ggplot2 画 Q-Q图

qq plot 是为了检验实际分布与假设分布是否相同。

我的数据来自于plink处理后生成的p值，所以不同的分布根据实际情况修改。

下面函数来自于 qqman 包，可定制性太差，就改下用ggplot2画。

qq = function(pvector, ...) {
    
    # Check for sensible input
    if (!is.numeric(pvector)) stop("Input must be numeric.")
    
    # limit to not missing, not nan, not null, not infinite, between 0 and 1
    pvector <- pvector[!is.na(pvector) & !is.nan(pvector) & !is.null(pvector) & is.finite(pvector) & pvector<1 & pvector>0]
    
    # Observed and expected
    o = -log10(sort(pvector,decreasing=FALSE))
    e = -log10( ppoints(length(pvector) ))
    
    
#     # The old way
#     plot(e, o, pch=20, 
#          xlab=expression(Expected~~-log[10](italic(p))), 
#          ylab=expression(Observed~~-log[10](italic(p))), 
#          ...)
    
    # The new way to initialize the plot.
    ## See http://stackoverflow.com/q/23922130/654296
    ## First, define your default arguments
    def_args <- list(pch=20, xlim=c(0, max(e)), ylim=c(0, max(o)), 
                     xlab=expression(Expected~~-log[10](italic(p))), 
                     ylab=expression(Observed~~-log[10](italic(p)))
    )
    ## Next, get a list of ... arguments
    #dotargs <- as.list(match.call())[-1L]
    dotargs <- list(...)
    ## And call the plot function passing NA, your ... arguments, and the default
    ## arguments that were not defined in the ... arguments.
    tryCatch(do.call("plot", c(list(x=e, y=o), def_args[!names(def_args) %in% names(dotargs)], dotargs)), warn=stop)

    # Add diagonal
    abline(0,1,col="red")
    
}

使用 ggplot2 作图

qq_dat <- data.frame(obs=-log10(sort(pd_dat$P,decreasing=FALSE)),
                     exp=-log10( ppoints(length(pd_dat$P))))
pd_qq <- ggplot(data=qq_dat,aes(exp,obs))+
  geom_point(alpha=0.7,color="#7F7F7FFF")+
  geom_abline(color="#D62728FF")+
  xlab("Expected -log10(P-value)")+
  ylab("Observed -log10(P-value)")+
  scale_x_continuous(limits = c(0,7))+
  scale_y_continuous(limits = c(0,7))+
  theme(
    axis.title = element_text(size=12,face="bold"),
    axis.text = element_text(face="bold",size=8,color = "black"),
    #axis.line = element_line(size=0.8,color="black"),
    axis.ticks= element_line(size=0.8,colour = "black"),
    panel.grid =element_blank(),
    panel.border = element_rect(fill=NA,size = 0.8),
    panel.background = element_blank())