Autoplots for gt_pcadapt objects — autoplot_gt

For gt_pcadapt, the following types of plots are available:

qq: a qunatile-quantile plot of the p-values from pcadapt (wrapping bigsnpr::snp_qq())
manhattan a manhattan plot of the p-values from pcadapt (wrapping bigsnpr::snp_manhattan())

Usage

# S3 method for class 'gt_pcadapt'
autoplot(object, type = c("qq", "manhattan"), ...)

Arguments

object: an object of class gt_pcadapt
type: the type of plot (one of "qq", and "mnahattan")
...: further arguments to be passed to bigsnpr::snp_qq() or bigsnpr::snp_manhattan().

Value

a ggplot2 object

Details

autoplot produces simple plots to quickly inspect an object. They are not customisable; we recommend that you use ggplot2 to produce publication ready plots.