changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / EBSeq / R / PolyFitPlot.R

diff --git a/EBSeq/R/PolyFitPlot.R b/EBSeq/R/PolyFitPlot.R
deleted file mode 100644 (file)
index 59fd29c..0000000
--- a/EBSeq/R/PolyFitPlot.R
+++ /dev/null
@@ -1,44 +0,0 @@
-PolyFitPlot <-
-function(X , Y , nterms , xname="Estimated Mean", yname="Estimated Var", pdfname="", xlim=c(-1,5), ylim=c(-1,7), ChangeXY=F,col="red"){
-       
-       b=rep(NA,nterms)
-       logX=matrix(rep(X, nterms),ncol=nterms, byrow=T)
-       for (i in 1:nterms)
-               logX[,i]=(log10(X))^i
-       colnames(logX)=paste("logmu^",c(1:nterms))
-       rownames(logX)=names(X)
-       NotUse=c(names(X)[X==0],names(Y)[Y==0],names(X)[rowMeans(logX)==-Inf],names(X)[rowMeans(logX)==Inf])
-       Use=names(X[!names(X)%in%NotUse])
-       Lm=lm(log10(Y[Use])~logX[Use,1:nterms])
-       b=summary(Lm)$coefficients[2:(nterms+1),1]
-       d=summary(Lm)$coefficients[1,1]
-       bvec=matrix(rep(b,length(X)),ncol=nterms,byrow=T)
-       fit=rowSums(logX*bvec)+d
-       main2=NULL
-       if (ChangeXY==T){
-               X.plot=log10(Y)
-               Y.plot=log10(X)
-               fit.X.plot=fit
-               fit.Y.plot=log10(X)
-       }
-       else{
-        X.plot=log10(X)
-        Y.plot=log10(Y)
-           fit.X.plot=log10(X)
-               fit.Y.plot=fit
-                                  }
-
-       for (i in 1:nterms)
-               main2=paste(main2,round(b[i],2),"*log(",xname,")^",i,"+")
-       main=pdfname
-       
-       smoothScatter(X.plot, Y.plot ,main=main,xlim=xlim,ylim=ylim,xlab=xname,ylab=yname,axes=F)
-       axis(1,at=seq(xlim[1],xlim[2],by=1), 10^seq(xlim[1],xlim[2],by=1))
-       axis(2,at=seq(ylim[1],ylim[2],by=2), 10^seq(ylim[1],ylim[2],by=2))
-       Sortit=order(fit.X.plot)
-       lines(fit.X.plot[Sortit],fit.Y.plot[Sortit],col=col,lwd=3)
-       output=list(b=b,d=d,lm=Lm,fit=fit,sort=Sortit)
-       names(output$b)=paste(xname,"^",c(1:length(output$b)))
-       output
-}
-