#' plot of HBD segment
#'
#' This function plots HBDsegments or ROHs for all the chromosoms of a given individual
#'
#' @param Submaps a list.submap object
#' @param ROH (optional) a data frame from which the segments will be plotted
#' @param unit the unit used to plot, "Bases" or "cM" (default is "CM")
#' @param id the individual id of the individual wanted
#' @param famid the family id of the individual wanted
#' @param regions a specific region to be highlighted in the plot (optional)
#' @param outfile a name for the plot (optional)
#' @param build the value of the genome build to use to plot chromosome in the plot (35, 36, 37,or 38, default is 37)
#'
#' @details If `ROH` is provided, it must be a data frame containing columns `FID`, `IID`, `CHR`, `POS1`, `POS2`, `PHE`.
#' Such a data frame can be obtained by reading the report generated by `plink` with the option `--homozyg`.
#' If `ROH` is not provided, the function will plot HBD segments defined in the Submaps object.
#' @details The `regions` argument is optional. If provided, it must be a matrix containing one line per region to be highlighted with in each line :
#' \itemize{
#' \item{the chromosome number}
#' \item{start}
#' \item{end}
#' }
#'
#' @return A plot of the individual's HBDsegments.
#'
#' @examples
#' #Please refer to vignette
#'
#' @export
HBDPlotId <- function(Submaps, ROH, unit= "cM", id, famid, quality = 95, regions, outfile, build = 37)
{
if(class(Submaps@submaps_list[[1]])[1] != "snpsMatrix" & class(Submaps@submaps_list[[1]])[1] != "HostspotsMatrix")
stop("need either an hotspots.segments list of submaps or a snpsSegments list of submaps.")
if(class(Submaps@bedmatrix)[1] != "bed.matrix")
stop("Need a bed.matrix.")
if(is.null(Submaps@HBD_recap))
stop("HBD_recap is empty cannot plot, make sure to have atleast one individual considered inbred.")
if(!missing(Submaps) & !missing(ROH))
{
plotROHSegmentsId(Submaps=Submaps, ROH, unit, id=id, famid=famid, regions, outfile=outfile, build=build)
}else{
if(!missing(Submaps))
plotHBDSegmentsId(Submaps = Submaps, id=id, famid=famid, quality=quality, unit=unit, regions, outfile=outfile, build=build)
}
}
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