拿到結(jié)果后，我們對結(jié)果進(jìn)行展示，一般 GWAS 的標(biāo)準(zhǔn)結(jié)果圖為 曼哈頓圖 和 QQ 圖，作圖代碼如下：

## 加載作圖包
library(qqman)

## 添加候選 SNP 標(biāo)記位點(diǎn)顯示
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
  )

曼哈頓圖

QQ 圖

數(shù)據(jù)示例入下：

作圖數(shù)據(jù)示例

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