R/autoplot_gt_pcadapt.R

In tidypopgen: Tidy Population Genetics

#' Autoplots for `gt_pcadapt` objects
#'
#' For `gt_pcadapt`, the following types of plots are available:
#' - `qq`: a quantile-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()])
#'
#' `autoplot` produces simple plots to quickly inspect an object. They are
#' not customisable; we recommend that you use `ggplot2` to produce publication
#' ready plots.
#'
#' @param object an object of class `gt_pcadapt`
#' @param type the type of plot (one of "qq", and "manhattan")
#' @param ... further arguments to be passed to [bigsnpr::snp_qq()] or
#' [bigsnpr::snp_manhattan()].
#' @returns a `ggplot2` object
#' @name autoplot_gt_pcadapt
#' @export
#' @examples
#' # Create a gen_tibble of lobster genotypes
#' bed_file <-
#'   system.file("extdata", "lobster", "lobster.bed", package = "tidypopgen")
#' lobsters <- gen_tibble(bed_file,
#'   backingfile = tempfile("lobsters"),
#'   quiet = TRUE
#' )
#'
#' # Remove monomorphic loci and impute
#' lobsters <- lobsters %>% select_loci_if(loci_maf(genotypes) > 0)
#' lobsters <- gt_impute_simple(lobsters, method = "mode")
#'
#' # Create PCA object
#' pca <- gt_pca_partialSVD(lobsters)
#'
#' # Create a gt_pcadapt object
#' pcadapt_obj <- gt_pcadapt(lobsters, pca, k = 2)
#'
#' # Plot the p-values from pcadapt
#' autoplot(pcadapt_obj, type = "qq")
#'
#' # Plot the manhattan plot of the p-values from pcadapt
#' autoplot(pcadapt_obj, type = "manhattan")
#'
autoplot.gt_pcadapt <- function(object, type = c("qq", "manhattan"), ...) {
  type <- match.arg(type)
  if (type == "qq") {
    bigsnpr::snp_qq(object, ...)
  } else if (type == "manhattan") {
    bigsnpr::snp_manhattan(
      object,
      infos.chr = attr(object, "loci")$chromosome,
      infos.pos = attr(object, "loci")$position,
      ...
    )
  }
}