Merge pull request #3 from ljljolinq1010/master

Add files via upload

R/PlotCIRatio.R

@@ -0,0 +1,54 @@
+PlotCIRatio <-function(ExpressionSet,measure,BootstrapNub) {
+  names(ExpressionSet)[2]<-"GeneID"
+  bootID<-replicate(BootstrapNub,sample(ExpressionSet$GeneID,replace=T))
+  rawIndex<-c()
+  logIndex<-c()
+  sqrtIndex<-c()
+  for (i in 1:BootstrapNub) {
+    tempID<-data.frame(bootID[,i])
+    names(tempID)<-"GeneID"
+    tempData<-merge(ExpressionSet,tempID,by="GeneID")
+    tempData<-tempData[c(2,1,3:ncol(ExpressionSet))]
+    if (measure=="TAI") {
+      ## raw expression value
+      rawIndex<-rbind(rawIndex,TAI(tempData))
+      ## log2 expression value
+      tempData_log2<-tf(tempData,log2)
+      logIndex<-rbind(logIndex,TAI(tempData_log2))
+      ## square root expression value
+      tempData_sqrt<-tf(tempData,sqrt)
+      sqrtIndex<-rbind(sqrtIndex,TAI(tempData_sqrt))
+    } 
+    if (measure=="TDI") {
+      ## raw expression value
+      rawIndex<-rbind(rawIndex,TDI(tempData))
+      ## log2 expression value
+      tempData_log2<-tf(tempData,log2)
+      logIndex<-rbind(logIndex,TDI(tempData_log2))
+      ## square root expression value
+      tempData_sqrt<-tf(tempData,sqrt)
+      sqrtIndex<-rbind(sqrtIndex,TDI(tempData_sqrt))
+    }  
+  }
+  ## interval ratio
+  rawRatio<-apply(rawIndex, 2,function(x) quantile(x,  probs =0.975))/
+    apply(rawIndex, 2,function(x) quantile(x,  probs =0.025)) 
+  logRatio<-apply(logIndex, 2,function(x) quantile(x,  probs =0.975))/
+    apply(logIndex, 2,function(x) quantile(x,  probs =0.025)) 
+  sqrtRatio<-apply(sqrtIndex, 2,function(x) quantile(x,  probs =0.975))/
+    apply(sqrtIndex, 2,function(x) quantile(x,  probs =0.025)) 
+  ## plot
+  par(mfrow=c(1,1))
+  par(mar=c(7,5,2,2))
+  allRatio<-c(rawRatio,logRatio,sqrtRatio)
+  plot(logRatio,type = "l",col="black",lwd=5,ylim=c(min(allRatio),max(allRatio)+max(allRatio)*0.05),
+       xlab="",ylab=" CI boundary ratio",cex.lab=1.4,cex.axis=1.2,xaxt='n')
+  lines(sqrtRatio,col="black",lty=2,lwd=5)
+  lines(rawRatio,col="black",lty=3,lwd=5)
+  legend("topleft",c("Without transformation","Srqt transformation","Log transformation"),lty=c(3,2,1),col="black",lwd=2,cex=1.4,bty = "n")
+  devNames<-colnames(ExpressionSet)[c(-1,-2)]
+  for (j in 1:length(devNames)) {
+    axis(side=1, at=j,labels=devNames[j], las=2,cex.axis=1.2) # Add development stages as labels, each color represents one meta development stage 
+  } 
+}
+