R/plot_slide_clusters.R

In Kevin-Haigis-Lab/PackageBluishgreen: Classify cells by fluorescence

#' Plot the clusters on the slide
#'
#' @param ts A tissue slide object
#' @param method The classification method to use. The classification should
#'   have already been done.
#' @param prop The proportion of cells to include in the plot (too many cells
#'   can impact performance).
#' @param point_size Size of each point.
#' @param alpha_values A two-value vector where each value indicates the
#'   transparency of points coming from the two clusters.
#'
#' @return A ggplot2 object.
#'
#' @examples
#' pancreas_slide <- tissue_slide(pancreas)
#' pancreas_slide <- cluster_manually(pancreas_slide,
#'   fitc,
#'   cutoff = 4,
#'   transform = log10
#' )
#' plot_slide_clusters(pancreas_slide)
#' @import ggplot2
#' @export plot_slide_clusters
plot_slide_clusters <- function(ts,
                                method = "manual",
                                prop = 0.25,
                                point_size = 0.5,
                                alpha_values = c(0.2, 0.7)) {
  if (method == "manual") {
    if (is.na(get_manual_classification_cutoff(get_manual_classification(ts)))) {
      stop("Cannot plot clusters without first applying a manual classification to the tissue slide.")
    }
    ts$.cluster <- get_manual_classification(ts)
  } else {
    stop(paste(
      "Only 'manual' is currently supported.",
      "To request a new clusering method, please open an issue (linked below)",
      " and comprehensively describe your desired use case.",
      paste0("=> ", link_to_github_issues()),
      sep = "\n"
    ))
  }

  ts <- dplyr::slice_sample(ts, prop = prop)

  ggplot2::ggplot(ts, ggplot2::aes(x = x, y = y)) +
    ggplot2::geom_point(
      ggplot2::aes(color = .cluster, alpha = .cluster),
      size = point_size
    ) +
    ggplot2::scale_x_continuous(expand = ggplot2::expansion(mult = c(0, 0))) +
    ggplot2::scale_y_continuous(expand = ggplot2::expansion(mult = c(0, 0))) +
    ggplot2::scale_color_brewer(
      type = "qual",
      palette = "Set1",
      direction = -1,
      guide = ggplot2::guide_legend(override.aes = list(size = 1, alpha = 1))
    ) +
    ggplot2::scale_alpha_manual(values = alpha_values, guide = FALSE) +
    theme_tissue_slide() +
    ggplot2::labs(color = "cluster")
}

utils::globalVariables(c("x", "y", ".cluster"), add = TRUE)