plot_geno: Make a genotype plot.
In dcgerard/updogAlpha: Using Parental Data for Offspring Genotyping

Description Usage Arguments Details Author(s)

The x-axis will be the counts of the non-reference allele, and the y-axis will be the counts of the reference allele. Transparency is controlled by the prob_ok vector, size is controlled by the maxpostprob vector.

plot_geno(ocounts, osize, ploidy, p1counts = NULL, p1size = NULL,
  p2counts = NULL, p2size = NULL, ogeno = NULL, seq_error = 0,
  bias_val = 1, prob_ok = NULL, maxpostprob = NULL, p1geno = NULL,
  p2geno = NULL, use_colorblind = TRUE)

`ocounts`	A vector of non-negative integers. The number of reference alleles observed in the offspring.
`osize`	A vector of positive integers. The total number of reads in the offspring.
`ploidy`	A non-negative integer. The ploidy of the species.
`p1counts`	A vector of non-negative integers. The number of reference alleles observed in parent 1.
`p1size`	A vector of positive integers. The total number of reads in parent 1.
`p2counts`	A vector of non-negative integers. The number of reference alleles observed in parent 2.
`p2size`	A vector of positive integers. The total number of reads in parent 2.
`ogeno`	The child genotypes
`seq_error`	The average sequencing error rate.
`bias_val`	The bias parameter.
`prob_ok`	A vector of posterior probabilities of not being a mistake.
`maxpostprob`	A vector of the posterior probabilities of begin at the modal probability.
`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`)?

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

David Gerard

dcgerard/updogAlpha documentation built on May 14, 2019, 3:10 a.m.