README.md

In YuLab-SMU/ggtreeExtra: An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

ggtreeExtra: An R Package To Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”.

‘ggtreeExtra’ extends the method for mapping and visualizing associated data on phylogenetic tree using ‘ggtree’. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by ‘ggtree’ with the grammar of ‘ggplot2’.

:writing_hand: Author

Shuangbin Xu and GuangChuang Yu

School of Basic Medical Sciences, Southern Medical University.

If you use ggtreeExtra in published research. Please cite the paper:

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang*, X Bo* and G Yu*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166.

• Source code to produce Supplementary Material

:arrow_double_down: Installation

The development version from github:

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("xiangpin/ggtreeExtra")

The released version from Bioconductor:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggtreeExtra")

:beginner: Usage

Please refer to the online vignette.

:sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

YuLab-SMU/ggtreeExtra documentation built on April 15, 2024, 6:25 p.m.