R/autoplot_gt_admix.R

In tidypopgen: Tidy Population Genetics

#' Autoplots for `gt_admix` objects
#'
#' For `gt_admix`, the following types of plots are available:
#' - `cv`: the cross-validation error for each value of `k`
#' - `barplot` a standard barplot of the admixture proportions
#'
#' `autoplot` produces simple plots to quickly inspect an object. They are not
#' customisable; we recommend that you use `ggplot2` to produce publication
#' ready plots.
#'
#' This autoplot will automatically rearrange individuals according to their id
#' and any grouping variables if an associated 'data' gen_tibble is provided. To
#' avoid any automatic re-sorting of individuals, set `arrange_by_group` and
#' `arrange_by_indiv` to FALSE. See `autoplot.q_matrix` for further details.
#'
#' @param object an object of class `gt_admixture`
#' @param type the type of plot (one of "cv", and "barplot")
#' @param k the value of `k` to plot (for `barplot` type only) param repeat the
#'   repeat to plot (for `barplot` type only)
#' @param run the run to plot (for `barplot` type only)
#' @param ... additional arguments to be passed to autoplot method for
#'   q_matrices [autoplot_q_matrix()], used when type is `barplot`.
#' @returns a `ggplot2` object
#' @name autoplot_gt_admix
#' @export
#' @examples
#' # Read example gt_admix object
#' admix_obj <-
#'   readRDS(system.file("extdata", "anolis", "anole_adm_k3.rds",
#'     package = "tidypopgen"
#'   ))
#' # Cross-validation plot
#' autoplot(admix_obj, type = "cv")
#'
#' # Basic barplot
#' autoplot(admix_obj, k = 3, run = 1, type = "barplot")
#'
#' # Barplot with individuals arranged by Q proportion
#' # (using additional arguments, see `autoplot.q_matrix` for details)
#' autoplot(admix_obj,
#'   k = 3, run = 1, type = "barplot", annotate_group = TRUE,
#'   arrange_by_group = TRUE, arrange_by_indiv = TRUE,
#'   reorder_within_groups = TRUE
#' )
#'
autoplot.gt_admix <- function(
    object,
    type = c("cv", "barplot"),
    k = NULL,
    run = NULL,
    ...) {
  type <- match.arg(type)
  if (type == "cv") {
    if (is.null(object$cv)) {
      stop("No cross validation error available")
    }

    if (object$algorithm == "SNMF") {
      ggplot2::ggplot(
        data.frame(k = object$k, cv = object$cv),
        ggplot2::aes(x = .data$k, y = .data$cv)
      ) +
        ggplot2::geom_point() +
        ggplot2::geom_line() +
        ggplot2::labs(x = "k", y = "Cross-Entropy")
    } else {
      ggplot2::ggplot(
        data.frame(k = object$k, cv = object$cv),
        ggplot2::aes(x = .data$k, y = .data$cv)
      ) +
        ggplot2::geom_point() +
        ggplot2::geom_line() +
        ggplot2::labs(x = "k", y = "Cross validation error")
    }
  } else if (type == "barplot") {
    # check that k is specified
    if (is.null(k)) {
      stop("You must specify a value for k")
    }
    # check that run is specified
    if (is.null(run)) {
      stop("You must specify a value for repeat")
    }
    # get the Q matrix for the specified k and repeat
    q <- get_q_matrix(object, k = k, run = run)
    autoplot(q, ...)
  }
}