csDendro {cummeRbund} | R Documentation |
Creates a grid graphics plot of a dendrogram of Jensen-Shannon distances between conditions of a CuffFeatureSet or CuffGeneSet object.
## S4 method for signature 'CuffFeatureSet' csDendro(object,logMode=T,pseudocount=1,replicates=FALSE) ## S4 method for signature 'CuffData' csDendro(object,logMode=T,pseudocount=1,replicates=FALSE,...)
object |
An object of class 'CuffFeatureSet' or 'CuffGeneSet' |
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) |
replicates |
A logical value whether or not to plot individual replicates or aggregate condition values. |
... |
Additional arguments to csHeatmap |
None
Returns a dendrogram object and plots that object by default.
None
Loyal A. Goff and Cole Trapnell
None.
data(sampleData) csDendro(sampleGeneSet)