csDensity: Density plot of CuffData

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.