R/pipelines.r

In ceas: Cellular Energetics Analysis Software

#' Bioenergetic Scope Plot Shortcut
#'
#' Wrapper to create a 2D plot visualizing the mean and standard deviation
#' basal and maximal ATP production from glycolysis and OXPHOS for each
#' experimental group Create a Bioenergetic scope plot from input Seahorse Wave
#' export, long-form rates excel files
#'
#' @param rep_list A list of Seahorse Wave excel export files. One file per
#' replicate. Group all replicates for a given experiment in a single folder,
#' and write that folder's path in "seahorse_data". You can use
#' `list.files("seahorse_data") "full.names=TRUE") to get the paths to the
#' files.
#' @param ph pH value for energetics calculation (for XF Media, 7.5)
#' @param pka pKa value for energetics calculation (for XF Media, 6.063)
#' @param buffer buffer for energetics calculation (for XF Media, 0.1 mpH/pmol H+)
#' @param sheet The number of the excel sheet containing the long-form Seahorse
#' data. Default is 2 because the long-form output from Seahorse Wave is on
#' sheet 2
#' @return a ggplot
#'
#' @importFrom ggplot2 ggplot aes geom_point labs xlab ylab geom_linerange xlim ylim scale_color_discrete
#' @export
#'
#' @examples
#' rep_list <- system.file("extdata", package = "ceas") |>
#'   list.files(pattern = "*.xlsx", full.names = TRUE)
#' make_bioscope_plot(rep_list, ph = 7.4, pka = 6.093, buffer = 0.1)
make_bioscope_plot <- function(rep_list, ph, pka, buffer, sheet = 2) {
  read_data(rep_list, sheet = sheet) |>
    partition_data() |>
    get_energetics(ph = ph, pka = pka, buffer = buffer) |>
    bioscope_plot()
}