R/breaks-major.R

In teunbrand/ggnomics: ggnomics

#' @name S4BreaksMajor
#' @title Major breaks for Vectors
#' @description Produces major breaks for use on plot axes.
#'
#' @param x A object describing the range of values
#' @param n A desired number of breaks
#' @param ... Arguments passed to downstream functions
#'
#' @return A vector with major breaks positions
#'
#' @details The downstream function that arguments are typically passed to is
#' the \code{\link[labeling]{extended}} function, except when ranges
#' are given as \code{\linkS4class{GenomicRanges}}.
#'
#' @export
#'
#' @examples
#' # For simple numerics
#' S4BreaksMajor(c(0, 12))
#'
#' # Gives GPos extremes for GRanges
#' require(GenomicRanges)
#' S4BreaksMajor(GRanges(c("chr1:100-200", "chr2:140-260")))
setGeneric(
    "S4BreaksMajor",
    function(x, n = 5L, ...) {
        standardGeneric("S4BreaksMajor")
    }
)

# Equivalent to the scales::extended_breaks() method
# S4 classes that have a projection on the real number line, e.g. IRanges or
# numeric-Rle should give limits in numeric terms, so they also go through this
# breaks method.

#' @rdname S4BreaksMajor
setMethod(
    "S4BreaksMajor",
    signature(x = "numeric"),
    function(x, n = 5L, ...) {
        x <- x[is.finite(x)]
        if (length(x) == 0) {
            return(numeric())
        }
        rng <- range(x)
        labeling::extended(rng[1], rng[2], n, ...)
    }
)


# Takes chromosome starts and ends as breaks. Should thus give appropriate
# positions for major gridlines.

#' @rdname S4BreaksMajor
setMethod(
    "S4BreaksMajor",
    signature(x = "GRanges"),
    function(x, n = 5L, ...) {
        if (length(x) == 0) {
            return(GreekSoldier(GRanges()))
        }
        br <- sort(GPos(seqnames = rep(seqnames(x), 2),
                        pos = c(start(x), end(x))))
        GreekSoldier(br)
    }
)