assessCorrectBATCH <-
function(rerun2,qopt,nt,rerun22,theme){
if(nt!=1){
#### Detect biological effect
pnames=colnames(rerun22$coefficients)
for(i in 2:ncol(rerun22$coefficients)){
blci<-data.frame(matrix(paste0("pPC-",1:qopt)),matrix(rerun22$coefficients[,i]),rerun22$coeffCI[,(2*i-1):(2*i)])
colnames(blci)<-c("x","y","ylo","yhi")
bldat<-blci[,-1]
rownames(bldat)<-blci[,1]
colnames(bldat)<-c("Effect","LowerCI","UpperCI")
filnamep1=paste0(getwd(),"/assessCorrectBATCH/",Sys.Date(),"_BioEFFECT.txt")
write.table(bldat,filnamep1,quote=TRUE,sep="\t",row.names=TRUE)
bpl <- ggplot(blci, aes(x=x, y=y, ymin=ylo, ymax=yhi))+geom_pointrange()+labs(title="",x="",y="Biological effect")+
theme_bw()+theme+coord_flip()+geom_hline(aes(yintercept=0),lty=5,col=2,size=1.5)
suppressMessages(ggsave(filename=paste0(getwd(),"/assessCorrectBATCH/BioEFFECT-",pnames[i],".png"),plot = bpl))}}
#### Detect batch effect
lci<-data.frame(matrix(paste0("pPC-",1:qopt)),matrix(rerun2$coefficients[,2]),rerun2$coeffCI[,3:4])
colnames(lci)<-c("x","y","ylo","yhi")
ldat<-lci[,-1]
rownames(ldat)<-lci[,1]
colnames(ldat)<-c("Effect","LowerCI","UpperCI")
write.table(ldat,paste0("assessCorrectBATCH/",Sys.Date(),"batchEffect.txt"),quote=TRUE,sep="\t",row.names=TRUE)
pl <- ggplot(lci, aes(x=x, y=y, ymin=ylo, ymax=yhi))+geom_pointrange()+labs(title="",x="",y="Batch effect")+
theme_bw()+theme+coord_flip()+geom_hline(aes(yintercept=0),lty=5,col=2,size=1.5)
suppressMessages(ggsave(filename="assessCorrectBATCH/BatchEffect.png",plot = pl))
}
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