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Make a genotype plot.

Source: R/plot_geno.R
plot_geno.Rd

The x-axis is the counts of the non-reference allele, and the y-axis is the counts of the reference allele. Transparency is controlled by the maxpostprob vector. These types of plots are used in Gerard et. al. (2018) and Gerard and Ferrão (2020).

Usage

plot_geno(
  refvec,
  sizevec,
  ploidy,
  p1ref = NULL,
  p1size = NULL,
  p2ref = NULL,
  p2size = NULL,
  geno = NULL,
  seq = 0,
  bias = 1,
  maxpostprob = NULL,
  p1geno = NULL,
  p2geno = NULL,
  use_colorblind = TRUE
)

Arguments

refvec

A vector of non-negative integers. The number of reference reads observed in the individuals

sizevec

A vector of positive integers. The total number of reads in the individuals.

ploidy

A non-negative integer. The ploidy of the species.

p1ref

A vector of non-negative integers. The number of reference reads observed in parent 1 (if the individuals are all siblings).

p1size

A vector of positive integers. The total number of reads in parent 1 (if the individuals are all siblings).

p2ref

A vector of non-negative integers. The number of reference reads observed in parent 2 (if the individuals are all siblings).

p2size

A vector of positive integers. The total number of reads in parent 2 (if the individuals are all siblings).

geno

The individual genotypes.

seq

The sequencing error rate.

bias

The bias parameter.

maxpostprob

A vector of the posterior probabilities of being at the modal genotype.

p1geno

Parent 1's genotype.

p2geno

Parent 2's genotype.

use_colorblind

A logical. Should we use a colorblind safe palette (TRUE), or not (FALSE)? Only allowed if ploidy <= 6.

Value

A ggplot object for the genotype plot.

Details

If parental genotypes are provided (p1geno and p2geno) then they will be colored the same as the offspring. Since they are often hard to see, a small black dot will also indicate their position.

References

  • Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789-807. doi:10.1534/genetics.118.301468 .

  • Gerard, David, and Luís Felipe Ventorim Ferrão. "Priors for genotyping polyploids." Bioinformatics 36, no. 6 (2020): 1795-1800. doi:10.1093/bioinformatics/btz852 .

Author

David Gerard

Examples

data("snpdat")
refvec  <- snpdat$counts[snpdat$snp == "SNP1"]
sizevec <- snpdat$size[snpdat$snp == "SNP1"]
ploidy  <- 6
plot_geno(refvec = refvec, sizevec = sizevec, ploidy = ploidy)