R/purity.R

In ddiez/scmisc: Miscellaneus Tools for the Analysis of Single Cell Data

#' compute_purity
#'
#' @param x object to compute purity on.
#' @param col.x name of column.
#' @param col.y name of column.
#' @param ... arguments passed down to methods.
#'
#' @export
compute_purity <- function(x, ...) {
  UseMethod("compute_purity")
}

#' @rdname compute_purity
#' @export
compute_purity.SingleCellExperiment <- function(x, ...) {
  compute_purity(colData(x), ...)
}

#' @rdname compute_purity
#' @export
compute_purity.DataFrame <- function(x, ...) {
  compute_purity(as.data.frame(x), ...)
}

#' @rdname compute_purity
#' @export
compute_purity.data.frame <- function(x, col.x, col.y, ...) {
  if (missing(col.x)) stop("col.x is missing.")
  if (missing(col.y)) stop("col.y is missing.")

  x |> select_at(.vars = c(col.x, col.y)) |>
    group_by_at(.vars = col.y) |>
    mutate(total = n()) |>
    group_by_at(.vars = c(col.x, col.y)) |>
    summarize(count = n(), purity = count / first(.data$total))
}