updog (version 1.2.0)

plot.mupdog: Draw a genotype plot from the output of mupdog.

Description

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

Usage

# S3 method for mupdog
plot(x, index, use_colorblind = TRUE, ...)

Arguments

x

A mupdog object.

index

The column number of the gene to plot.

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.

Value

A ggplot object for the genotype plot.

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 Ferr<U+00E3>o (2019).

References

• Gerard, D., Ferr<U+00E3>o, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789-807. doi: 10.1534/genetics.118.301468.

• Gerard, D. and Ferr<U+00E3>o, L. F. V. (2019). Priors for Genotyping Polyploids. Bioinformatics. doi: 10.1093/bioinformatics/btz852.

See Also

plot_geno

The underlying plotting function.

mupdog

Creates a mupdog object.

Examples

# NOT RUN {
data("mupout")
plot(mupout, 4)

# }