MAplot {cummeRbund} | R Documentation |
Creates an M vs A plot (Avg intensity vs log ratio) for a given pair of conditions across all fpkms
## S4 method for signature 'CuffData' MAplot(object,x,y,logMode=T,pseudocount=1,smooth=FALSE,useCount=FALSE)
object |
An object of class 'CuffData'. |
x |
Sample name from 'samples' table for comparison |
y |
Sample name from 'samples' table for comparison |
logMode |
A logical argument to log10-transform FPKM values prior to plotting. |
pseudocount |
Value to be added to FPKM for appropriate log transformation and clustering. (Avoids zero-based errors) |
smooth |
Logical argument whether or not to draw a smoothed line fit through data. |
useCount |
Logical argument whether or not to use mean counts instead of FPKM values. |
None
Returns a ggplot MvsA plot object.
None
Loyal A. Goff and Cole Trapnell
None.
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