##
# mae.loessPlot() - generate loess line and fitted plots for 
# for two samples if doPlot is true. The plots include:
#      M vs A (loess line)
#      M vs A (loess fitted) plots
# Parameters:
#   x and y single sample matrices or data frames
#   xName and yName are sample names
#   doPlot = TRUE, if do a plot, else just compute the loess data
# Return:
#   AValue is c(log10(as.matrix(x)) + log10(as.matrix(y)))/2
#   MValue is c(log2(as.matrix(x)/as.matrix(y)))
#   dMvsA is data.frame(ID=(cbind(x,y)[,1]),AVAL=AValue, MVAL=MValue)
#   dMvsA.lo is loess fit of (MValue ~ AValue)
#   fitted is (MValue-dMvsA.lo$fitted) 
#   sNames is c(xName,yName)
#
# Developer: S. Sundaram, P. Lemkin, G. Thornwal
# Date: 06/30/2003
##
mae.loessPlot <- function(x,y,xName,yName,doPlot=TRUE)
{ # mae.loessPlot
  AValue <- c(log10(as.matrix(x)) + log10(as.matrix(y)))/2
  MValue <- c(log2(as.matrix(x)/as.matrix(y)))
  dMvsA <- data.frame(ID=(cbind(x,y)[,1]), AVAL=AValue, MVAL=MValue)
  dMvsA.lo <- loess(MVAL ~ AVAL, dMvsA, degree=1, span=.5)
  samplesTitle <- paste(xName,"vs.",yName)
  #
  mTitleL <- paste("M vs A (loess line for",samplesTitle,")")
  if(doPlot) plot(AValue,MValue,main=mTitleL,xlab="A(log10)",ylab="M(log2)")
  points(AValue,dMvsA.lo$fitted, col="red", pch=18);
  mTitleF <- paste("M vs. A (loess fitted for",samplesTitle,")")
  fitted <- MValue-dMvsA.lo$fitted
  if(doPlot) plot(AValue,fitted,main=mTitleF,xlab="A(log10)", ylab="M(log2)")
  sNames=c(xName,yName)
  return(AValue=AValue, MValue=MValue, dMvsA=dMvsA, dMvsA.lo=dMvsA.lo,
         fitted=fitted, sNames=sNames)
} # end of mae.loessPlot