plot_geno: Make a genotype plot.

Description Usage Arguments Details Author(s)

View source: R/generics.R

Description

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.

Usage

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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)

Arguments

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)?

Details

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.

Author(s)

David Gerard


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