csDensity {cummeRbund} | R Documentation

## Density plot of CuffData

### Description

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

### Usage

    ## S4 method for signature 'CuffData'
    csDensity(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)
    ## S4 method for signature 'CuffFeatureSet'
    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

### Details

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

### Value

A ggplot2 plot object

### Note

None

### Author(s)

Loyal A. Goff

### 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

[Package cummeRbund version 2.30.0 Index]