R/plot_genome_vs_map.R

In mappoly: Genetic Linkage Maps in Autopolyploids

#' Physical versus genetic distance 
#' 
#' This function plots scatterplot(s) of physical distance (in Mbp) versus the genetic 
#' distance (in cM). Map(s) should be passed as a single object or a list of objects 
#' of class \code{mappoly.map}.
#'
#' @param  map.list A list or a single object of class \code{mappoly.map}
#' 
#' @param phase.config A vector containing which phase configuration should be
#'  plotted. If \code{'best'} (default), plots the configuration
#'  with the highest likelihood for all elements in \code{'map.list'} 
#'     
#' @param same.ch.lg Logical. If \code{TRUE} displays only the scatterplots between the 
#'   chromosomes and linkage groups with the same number. Default is \code{FALSE}.   
#'
#' @param alpha transparency factor for SNPs points
#' 
#' @param size size of the SNP points
#'    
#' @examples
#'   plot_genome_vs_map(solcap.mds.map, same.ch.lg = TRUE)
#'   plot_genome_vs_map(solcap.mds.map, same.ch.lg = FALSE, 
#'                      alpha = 1, size = 1/2)
#'  
#' @author Marcelo Mollinari, \email{mmollin@ncsu.edu}
#'
#' @references
#'     Mollinari, M., and Garcia, A.  A. F. (2019) Linkage
#'     analysis and haplotype phasing in experimental autopolyploid
#'     populations with high ploidy level using hidden Markov
#'     models, _G3: Genes, Genomes, Genetics_. 
#'     \doi{10.1534/g3.119.400378}
#'
#' @export plot_genome_vs_map
plot_genome_vs_map <- function(map.list, phase.config = "best", 
                               same.ch.lg = FALSE, alpha = 1/5, 
                               size = 3){
  if(inherits(map.list, "mappoly.map")) 
    map.list <- list(map.list)
  if(!inherits(map.list, "list"))
    stop("All elemnts in 'map.list' should be of class 'mappoly.map'")
  if (any(!sapply(map.list, inherits, "mappoly.map"))) 
    stop("All elemnts in 'map.list' should be of class 'mappoly.map'")
  if(length(phase.config) != length(map.list))
    phase.config <- rep(phase.config[1], length(map.list))
  if(any(sapply(map.list, function(x) is.null(x$info$genome.pos))))
    stop("All elemnts in 'map.list' should have the genomic position of the markers")
  geno.vs.map <- NULL
  for(i in 1:length(map.list)){
    ## Get linkage phase configuration
    LOD.conf <- get_LOD(map.list[[i]], sorted = FALSE)
    if(phase.config[i]  ==  "best") {
      i.lpc <- which.min(LOD.conf)
    } else if(is.numeric(phase.config[i])){
      i.lpc <- phase.config[i]
      if(i.lpc > length(LOD.conf))
        stop("invalid linkage phase configuration")
    } else stop("invalid linkage phase configuration")
    LG <- genomic.pos <- map.pos <- NULL
    geno.vs.map <- rbind(geno.vs.map,
                         data.frame(mrk.names = map.list[[i]]$info$mrk.names,
                                    map.pos = cumsum(imf_h(c(0, map.list[[i]]$maps[[i.lpc]]$seq.rf))),
                                    genomic.pos = map.list[[i]]$info$genome.pos/1e6, 
                                    LG = as.factor(i),
                                    chr = as.factor(map.list[[i]]$info$chrom)))
  }
  geno.vs.map$chr <- factor(geno.vs.map$chr, levels = sort(levels(geno.vs.map$chr))) 
  if(same.ch.lg){
    p <- ggplot2::ggplot(geno.vs.map, ggplot2::aes(genomic.pos, map.pos)) +
      ggplot2::geom_point(alpha = alpha, ggplot2::aes(colour = LG), size = size) +
      ggplot2::facet_wrap(~LG, nrow = floor(sqrt(length(map.list)))) +  
      ggplot2::labs(subtitle = "Linkage group", x = "Genome position (Mbp)", y = "Map position (cM)") +
      ggplot2::theme_bw() +
      ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1), 
                     legend.position = "none", plot.subtitle = ggplot2::element_text(hjust = 0.5)) 
    
  } else {
    p <- ggplot2::ggplot(geno.vs.map, ggplot2::aes(genomic.pos, map.pos)) +
      ggplot2::geom_point(alpha = alpha, ggplot2::aes(colour = LG), size = size) +
      ggplot2::facet_grid(LG~chr) + 
      ggplot2::labs(x = "Genome position (Mbp)", y = "Map position (cM)") +
      ggplot2::theme_bw() +
      ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1), legend.position = "none") 
  }
  p
}