plotTargetAnnotation {genomation} | R Documentation

## 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, ...)

    ## S4 method for signature '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)

[Package genomation version 1.11.3 Index]