Venn diagram for annotated regions given the genomic state

Description

Makes a venn diagram for the regions given the genomic state showing how many regions overlap introns, exons, intergenic regions, none or multiple groups.

Usage

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vennRegions(annotatedRegions, subsetIndex = NULL, ...)

Arguments

annotatedRegions

The output from annotateRegions used on regions.

subsetIndex

A vector of to use to subset the regions to use for the venn diagram. It can be a logical vector of length equal to the number of regions or an integer vector. If NULl, then it's ignored.

...

Arguments passed to vennDiagram.

Value

Makes a venn diagram plot for the annotation given the genomic state and the actual venn counts used to make the plot.

Author(s)

Leonardo Collado-Torres

See Also

annotateRegions, vennCounts, vennDiagram

Examples

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## Load data
library('derfinder')

## Annotate regions
annotatedRegions <- annotateRegions(regions = genomeRegions$regions, 
    genomicState = genomicState$fullGenome, minoverlap = 1)

## Make venn diagram
venn <- vennRegions(annotatedRegions)

## Add title and choose text color
venn2 <- vennRegions(annotatedRegions, main = 'Venn diagram', counts.col = 
    'blue')

## Subset to only significant regions, so you don't have to annotate them
## again
venn3 <- vennRegions(annotatedRegions, subsetIndex = 
    genomeRegions$regions$significant == 'TRUE', main = 'Significant only')