plot_genome_vs_map {mappoly}

Physical versus genetic distance

Description

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 mappoly.map.

Usage

plot_genome_vs_map(
  map.list,
  phase.config = "best",
  same.ch.lg = FALSE,
  alpha = 1/5,
  size = 3
)

Arguments

map.list

A list or a single object of class mappoly.map

phase.config

A vector containing which phase configuration should be plotted. If 'best' (default), plots the configuration with the highest likelihood for all elements in 'map.list'

same.ch.lg

Logical. If TRUE displays only the scatterplots between the chromosomes and linkage groups with the same number. Default is FALSE.

alpha

transparency factor for SNPs points

size

size of the SNP points

Author(s)

Marcelo Mollinari, [e-mail]

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

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)