csClusterPlot {cummeRbund} | R Documentation |
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.
csClusterPlot(clustering, pseudocount=1.0,logMode=FALSE,drawSummary=TRUE,sumFun=mean_cl_boot)
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) |
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.
A ggplot2 object of expressionProfiles faceted by cluster ID.
None.
Loyal A. Goff
None.
data(sampleData) myClustering<-csCluster(sampleGeneSet,k=4) csClusterPlot(myClustering)