ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data

By Guangchuang Yu, David K. Smith, Huachen Zhu, Yi Guan, T. T. Lam. 2017

4,268 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/01e649ac2ba9f6dfed9adad99256b14ac9f4482e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

1. Guangchuang Yu
2. Zehan Dai
3. Li Zhan
4. Meijun Chen
5. Wenli Tang
6. Yi Guan
7. T. T. Lam
8. Shuangbin Xu

In Molecular Biology

1. Guangchuang Yu
2. Zehan Dai
3. Li Zhan
4. Tianzhi Wu
5. Erqiang Hu
6. Meijun Chen
7. Wenli Tang
8. Yi Guan

In Paleontology

1. Guangchuang Yu
2. Zehan Dai
3. Yi Guan
4. T. T. Lam
5. François Balloux
6. Casey W. Dunn
7. Huachen Zhu

Citations in the corpus

• Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 (2020, positive): “The resulting phylogeny was viewed and annotated using ggtree (10) (Figures S1-S2).”
• Using ggtree to Visualize Data on Tree‐Like Structures (2020, methodology): “The ggtree package is designed to fill this gap by facilitating tree-data integration and visualization (Yu, Smith, Zhu, Guan, & Lam, 2017).”
• microViz: an R package for microbiome data visualization and statistics (2021, methodology): “Other packages in R, such as ggtree (Yu et al., 2017) or metacoder (Foster et al., 2017), can be used to make annotated cladograms similar to the microViz taxonomic association tree visualizations, but the microViz style has a few advantages for the purpose of reporting multivariable model results:…”
• treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. (2019, methodology): “We previously addressed this by implementing a number of parser functions and classes in ggtree (Yu et al. 2017).”
• ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data (2021, methodology): “Couple with the inward circular tree layout supported by ggtree (Yu et al. 2017), ggtreeExtra allows displaying flows or connections between taxa, such as syntenic linkage among genes and genomes, and reticulate evolutionary relationships including horizontal gene transfer, hybridization, and inters”
• Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree. (2018, background): “Ggtree (Yu et al. 2017) parses tree data from various file formats, especially model-based statistical inferences from commonly used programs.”
• Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data (2022, methodology): “Ggtree is an R/Bioconductor package for the visualization and annotation of phylogenetic trees with diverse associated data [3].”
• Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures (2019, methodology): “R package ggtree (51) was used to visualize phylogenetic trees of the TME signature genes.”