flexdog.A wrapper for plot_geno. This will create a genotype plot for a single SNP.
# S3 method for flexdog
plot(x, use_colorblind = TRUE, ...)A ggplot object for the genotype plot.
A flexdog object.
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.
David Gerard
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).
Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789-807. 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. tools:::Rd_expr_doi("10.1093/bioinformatics/btz852").
plot_genoThe underlying plotting function.
flexdogCreates a flexdog object.