genomation (version 1.4.2)

plotTargetAnnotation: Plot annotation categories from AnnotationByGeneParts 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 = getColors(length(x@annotation)), cex.legend = 1, ...)
## S3 method for class 'AnnotationByFeature':
plotTargetAnnotation(x, precedence = TRUE,
  col = getColors(length(x@annotation)), cex.legend = 1, ...)

Arguments

x

a AnnotationByFeature or AnnotationByGeneParts 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 AnnotationByGeneParts object

col

a vector of colors for piechart or the bar plot

cex.legend

a numeric value of length 1 to specify the size of the legend. By default 1.

...

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

data(cage)

bed.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
gene.parts = readTranscriptFeatures(bed.file)
annot = annotateWithGeneParts(cage, gene.parts, intersect.chr=TRUE)
plotTargetAnnotation(annot)