library(sva)
library("FactoMineR")
library("factoextra")
setwd("//Users//xiaoyezzy//Desktop")                #设置工作目录
pheno=read.table("pheno.txt",header=T,sep="\t",row.names=1)
data = read.table("matrix.txt",header=T,sep="\t",row.names=1)  

#设置pca函数
pca.plot = function(data,col){
  df.pca <- PCA(t(data), graph = FALSE)
  fviz_pca_ind(df.pca,
               geom.ind = "point",
               col.ind = col ,
               addEllipses = TRUE,
               legend.title = "Groups"
  )
}
#查看校正前的PCA图
pca.plot(data,factor(pheno$batch))

combat_data <- ComBat(dat = as.matrix(data), batch = pheno$batch)
#查看校正后的PCA图
pca.plot(combat_data,factor(pheno$batch))