correctComBat <-function(Ys,batchCL,grps,cGsub,Conf,theme,type)
{
comdat<-t(Ys);
comres<-ComBat(dat=comdat,batch=batchCL,mod=NULL, par.prior=TRUE, prior.plots=FALSE) # run combat
write.table(t(comres),paste0("correctComBat/",Sys.Date(),"combatCorrectedData.txt"),quote=TRUE,sep="\t",row.names=TRUE)
## compare combat predicted data with observed data
x <- c(comres)
y <- c(comdat)
tdat4<-sdat4<-data.frame(x,y)
colnames(tdat4)<-c("Combat_predictedData","ObservedData")
write.table(tdat4,paste0("correctComBat/",Sys.Date(),"Combat_predicted_vs_ObservedData.txt"),quote=TRUE,sep="\t",row.names=TRUE)
fig5<-ggplot(data=sdat4, aes(x, y,colour=c("orange")[rep(1,length(y))])) +
geom_point(aes(shape=factor(16)),size=3,alpha=.2)+scale_colour_manual("",values="orange")+theme(legend.key = element_blank())+
labs(title=paste0("Correlation: ",round(cor(x,y),2)),x="Combat predicted data",y="Observed data") +theme_bw()+theme+
theme(legend.position = c(10000, 10000))+theme(legend.key = element_blank())+theme(legend.title=element_blank())+
guides(colour = guide_legend(override.aes = list(linetype=0)))
ggsave(filename ="correctComBat/Combat_predicted_vs_ObservedData.pdf", device=cairo_pdf,plot = fig5)
### pca on combat batch corrected
res5<-prcomp(t(comres),scale=TRUE)
x <- res5$x[,1]
y <- res5$x[,2]
sdat6 <- data.frame(x=x,y=y,group=grps[batchCL])
tdat6<-data.frame(sdat6[,1:2],grps[batchCL],Conf)
colnames(tdat6)<-c("PC-1","PC-2","Batch","Type")
rownames(tdat6)<-rownames(Ys)
write.table(tdat6,paste0("correctComBat/",Sys.Date(),"pca_After_Combat_Correction.txt"),quote=TRUE,sep="\t",row.names=TRUE)
fig7<-ggplot(data= sdat6, aes(x, y,colour=cGsub[batchCL])) +
geom_point(aes(shape=factor(c(16,15)[Conf],labels=type)),size=8,alpha=.7)+
scale_shape_manual(values=c(16,15),guide=guide_legend(override.aes=aes(size=6)))+
labs(title="",x="PC-1",y="PC-2") +theme_bw()+theme+
scale_colour_manual("Batch",labels=grps,values=cGsub)+theme(legend.key = element_blank())+
theme(legend.title=element_blank())+guides(colour = guide_legend(override.aes = list(linetype=0)))
ggsave(filename ="correctComBat/pca_After_Combat_Correction.pdf", device=cairo_pdf,plot = fig7)
comres
}
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