csClusterPlot: csClusterPlot

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

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)

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.