CMplot Manhattan/QQplot

CMplot重画Manhattan

 install.packages("CMplot")

 library("CMplot")

包里带的演示数据

data(pig60K)

head(pig60K)

数据读入

data14 <- read.table("D:/0-WangZY/1.农科院作科所/邹新宇师姐产量品质协同 
GWAS/GWAS结果0611/Wglutein_23_BJ_150_RESULT.txt")

data13 <- read.table("D:/0-WangZY/1.农科院作科所/邹新宇师姐产量品质协同 
GWAS/GWAS结果0611/Wglutein_22_XX_150_RESULT.txt")

head(data)

染色体名称修改

        data14$V2= c('1'="1A",'2'="1B",'3'="1D", 

        '4'="2A", '5'="2B", '6'="2D",

        '7'="3A", '8'="3B", '9'="3D",

        '10'="4A",'11'="4B",'12'="4D",

        '13'="5A",'14'="5B",'15'="5D",

        '16'="6A",'17'="6B",'18'="6D",

        '19'="7A",'20'="7B",'21'="7D")[as.character(data14$V2)]

单条染色体manhattan

  CMplot(data14, plot.type = "m",LOG10 = TRUE, band = 0,

  threshold = 1e-05, threshold.lwd = 1, threshold.lty = 1,

  signal.cex = c(1.5, 1.5), signal.pch = c(19,19),

  chr.den.col = NULL, cex = 0.7, bin.size = 1e5,

  axis.cex = 1.5,

  file = "jpg", dpi = 300, file.output = TRUE, width = 18, height = 9, verbose = TRUE)

QQplot

  CMplot(data2, plot.type = "q", box = FALSE,

  conf.int = TRUE, conf.int.col = NULL, threshold.col = "red", threshold.lty = 2,

  main = "QQplot",

  file = "jpg", dpi = 600, file.output = TRUE, verbose = TRUE, width = 5, height = 5)

以下均为代码暂存

  file.output = FALSE

  CMplot(pig60K,plot.type="q",box=FALSE,file="jpg",file.name="",dpi=300,

  conf.int=TRUE,conf.int.col=NULL,threshold.col="red",threshold.lty=2,

  file.output=TRUE,verbose=TRUE,width=5,height=5)

  CMplot(data1,plot.type="m",band=0,threshold =1e-05,threshold.col="black",amplify=TRUE,

  signal.col=c("red","green"), 
 signal.cex=c(1.7,1.7),signal.pch=c(19,19),LOG10=TRUE,ylab=expression(-log[10](P.value)),

  pch=19,cex = 0.5,dpi=100,file.output=TRUE,conf.int=F)

 CMplot(data,plot.type = "q",cex = 0.5,conf.int=F,dpi=100,memo= paste(i,".trait",name_data[i,3],sep="_"))

 CMplot(pig60K, plot.type = "m", LOG10 = TRUE, ylim = NULL, threshold = c(1e-06, 1e-04),

  threshold.lty = c(1, 2), threshold.lwd = c(1, 1), threshold.col = c("black","grey"),

  amplify = TRUE, bin.size = 1e+06,

  chr.den.col = c("darkgreen", "yellow", "red"),

  signal.col = c("red", "green"), signal.cex = c(1.5, 1.5), signal.pch = c(19,19),

  file = "jpg", memo = "", dpi = 300, file.output = TRUE, verbose = TRUE,

  width = 14, height = 6)



  CMplot(data, plot.type="m", LOG10=TRUE, ylim=NULL,

  threshold=c(1e-6,1e-4),

  threshold.lty=c(1,2),threshold.lwd=c(1,1),

  threshold.col=c("black","grey"), amplify=F,

  bin.size=1e6,chr.den.col=c("darkgreen", "yellow","red"),

  signal.col=c("red","green"),signal.cex=c(1,1),

  signal.pch=c(19,19),

  highlight = c('MARC0066784','MARC0040492'),highlight.col = 'black',

  highlight.cex = 1,

  file="jpg",dpi=300,

  file.output=TRUE,verbose=TRUE)

threshold设置阈值，如4和6(log以后的)

signal设置超过阈值的点，如绿色和红色的点

highlight个性化某些点，如图中的两个黑色的点

highlight.text为某些点添加标签

最后编辑于：2024.07.08 14:24:45