如何在R中绘制迈阿密图(GWAS)？

Question

我正在寻找一个函数来运行迈阿密图(GWAS)，它看起来像这样：

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我会有2个不同的GWASes的数据。要模拟绘图，可以使用此数据集(https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html)：

require(qqman)
head(gwasResults)

任何帮助都将不胜感激！非常感谢!

Answer 1

你可以做类似这样的事情

library(qqman)
par(mfrow=c(2,1))
par(mar=c(0,5,3,3))
manhattan(gwasResults,ylim=c(0,10),cex=2.2,cex.lab=2.5,font.lab=2,font.axis=2,cex.axis=1.6,las=2,font=4)
par(mar=c(5,5,3,3))
manhattan(gwasResults,ylim=c(10,0),cex=2.2,cex.lab=2.5,font.lab=2,font.axis=2,cex.axis=1.6,las=2,font=4,xlab="",xaxt="n")
dev.off()

R中的迈阿密图(GWAS)

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Answer 2

你可以试试

library(tidyverse)
library(ggfastman)
data("gwas_data")
gwas_data %>% 
  mutate( gr= "Study 1") %>% 
  mutate(pvalue=-log10(pvalue)) %>% 
  # rbind a second study with pvalues with other sign.
  bind_rows(., mutate(., gr= "Study 2",
                      pvalue = -pvalue)) %>% 
  # plot the points 
  fast_manhattan(., build = "hg18", speed = "fast",log10p = F, dodge_x = T,pointsize = 2.1, pixels = c(1000,500)) + 
  # add significance line
  geom_hline(data= . %>% group_by(gr) %>% slice(1), aes(yintercept = ifelse(pvalue>0, -log10(5e-08),log10(5e-08))),color ="deeppink") + 
  facet_wrap(~gr, scales = "free_y",ncol = 1,strip.position = "right")+
  scale_y_continuous(expression(-log[10](italic(p))),breaks= seq(-90,80,10), labels = abs(seq(-90,80,10)), expand = c(0.01, 0))

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Answer 3

用于创建镜像曼哈顿图的R包是hudson (https://github.com/anastasia-lucas/hudson)，函数是hudson::gmirror。示例(在GitHub中提供)

library(hudson)
data(gwas.t)
data(gwas.b)
gmirror(top=gwas.t, bottom=gwas.b, tline=0.05/nrow(gwas.t), bline=0.05/nrow(gwas.b), 
toptitle="GWAS Comparison Example: Data 1", bottomtitle = "GWAS Comparison Example: Data 2", 
highlight_p = c(0.05/nrow(gwas.t),0.05/nrow(gwas.b)), highlighter="green")