plot.flexdog: Draw a genotype plot from the output of 'flexdog'.

In updog: Flexible Genotyping for Polyploids

Draw a genotype plot from the output of flexdog.

Description

A wrapper for plot_geno. This will create a genotype plot for a single SNP.

Usage

## S3 method for class 'flexdog'
plot(x, use_colorblind = TRUE, ...)

Arguments

x	A flexdog object.
use_colorblind	Should we use a colorblind-safe palette (TRUE) or not (FALSE)? TRUE is only allowed if the ploidy is less than or equal to 6.
...	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).

Value

A ggplot object for the genotype plot.

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

The underlying plotting function.

flexdog

Creates a flexdog object.

updog documentation built on Nov. 17, 2023, 9:06 a.m.