cummeRbund (version 2.14.0)

csClusterPlot: csClusterPlot

Description

Replaces the default plotting behavior of the old csCluster. Takes as an argument the output of csCluster and plots expression profiles of features facet by cluster.

Usage

csClusterPlot(clustering, pseudocount=1.0,logMode=FALSE,drawSummary=TRUE,sumFun=mean_cl_boot)

Arguments

clustering

The output of csCluster. (Must be the output of csCluster. Only this data format contains the necessary information for csClusterPlot.)

pseudocount

Value added to FPKM to avoid log transformation issues.

logMode

Logical argument whether to plot FPKM with log axis (Y-axis).

drawSummary

Logical value whether or not to draw a summary line for each cluster (by default this is the cluster mean)

sumFun

Summary function used to by drawSummary (default: mean_cl_boot)

Value

A ggplot2 object of expressionProfiles faceted by cluster ID.

Details

This replaces the default plotting behavior of the old csCluster() method. This was necessary so as to preserve the cluster information obtained by csCluster in a stable format. The output of csClusterPlot is a ggplot2 object of expressionProfiles faceted by cluster ID.

References

None.

Examples

	data(sampleData)
	myClustering<-csCluster(sampleGeneSet,k=4)
	csClusterPlot(myClustering)