R/plotting.R

In binmapr: Call Marker from Snp Data using Binmap

#' genotype plotting
#'
#' @importFrom graphics plot
#' @param geno genotype vector
#' @param pos.start position start index,
#' for exmaple, the pos.start of chr1_1234 is 6
#' @param xlab x lab
#' @param ylab y lab
#' @param title title
#'
#' @return a genotype distribution by the chromsome
#' 
#' @examples 
#' geno <- c(1,1,1,1,0,0,0,2,2,2)
#' names(geno) <- c("1_1","1_100","1_200","1_210","1_230","1_300","1_500","1_600","1_700","1_1000")
#' plotGeno(geno, pos.start = 3)
#' 
#' @export
#' @author Zhougeng Xu
plotGeno <- function(geno,
                     pos.start = 6,
                     xlab = "position",
                     ylab = NULL,
                     title = NULL){

  pos <- as.numeric(substring(names(geno), pos.start))

  plot(x=pos, y = geno, pch=20 , cex = 0.2,
       xlab = xlab, ylab = ylab, ylim = c(0,2),
       main = title)
}

#' QTL mapping plot
#'
#' @importFrom graphics plot
#' @importFrom graphics axis
#' @importFrom graphics lines
#' @param pos position of each p value
#' @param pvalue p value
#' @param ylab y lab
#' @param ymax y max
#' @param chr.name chromosome name
#' @param threshold QTL threshold
#' @param ... other parameter pass to base::plot
#' 
#' @return a LOD distribution by the chromsome
#' 
#' @examples 
#' pos <- c(1,100,200,210,230,300,500,600,700,1000)
#' pvalue <- c(0.1,0.05,0.05,0.05,0.01,0.001,0.01,0.05,0.05,0.1)
#' plotQtl(pos, pvalue, ymax = 3)
#' 
#' @export
#' @author Zhougeng Xu
plotQtl <- function(pos,
                    pvalue,
                    ylab = "LOD",
                    chr.name = "",
                    ymax = 10,
                    threshold = 2,
                    ...){


  # plot according to position
  df <- data.frame(pos = pos,
                   pvalue = pvalue,
                   lod = -log10(pvalue))

  plot(df$pos, df$lod,
       ylab = ylab,
       xlab = chr.name,
       axes = FALSE, xaxs = "i", yaxs = "i",
       ylim=c(0,ymax), pch=20 , cex = 0.2, type="l")

  max_pos <- ceiling(max(df$pos) / 1000000) + 1
  axis(1, at=seq(0,max_pos)* 1000000, labels = seq(0,max_pos))
  axis(2, at=seq(0,ymax))
  lines(x=c(0,max_pos*1000000),y=c(threshold,threshold), col = "red")

  # add start position and end position
  #start_index <- min(which(df$lod > threshold))
  #end_index <-  min(which(rev(df$lod) > threshold))

  #if ( length(start_index) > 0){
  #  text(grconvertX(0.2,"npc"), grconvertY(0.5, "npc"),
  #       labels = paste0("Start: ", df$pos[start_index]))
  #  text(grconvertX(0.2,"npc"), grconvertY(0.6, "npc"),
  #       labels = paste0("End: ", rev(df$pos)[end_index]))
  #}

}