R/LDheatmap.addGrob.R

In LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

#' @name LDheatmap.addGrob
#' @aliases LDheatmap.addGrob
#' @title Add a graphical object to an LDheatmap plot
#' @description Add a graphical object to an LDheatmap plot such that the x-axis corresponds
#'to the physical map on the heatmap.
#' @usage LDheatmap.addGrob(LDheatmap, grob, height = 0.2)
#' @param LDheatmap An object of class LDheatmap.
#' @param grob A graphical object of class\code{\link{grob}}.
#' @param height The height of the viewport in which the grob will be placed.
#' @return An object of class LDheatmap given as an argument, with the \code{grob}
#'\code{LDheatmapGrob} modified to inclue the new child grob.
#' @author Sigal Blay <sblay@sfu.ca>
#' @seealso \code{\link{LDheatmap}}
#' @examples # Add an empty rectangle frame
#'data(GIMAP5.CEU) 
#'ll<-LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position,flip=TRUE)
#'llplusgrob<-LDheatmap.addGrob(ll, grid::rectGrob())
#' @keywords hplot
#' @export

# ldheatmap - Plots measures of pairwise linkage disequilibria for SNPs
# Copyright (C) 2004  J.Shin, S. Blay, N. Lewin-Koh, J.Graham, B.McNeney

# To cite LDheatmap in publications use:
# Shin J-H, Blay S, McNeney B and Graham J (2006). LDheatmap: An R
# Function for Graphical Display of Pairwise Linkage Disequilibria
# Between Single Nucleotide Polymorphisms. J Stat Soft, 16 Code Snippet 3

# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

###########################################################################


#_______________________Add a user-defined grob_____________________________________##
LDheatmap.addGrob <- function(LDheatmap, grob, height=0.2) {
  requireNamespace("grid")
  flip <- !is.null(LDheatmap$flipVP)
  vp <- constructVP(LDheatmap$LDheatmapGrob, 0.03, flip)
  vp$height <- unit(height, "npc")
  vpstack <- vp; if(flip) vpstack <- vpStack(LDheatmap$flipVP,vp)
  grob <- gTree(children=gList(grob), vp=vpstack)
  LDheatmap$LDheatmapGrob <- addGrob(LDheatmap$LDheatmapGrob, grob)
  LDheatmap$LDheatmapGrob <- moveTitles(LDheatmap$LDheatmapGrob, vp)
  return(LDheatmap)
}