257 – Advances in Graphical Frameworks and Methods Part 1
Visualizing, Adjusting, and Comparing Dendrograms Using the Dendextend R Package
Tal Galili
Tel Aviv University
A dendrogram is a tree diagram which is often used to visualize a hierarchical clustering of items. Dendrograms are used in many disciplines, ranging from Phylogenetic Trees in computational biology to Lexomic Trees in text analysis. Hierarchical clustering in R is commonly performed using the hclust function. When a more sophisticated visualization is desired, the hclust object is often coerced into a dendrogram object, which in turn is modified and plotted.
The dendextend R package extends the palette of base R functions for the dendrogram class, offering easier manipulation of a dendrogram's shape, color and content through functions such as rotate, prune, color_labels, color_branches, cutree, and more. These can be plotted in based R and ggplot2.
dendextend also provides the tools for comparing the similarity of two dendrograms to one another: either graphically (using a tanglegram plot, or Bk plots), or statistically (with Cophenetic correlation, Baker's Gamma, etc) - while enabling bootstrap and permutation tests for comparing the trees. The dendextendRcpp package provides C++ faster implementations for some of the more computationally intensive functions.