Venn diagram for annotated regions given the genomic state

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

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.

See also

annotateRegions, vennCounts, vennDiagram

Author

Leonardo Collado-Torres

Examples

## Load data
library("derfinder")

## Annotate regions
annotatedRegions <- annotateRegions(
    regions = genomeRegions$regions,
    genomicState = genomicState$fullGenome, minoverlap = 1
)
#> 2023-05-07 05:31:42.784791 annotateRegions: counting
#> 2023-05-07 05:31:44.170766 annotateRegions: annotating

## 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"
)