18.2 pheatmap function from the pheatmap package

# install pheatmap package
install.package("pheatmap")

Get started:

# load package
library(pheatmap)

# create matrix
mat <- matrix(rnorm(1200), ncol=6)

# heatmap with the defaults parameters
pheatmap(mat)

Change the color palette / gradient

# with "rainbow" colors
pheatmap(mat, color=rainbow(50))

# with blue to red (middle color white)
pheatmap(mat, color=colorRampPalette(c("navy", "white", "red"))(50))

Do not cluster rows or columns

# remove the clustering by rows
pheatmap(mat, cluster_rows=FALSE)

# remove the clustering by columns
pheatmap(mat, cluster_cols=FALSE)

# remove both clusterings
pheatmap(mat, cluster_rows=FALSE, cluster_cols=FALSE)

Add some annotation colored bar(s):

# add column names to mat
colnames(mat) <- paste0("Sample", 1:6)

# create data frame for annotation (in the case of samples, information about the experiment, for example)
annot_cols = data.frame(
                Group = c(rep("WT", 3), rep("KO", 3)), 
                TimePoint = rep(c(0, 5, 10), each=2),
        row.names = colnames(mat)
                )
# plot
pheatmap(mat, annotation_col = annot_cols)