Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree.

By Guangchuang Yu, T. T. Lam, Huachen Zhu, Yi Guan. Molecular biology and evolution, 2018

625 citations recorded by the source corpus.

Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external data on phylogenies with two general methods. Method 1 allows external data to be mapped on the tree structure and used as visual characteristic in tree and data visualization. Method 2 plots the data with the tree side by side using different geometric functions after reordering the data based on the tree structure. These two methods integrate data with phylogeny for further exploration and comparison in the evolutionary biology context. Ggtree is available from http://www.bioconductor.org/packages/ggtree.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/4958456ee54cac818ae967a78891a91cdbae9529

How researchers see this paper

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

In Genetics

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

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. Casey W. Dunn
6. Huachen Zhu

Citations in the corpus

• Using ggtree to Visualize Data on Tree‐Like Structures (2020, methodology): “An example presented in Yu et al. (2018) uses ggtree to visualize phylogenetic trees with species abundance distribution stored in the phy-loseq object.”
• Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data (2022, methodology): “We previously proposed two methods for mapping and visualizing associated data on the phylogeny [4].”
• ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data (2021, methodology): “We proposed and implemented this framework design originally in ggtree (Yu et al. 2018) and ggtreeExtra fully embraces the design concept.”
• treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. (2019, methodology): “In addition to incorporating data into a tree object with the full_join method, users can visualize the data mapped onto the tree using ggtree (Yu et al. 2018).”