plot.multidog: Plot the output of 'multidog'.

In updog: Flexible Genotyping for Polyploids

Plot the output of multidog.

Description

Produce genotype plots from the output of multidog. You may select which SNPs to plot.

Usage

## S3 method for class 'multidog'
plot(x, indices = seq(1, min(5, nrow(x$snpdf))), ...)

Arguments

x	The output of multidog.
indices	A vector of integers. The indices of the SNPs to plot.
...	not used.

Details

On a genotype plot, the x-axis contains the counts of the non-reference allele and the y-axis contains the counts of the reference allele. The dashed lines are the expected counts (both reference and alternative) given the sequencing error rate and the allele-bias. The plots are color-coded by the maximum-a-posterior genotypes. Transparency is proportional to the maximum posterior probability for an individual's genotype. Thus, we are less certain of the genotype of more transparent individuals. These types of plots are used in Gerard et. al. (2018) and Gerard and Ferrão (2020).

Author(s)

David Gerard

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301468")}.

• Gerard, David, and Luís Felipe Ventorim Ferrão. "Priors for genotyping polyploids." Bioinformatics 36, no. 6 (2020): 1795-1800. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btz852")}.

See Also

plot_geno.

updog documentation built on May 29, 2024, 8:13 a.m.