plotCluster
(Package: derfinderPlot) :
Plot the coverage information surrounding a region cluster
For a given region found in calculatePvalues, plot the coverage for the cluster this region belongs to as well as some padding. The mean by group is shown to facilitate comparisons between groups. If annotation exists, you can plot the trancripts and exons (if any) overlapping in the vicinity of the region of interest.
plotOverview
(Package: derfinderPlot) :
Plot a karyotype overview of the genome with the identified regions
Plots an overview of the genomic locations of the identified regions (see calculatePvalues) in a karyotype view. The coloring can be done either by significant regions according to their p-values, significant by adjusted p-values, or by annotated region if using annotateNearest.
This function takes the regions found in calculatePvalues and assigns them genomic states contructed with makeGenomicState. The main workhorse functions are countOverlaps and findOverlaps. For an alternative plot check plotCluster which is much slower and we recommend it's use only after quickly checking the results with this function.
vennRegions
(Package: derfinderPlot) :
Venn diagram for annotated regions given the genomic state
Makes a venn diagram for the regions given the genomic state showing how many regions overlap introns, exons, intergenic regions, none or multiple groups.
providing 
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