = seq(-3,3), 
                                colors = paint_palette("Twilight",7,"continuous"))
ComplexHeatmap::Heatmap(dum.mat, 
                        name="mat", 
                        col=col_fun, 
                        heatmap_legend_param = list(at = c(-3,-1.5,0,1.5,3)) # control breaks of heatmap legend
                        )