CMplot 绘制曼哈顿图和QQ图

#!/usr/bin/env Rscript
# cat ../manhattan_cmplot2.R
# Rscript ../manhattan_cmplot2.R gwas_output.snp gwas_output.png
library(tidyverse)
args=commandArgs(TRUE)
if (length(args) != 2) {
          print ("usage: <gwas file(4 column)>   <out.prefix> ")
  q()
}

input <- args[1]
#max_y <- as.numeric(args[3])
prefix <- args[2]

library(CMplot)

gwas<- read.table(input, header = T);

png(paste(prefix, "_manhattan.png", sep = ""), width=600, height=300)
CMplot(gwas,
       plot.type = "m",
       LOG10 = T,
       col = c("#808080","#000000"),
       cex = 0.3,
       ylab.pos = 2, 
       cex.axis = 1.2,
  #  chr.labels=paste("Chr",c(1:21),sep=""),
       chr.labels.angle=45,
       threshold = c(1e-5,1e-8), ## 显著性阈值, the Bonfferoni adjustment methodc(0.05,0.01)/nrow(gwas)
       threshold.col=c('red','black'),  ## 阈值线颜色
       threshold.lty = c(2,2), ## 阈值线线型
       threshold.lwd = c(2,1), ## 阈值线粗细
       amplify = T,  ## 放大显著SNP
       highlight.cex=1,
       highlight.pch=19,
       main=prefix,
       chr.den.col=c("darkgreen", "yellow","red"),
       signal.cex = c(1,1), ## 点大小
       signal.pch = c(20,20), ## 点形状
       signal.col = c("#A2C39A","#6AA84F","#3E7D21"), ## 点颜色
       file.output = F )
dev.off()

png(paste(prefix, "_qq.png", sep = ""), width=300, height=300)
CMplot(gwas,
       plot.type = "q", ## 绘制QQplot
       box=T, ## 是否加边框
       conf.int=T, ## 是否绘制置信区间
       conf.int.col=NULL, ## 置信区间颜色
       threshold.col="red", ## 对角线颜色
       threshold.lty=2,  ## 线型
       cex = 0.8,
       ylab.pos = 2, 
       cex.axis = 1.5,
       main = "QQ-plot",
       file.output = F )

dev.off()