@@ -1,48 +1,55 @@

-#' kpAddChromosomeNames

-#' 

-#' @description 

-#' 

-#' Plots the chromosome names in the karyoplot

-#' 

-#' @details 

-#' 

-#' Given a KaryoPlot object, plot the names of the depicted chromosomes. This 

-#' function is usually automatically called by plotKaryotype unless 

-#' \code{labels.plotter} is NULL.

-#' 

-#' @usage kpAddChromosomeNames(karyoplot, xoffset=0, yoffset=0, ...)

-#' 

-#' @param karyoplot    a \code{karyoplot} object returned by a call to \code{plotKaryotype}

-#' @param xoffset    (numeric) a number of units to move the the chromosome names on the x axis with respect to their standard position (defaults to 0)

-#' @param yoffset    (numeric) a number of units to move the the chromosome names on the y axis with respect to their standard position (defaults to 0)

-#' @param ...  any additional parameter to be passed to the text plotting. All R base graphics params are passed along.

-#' 

-#' @return

-#' invisibly returns the given karyoplot object

-#'  

-#' @seealso \code{\link{plotKaryotype}}, \code{\link{getChromosomeNamesBoundingBox}}

-#' 

-#' @examples

-#'

-#' kp <- plotKaryotype(labels.plotter = NULL)

-#' kpAddChromosomeNames(kp, col="red", srt=30)

-#'  

-#' @export kpAddChromosomeNames

-#' 

-

-kpAddChromosomeNames <- function(karyoplot, xoffset=0, yoffset=0, ...) {

-  karyoplot$beginKpPlot()

-  on.exit(karyoplot$endKpPlot())

-  

-  bb <- getChromosomeNamesBoundingBox(karyoplot)

-  

-  chr.labels <- karyoplot$chromosomes

-

-  x <- (bb$x0+bb$x1)/2 + yoffset

-  y <- (bb$y0+bb$y1)/2 + xoffset

-  

-  graphics::text(x=x, y=y, labels=chr.labels, ...)

-  

-  invisible(karyoplot)

-}

-

+#' kpAddChromosomeNames

+#' 

+#' @description 

+#' 

+#' Plots the chromosome names in the karyoplot

+#' 

+#' @details 

+#' 

+#' Given a KaryoPlot object, plot the names of the depicted chromosomes. This 

+#' function is usually automatically called by plotKaryotype unless 

+#' \code{labels.plotter} is NULL.

+#' 

+#' @usage kpAddChromosomeNames(karyoplot, names=NULL, xoffset=0, yoffset=0, ...)

+#' 

+#' @param karyoplot    a \code{karyoplot} object returned by a call to \code{plotKaryotype}

+#' @param names      (character vector) the names to use for the chromosomes. If NULL, the chromosome names in the original genome will be used. (defaults to NULL)

+#' @param xoffset    (numeric) a number of units to move the the chromosome names on the x axis with respect to their standard position (defaults to 0)

+#' @param yoffset    (numeric) a number of units to move the the chromosome names on the y axis with respect to their standard position (defaults to 0)

+#' @param ...  any additional parameter to be passed to the text plotting. All R base graphics params are passed along.

+#' 

+#' @return

+#' invisibly returns the given karyoplot object

+#'  

+#' @seealso \code{\link{plotKaryotype}}, \code{\link{getChromosomeNamesBoundingBox}}

+#' 

+#' @examples

+#'

+#' kp <- plotKaryotype(labels.plotter = NULL)

+#' kpAddChromosomeNames(kp, col="red", srt=30)

+#'  

+#' @export kpAddChromosomeNames

+#' 

+

+kpAddChromosomeNames <- function(karyoplot, chr.names=NULL, xoffset=0, yoffset=0, ...) {

+  #Validate parameters

+  if(!methods::is(karyoplot, "KaryoPlot")) stop("'karyoplot' must be a valid 'KaryoPlot' object")

+  

+  if(is.null(chr.names)) chr.names <- karyoplot$chromosomes

+  if(length(chr.names)==0) stop("In kpAddChromosomeNames: chr.names must have at least one element.")

+  if(!all(methods::is(chr.names, "character"))) stop("In kpAddChromosomeNames: all elements of chr.names must be characters.")

+

+  #Begin plotting

+  karyoplot$beginKpPlot()

+  on.exit(karyoplot$endKpPlot())

+  

+  bb <- getChromosomeNamesBoundingBox(karyoplot)

+  

+  x <- (bb$x0+bb$x1)/2 + xoffset

+  y <- (bb$y0+bb$y1)/2 + yoffset

+  

+  graphics::text(x=x, y=y, labels=chr.names, ...)

+  

+  invisible(karyoplot)

+}

+