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

BiocManager::install("yeastCC")

x <- matrix(rnorm(100), nrow = 5)
dim(x)

[1]  5 20

heatmap(x)

Remove dendogram

heatmap(x, Colv = NA)

Returns pairwise distance matrix between rows of a data matrix

dist(x)

         1        2        3        4
2 5.728357                           
3 7.435952 7.348611                  
4 6.681600 6.464734 8.268792         
5 5.337119 6.253327 7.095763 5.704023

Clusters using a distance matrix

hclust(dist(x))

Call:
hclust(d = dist(x))

Cluster method   : complete 
Distance         : euclidean 
Number of objects: 5 

Clusters using a distance matrix

plot(hclust(dist(x)))

heatmap(x, Colv = NA)

Cuts a tree, e.g., as resulting from hclust, into the desired number(s) of groups

cutree(tree, no. of clusters)

tree <- hclust(dist(x))
cutree(tree,2)

[1] 1 1 2 1 1

tree <- hclust(dist(x))
cutree(tree,5)

[1] 1 2 3 4 5

• heatmap
• dist
• hclust
• cutree
• pbinom