csClusterPlot {cummeRbund} | R Documentation

## 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)

### 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.

### Value

A ggplot2 object of expressionProfiles faceted by cluster ID.

### Note

None.

### Author(s)

Loyal A. Goff

### References

None.

### Examples

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

[Package cummeRbund version 2.34.0 Index]