oracle_plot: Construct an oracle plot from the output of 'oracle_joint'.

In updog: Flexible Genotyping for Polyploids

Construct an oracle plot from the output of oracle_joint.

Description

After obtaining the joint distribution of the true genotype with the estimated genotype from the oracle estimator using oracle_joint, you can use oracle_plot to visualize this joint distribution.

Usage

oracle_plot(jd)

Arguments

jd	A matrix containing the joint distribution of the true genotype and the oracle estimator. Usually, this is obtained by a call from oracle_joint.

Value

A ggplot object containing the oracle plot. The x-axis indexes the possible values of the estimated genotype. The y-axis indexes the possible values of the true genotype. The number in cell (i, j) is the probability that an individual will have true genotype i but is estimated to have genotype j. This is when using an oracle estimator. The cells are also color-coded by the size of the probability in each cell. At the top are listed the oracle misclassification error rate and the correlation of the true genotype with the estimated genotype. Both of these quantities may be derived from the joint distribution.

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")}.

See Also

oracle_joint for obtaining jd.

Examples

ploidy <- 6
dist <- stats::dbinom(0:ploidy, ploidy, 0.75)
jd <- oracle_joint(n = 100, ploidy = ploidy, seq = 0.001,
                   bias = 0.7, od = 0.01, dist = dist)
pl <- oracle_plot(jd = jd)
print(pl)

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