Is there a function in pheatmap or some complementary package where you can color the branches of the dendrogram used to cluster the rows?

Hi, you should be able to do this by first creating the dendrogram and hclust object via CRAN's dendextend package, and then supplying these hclust objects to pheatmap via cluster_rows and cluster_cols.

One function to colour the dendrogram in dendextend is color_branches()

There is an example with gplots::heatmap.2() in the vignette: https://cran.r-project.org/web/packages/dendextend/vignettes/Cluster_Analysis.html

Kevin