cummeRbund (version 2.14.0)

csDensity: Density plot of CuffData

Description

Creates a smoothed density plot, by sample, for log10 FPKM values from a cuffdiff run.

Usage

"csDensity"(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)
"csDensity"(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)

Arguments

object

An object of class CuffData.

logMode

A logical value of whether or not to log10-transform FPKM values. By default this is TRUE.

pseudocount

Pseudocount value added to FPKM to avoid errors in log-transformation of true zero values.

labels

A list of tracking_id values or gene_short_name values used for 'callout' points on the density plot for reference. (Not implemented yet).

features

Will include all fields from 'features' slot in returned ggplot object. Useful for further manipulations of plot object using feature-level attributes (e.g. gene_type, class_code, etc)

replicates

A logical value whether or not to plot individual replicates or aggregate condition values.

...

Additional arguments

Value

A ggplot2 plot object

Details

Creates a density plot, by sample, for log10-transformed FPKM values from a cuffdiff run.

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<-csDensity(genes) #Create csDensity plot
	d #Render plot