csDensity {cummeRbund} | R Documentation |
Creates a smoothed density plot, by sample, for log10 FPKM values from a cuffdiff run.
## 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,...)
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 |
Creates a density plot, by sample, for log10-transformed FPKM values from a cuffdiff run.
A ggplot2 plot object
None
Loyal A. Goff
None
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