Abstract
We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree in a circular or rectangular layout (https://www.bioconductor.org/packages/ggtreeExtra). The package supports more data types and visualization methods than other tools. It supports using the grammar of graphics syntax to present data on a tree with richly annotated layers and allows evolutionary statistics inferred by commonly used software to be integrated and visualized with external data. GgtreeExtra is a universal tool for tree data visualization. It extends the applications of the phylogenetic tree in different disciplines by making more domain-specific data to be available to visualize and interpret in the evolutionary context.
Highlights
Phylogenetic tree is widely used in a number of biological fields, including comparative genomics, epidemiology and microbiome
A recent research constructed a phylogenetic tree of SARS-CoV-2 and integrated the state information of initial diagnosis of Australian SARS-CoV-2 genomes and country information of the origin of the GISAID genomes to investigate origins and transmission pathways of the COVID-19 strains in Australia[1]
The ggtreeExtra package implemented a layer function, geom_fruit, which is a universal function for aligning graphic layer to phylogenetic tree (Supplemental Fig. S1, S2 and Tab S1)
Summary
Phylogenetic tree is widely used in a number of biological fields, including comparative genomics, epidemiology and microbiome. To fully extend ggtree to support visualizing phylogenetic data from multiple sources in the big data era especially for circular layout, we developed the ggtreeExtra package.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
