全基因组关联分析流程（三）

拿到结果后，我们对结果进行展示，一般 GWAS 的标准结果图为 曼哈顿图 和 QQ 图，作图代码如下：

## 加载作图包
library(qqman)

## 添加候选 SNP 标记位点显示
candidate_Gene <- c("SYN2040", "SYN25096",
                    "SYN6161","PZE-108000718",
                    "SYN28779","PZE-108000725","SYN25098",
                    "PHM7953.11","SYN10050",
                    "SYN35436","SYN28782",
                    "SYN25094","SYN17706",
                    "PZE-109109509", "PZE-109109408",
                    "PZE-107060597", "PZE-107061311",
                    "PZE-105106278", "PZE-104065772"
                    )

YN <- read.table("YN_Adjust.txt", header = T)

manhattan(WJ2, main = "Manhattan Plot", 
          ylim = c(0, 10), cex = 0.6, 
          cex.axis = 0.9, 
          col = c("blue4", "orange3"), 
          suggestiveline = F, genomewideline = 4.6,
#          chrlabs = c(1:10),
          highlight = candidate_Gene          
)

qq(WJ2$P, main = "Q-Q plot of GWAS p-values", 
   xlim = c(0, 6), ylim = c(0, 9), pch = 18, 
   col = "blue4", cex = 1.1, las = 1
  )

曼哈顿图

QQ 图

数据示例入下：

作图数据示例

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