MAplot {cummeRbund} | R Documentation

## MAplot

### Description

Creates an M vs A plot (Avg intensity vs log ratio) for a given pair of conditions across all fpkms

### Usage

    ## S4 method for signature 'CuffData'
    MAplot(object,x,y,logMode=T,pseudocount=1,smooth=FALSE,useCount=FALSE)

### Arguments

`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.

### Details

None

### Value

Returns a ggplot MvsA plot object.

### Note

None

### Author(s)

Loyal A. Goff and Cole Trapnell

### References

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

[Package cummeRbund version 2.30.0 Index]