plot_Manhantan.R

library(CMplot)
data1 <- read.table("IHS.csv",header = T,sep = ',') 
color_set <- c("#801e91","#344fa8","#f7cb34","#a8a8aa","#ffe4c7")
CMplot(data1, plot.type="m", LOG10=F,       
       chr.den.col=NULL, col = color_set,      
       threshold = 0.186813, threshold.col = "red", threshold.lwd= 2, threshold.lty =1,      
       amplify = FALSE, file.output=T, height=5, width = 10,     
       ylab = "iHS",
       ###ylab = expression(paste(italic('F'),st)),
       pch =".", cex =4, dpi = 600, file = "jpg",memo = "IHS")


## circol 图
#SNP chr    pos Somatic cell score  Milk yield Fat percentage
#1 SNP1   1  59082        0.000244361 0.000484255    0.001379210
#2 SNP2   1 118164        0.000532272 0.000039800    0.000598951
data1 <- read.table("wag_A-H.windowed.weir.fst",sep='\t', header = TRUE)
data2 <- read.table("A_H-Wag.norm.XPEHH",sep='\t', header = TRUE)
data3 <- read.table("wag_A-H-lnratio.txt", sep='\t', header = TRUE)

merged_data <- merge(merge(data1, data2, by=c("CHR","BP")), 
                     data3, by=c("CHR","BP"))
input_data <- merged_data[,c(3,1,2,4,6,8)]
CMplot(input_data,type="p",plot.type="c",LOG10=FALSE,outward=TRUE,
       col=matrix(c("#4DAF4A", NA, NA,
                    "dodgerblue4","deepskyblue", NA,
                    "dodgerblue1", "olivedrab3", "darkgoldenrod1"), 
                    nrow=3, byrow=TRUE),
       chr.labels=paste("Chr",c(1:29),sep=""),threshold=NULL,r=1.5,cir.chr.h=1.5,
       cir.band=1,file="jpg", dpi=600,chr.den.col="black",
       file.output=T,verbose=TRUE,width=10,height=10)


## 可视化在每个染色体上选择信号的值
library(ggplot2)

data<-read.table("Fst_JBC-EU.windowed.weir.fst",header=T)
sc3 = subset(data,CHROM=="10")
p <- ggplot(sc3,aes(x=BIN_END/1000000,y=WEIGHTED_FST)) + 
  geom_point(size=0.5, colour="blue") + xlab("Physical distance (Mb)")+ ylab("Fst") + ylim(0,1)
p + theme_bw()