I recently was using the R package
pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While
pvclust provides it’s own plots via
plot() on a
pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages
ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the
pvclust object and integrate them into a generic R
phylo object for plotting the dendrogram in ggtree.