# ggtreeExtra

**Repository Path**: mloine/ggtreeExtra

## Basic Information

- **Project Name**: ggtreeExtra
- **Description**: 搬运  方便下载
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-09-09
- **Last Updated**: 2024-05-02

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

<!-- README.md is generated from README.Rmd. Please edit that file -->

# 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
mapped to circular layout, fan layout, or other layout tree built by
‘ggtree’ with the grammar of ‘ggplot2’.

# :writing\_hand: Author

[Shuangbin Xu](https://github.com/xiangpin) and [GuangChuang
Yu](https://guangchuangyu.github.io)

School of Basic Medical Sciences, Southern Medical University.

`ggtreeExtra` has not been published, if you use `ggtreeExtra` in
published research. Please cite the most appropriate paper(s) from this
list:

1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
    ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
    [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
      - [Source code and data to reproduce figures in the
        article](https://github.com/GuangchuangYu/ggtree-current-protocols)
2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
    methods for mapping and visualizing associated data on phylogeny
    using ggtree. ***Molecular Biology and Evolution***, 2018,
    35(2):3041-3043. doi:
    [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
      - [Source code to produce Supplementary
        Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
    R package for visualization and annotation of phylogenetic trees
    with their covariates and other associated data. ***Methods in
    Ecology and Evolution***. 2017, 8(1):28-36. doi:
    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

# :arrow\_double\_down: Installation

The development version from `github`:

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

The released version from
[`Bioconductor`](https://bioconductor.org/packages/ggtreeExtra):

``` r
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](https://bioconductor.org/packages/devel/bioc/vignettes/ggtreeExtra/inst/doc/ggtreeExtra.html).

<!-- <img src="inst/extdata/fig1.png" style="display: block; margin: auto;" /> -->

# :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](CONDUCT.md).