vennRegions: Venn diagram for annotated regions given the genomic state

In derfinderPlot: Plotting functions for derfinder

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

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

## 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"
)

derfinderPlot documentation built on Dec. 20, 2020, 2:01 a.m.