Heat map in R

The heatmap function

The heatmap function can draw a heat map in R from a matrix. In the following examples we are going to use a square matrix but note that the number of rows and columns doesn’t need to be the same.

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m)

Basic heat map in R

Data normalization

The data is normalized by rows by default. However, you might need to normalize it in the column direction ("column") or if no normalization must be carried at all ("none").

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m, scale = "column")

Heat map normalization in R

Color customization

You can pass a color palette to the col argument of the heatmap function. In the following example we are using the viridis palette via hcl.colors.

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m, col = hcl.colors(50))

Heat map color customization in R

Side colors

It is possible to pass a vector of colors to the ColSideColors and RowSideColors argument to annotate the columns and the rows of the matrix, respectively.

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m,
        ColSideColors = rainbow(ncol(m)),
        RowSideColors = rainbow(nrow(m)))

ColSideColors and RowSideColors arguments of the heatmap function

Heat map dendrograms

Remove the row dendrogram of the heat map

Remove row dendrogram

The Rowv argument controls if the row dendrogram should be computed and how. You can pass a dendrogram or a vector specifying the order. Setting it to NA will remove the dendrogram.

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m, Rowv = NA)

Remove the column dendrogram of heatmap in R

Remove column dendrogram

The Colv argument is the equivalent of Rowv but for columns. Set it to NA to remove the column dendrogram.

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m, Colv = NA)

Remove the dendrograms of the heatmap function in R

Remove both dendrograms

Setting Rowv and Colv to NA will remove both dendrograms of the heat map and no reordering will be computed.

# Matrix
m <- matrix(rnorm(100), ncol = 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)

heatmap(m, Rowv = NA, Colv = NA)
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See also