R/pcr_plot.R

In KaiAragaki/amplify: Automate PCR Tasks Reproducibly

#' Plot qPCR results
#'
#' @param x a `pcr` object or `data.frame`
#'
#' @return a `ggplot`
#' @export
#'
#' @importFrom rlang .data
#'
#' @examples
#' system.file("extdata", "untidy-pcr-example.xls", package = "amplify") |>
#'   pcr_tidy() |>
#'   pcr_rq("RD1") |>
#'   pcr_plot()
pcr_plot <- function(x, ...) {
  UseMethod("pcr_plot")
}


#' @rdname pcr_plot
#' @export
pcr_plot.pcr <- function(x, ...) {
  x |>
    tidy_if_not() |>
    mop::scrub() |>
    pcr_plot()
}

#' @rdname pcr_plot
#' @export
pcr_plot.data.frame <- function(x, ...) {

  x |>
    dplyr::filter(!is.na(.data$sample_name)) |>
    rm_dupes() |>
    ggplot2::ggplot(ggplot2::aes(x = .data$sample_name, y = .data$rq, fill = .data$target_name)) +
    ggplot2::geom_col() +
    ggplot2::geom_errorbar(ggplot2::aes(ymin = .data$rq_min, ymax = .data$rq_max)) +
    ggplot2::facet_wrap(~.data$target_name, scales = "free") +
    ggplot2::scale_fill_viridis_d(begin = 0.1, end = 0.9) +
    ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, hjust = 1, vjust = 0.5),
                   axis.title.x = ggplot2::element_blank())
}

rm_dupes <- function(x) {
  if ("..group" %in% colnames(x)) {
    x <- dplyr::distinct(
      x, .data$target_name, .data$sample_name, .data$..group, .keep_all = TRUE
    )
    return(x)
  }
  dplyr::distinct(x, .data$target_name, .data$sample_name, .keep_all = TRUE)
}