methylKit (version 0.99.2)

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)), ...)
# S4 method for annotationByFeature
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=readTranscriptFeatures(system.file("extdata", 
"refseq.hg18.bed.txt", package = "methylKit"))
ann=annotateWithGenicParts(methylDiff.obj, gene.obj)
plotTargetAnnotation(ann,precedence=FALSE)



# }