methylKit (version 0.9.5)

plotTargetAnnotation: Plot annotation categories from annotationByGenicParts or annotationByFeature

Description

This function plots a pie or bar chart for showing percentages of targets annotated by genic parts or other query features.

Usage

plotTargetAnnotation(x,precedence=TRUE,col=rainbow(length(x@annotation)),
    ...)

Arguments

x

an annotationByFeature or an annotationByGenicParts object

precedence

TRUE|FALSE. If TRUE there will be a hierachy of annotation features when calculating numbers (with promoter>exon>intron precedence). This option is only valid when x is a annotationByGenicParts object

col

a vector of colors for piechart or the bar plot

...

graphical parameters to be passed to pie or barplot functions

Value

plots a piechart or a barplot for percentage of the target features overlapping with annotation

Examples

# NOT RUN {
data(methylKit)
gene.obj=read.transcript.features(system.file("extdata", "refseq.hg18.bed.txt", package = "methylKit"))
ann=annotate.WithGenicParts(methylDiff.obj, gene.obj)
plotTargetAnnotation(ann,precedence=FALSE)
# }