Using ggtree to Visualize Data on Tree-Like Structures.

This article contains five basic protocols describing how to visualize trees using the grammar of graphics syntax, how to visualize hierarchical clustering results with associated data, how to estimate bootstrap values and visualize the values on the tree, how to estimate continuous and discrete ancestral traits and visualize ancestral states on the tree, and how to visualize a multiple sequence alignment with a phylogenetic tree. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Using grammar of graphics for visualizing trees Basic Protocol 2: Visualizing hierarchical clustering using ggtree Basic Protocol 3: Visualizing bootstrap values as symbolic points Basic Protocol 4: Visualizing ancestral status Basic Protocol 5: Visualizing a multiple sequence alignment with a phylogenetic tree.
PMID: 32162851 [PubMed - in process]

Source: Current Protocols in Bioinformatics - March 13, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research