Hierarchical clustering example

hclust_example.R

# Sample code for performing hierarchical clustering

# install.packages("gplots")
library(gplots)
library(RColorBrewer)

##### Use iris dataset ####
# See ?iris for more info

data <- as.matrix(iris[,1:4])

dr <- as.dist(1 - cor(t(data), method="spearman", use="pairwise.complete.obs"))
dc <- as.dist(1 - cor(data, method="spearman", use="pairwise.complete.obs"))

hr <- hclust(dr, method="complete")
hc <- hclust(dc, method="complete")


#### Plot heatmap ####
mycolors <- brewer.pal(9, "YlOrRd")

mycolhr <- rainbow(3) # generate 3 colors
names(mycolhr) <- unique(iris$Species)
mycolhr <- mycolhr[iris$Species]
    
mycolhc <- gray.colors(4)

pdf("test.pdf")
heatmap.2(data,  
          Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc),
          RowSideColors=mycolhr, ColSideColors=mycolhc,
          col=mycolors, trace="none", density.info="none",
          cexRow=0.6, cexCol=0.8, keysize=1,
          margins=c(5,10), 
          labRow=iris$Species, scale="none",
          sepwidth=c(0,0)
)
dev.off()