https://github.com/kehaowu/rmanhattanplot

Provide function to plot manhattan plot in R.
https://github.com/kehaowu/rmanhattanplot

Last synced: 3 months ago
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Provide function to plot manhattan plot in R.

• Host: GitHub
• URL: https://github.com/kehaowu/rmanhattanplot
• Owner: KehaoWu
• License: mit
• Created: 2015-10-13T14:11:11.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2015-10-13T20:00:58.000Z (about 9 years ago)
• Last Synced: 2023-10-20T20:55:54.414Z (about 1 year ago)
• Language: R
• Size: 168 KB
• Stars: 5
• Watchers: 2
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Rmanhattanplot

>

本代码用于做曼哈顿图。曼哈顿图一般用于在GWAS中集中展示全基因组p值。

> 

We provide codes to plot manhattan plot which is commonly used to display p values from GWAS.

!["Manhattan Plot"](Demo/manhattanplot.png "Manhattan Plot")

## 安装 / Installation

  

```R  

install.packages("devtools")

devtools::install_github("KehaoWu/Rmanhattanplot")

```

## 使用 / Usage

应提供全基因组数据：p值、染色体物理位置和染色体编号

如：

```R

# 以下代码仅提供示例数据，不要在真实的环境中运行

> pvalue = runif(100)

> bp = sample(10000:20000,100)

> chr = sample(1:22,100,replace=T)

> head(pvalue)

[1] 0.34011080 0.58690499 0.55647674 0.85494148 0.07878192 0.46782922

> head(bp)

[1] 10805 13579 19443 10023 19322 18355

> head(chr)

[1]  2  9 11 19  8 20

# 提供类似的数据运行以下代码

> library(Rmanhattanplot)

> p = manhattanPlot(pvalue = pvalue,bp = bp,chr = chr,cutoffline = T)

> plot(p) #返回gglot2对象

```

参考：[Make manhattan plot with ggplot2 script](https://pods.iplantcollaborative.org/wiki/display/eot/Make+manhattan+plot+with+ggplot2+script)