\name{MAplot}
 \alias{MAplot}
 \alias{MAplot,CuffData-method}
 
 \title{
 MAplot
 }
 \description{
 Creates an M vs A plot (Avg intensity vs log ratio) for a given pair of conditions across all fpkms
 }
 \usage{

 \S4method{MAplot}{CuffData}(object,x,y,logMode=T,pseudocount=1,smooth=FALSE,useCount=FALSE)

 }
 
 \arguments{
   \item{object}{
 An object of class 'CuffData'.
 }
   \item{x}{
 Sample name from 'samples' table for comparison
 }
   \item{y}{
 Sample name from 'samples' table for comparison
 }
   \item{logMode}{
 A logical argument to log10-transform FPKM values prior to plotting.
 }
   \item{pseudocount}{
 Value to be added to FPKM for appropriate log transformation and clustering. (Avoids zero-based errors)
 }

   \item{smooth}{
 Logical argument whether or not to draw a smoothed line fit through data.

 }
   \item{useCount}{
 Logical argument whether or not to use mean counts instead of FPKM values.

 }
  

  
 }
 \details{
 None
 }
 \value{
 Returns a ggplot MvsA plot object.
 }
 \references{
 None.
 }
 \author{
 Loyal A. Goff and Cole Trapnell
 }
 \note{
 None
 }
 
 \examples{
 	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
 	genes<-a@genes #Create CuffData object for all 'genes'
 	d<-MAplot(genes,'hESC','Fibroblasts') #Create csDensity plot
 	d #Render plot
 }
 
 \keyword{heatmap}