The following example performs hierarchical clustering on the rlog transformed expression matrix subsetted by the DEGs identified in the above differential expression analysis. It uses a Pearson correlation-based distance measure and complete linkage for cluster joining.

library(pheatmap)
geneids <- unique(as.character(unlist(DEG_list[[1]])))
y <- assay(rlog(dds))[geneids, ]
pdf("heatmap1.pdf")
pheatmap(y, scale = "row", clustering_distance_rows = "correlation", 
    clustering_distance_cols = "correlation")
dev.off()

Figure 6: Heat Map with Hierarchical Clustering Dendrograms of DEGs



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