R/vennRegions.R

In derfinderPlot: Plotting functions for derfinder

#' 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.
#'
#' @param annotatedRegions The output from [annotateRegions][derfinder::annotateRegions]
#' used on `regions`.
#' @param 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.
#' @param ... Arguments passed to [vennDiagram][limma::venn].
#'
#' @return Makes a venn diagram plot for the annotation given the genomic state
#'     and the actual venn counts used to make the plot.
#'
#' @author Leonardo Collado-Torres
#' @seealso [annotateRegions][derfinder::annotateRegions], [vennCounts][limma::venn],
#'     [vennDiagram][limma::venn]
#' @export
#'
#' @importFrom limma 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"
#' )
vennRegions <- function(annotatedRegions, subsetIndex = NULL, ...) {

    ## Check input
    stopifnot("countTable" %in% names(annotatedRegions))

    ## Subset if necessary
    if (!is.null(subsetIndex)) {
        annotatedRegions$countTable <- annotatedRegions$countTable[subsetIndex, ]
    }

    ## Get venn counts
    vennInfo <- vennCounts(annotatedRegions$countTable > 0)

    ## Make plot
    vennDiagram(vennInfo, ...)

    ## Return data
    return(vennInfo)
}