R/plots.r

In paulklemm/seqc: What the Package Does (One Line, Title Case)

#' Read in Cuffdiff result
#'
#' @export
#' @import cummeRbund magrittr
#' @param path Path to cuffdiff folder
#' @return cummeRbund cuff object
read_cuffdiff <- function(path) {
  cuff <- readCufflinks(dir = path)
  cuff %>% return()
}

#' Make cummeRbund report from Cuffdiff result
#'
#' @export
#' @import magrittr ggplot2 rmarkdown
#' @param cuffdiff_path Path to cuffdiff folder
#' @param output_path Path to HTML output
#' @param save_plots Save plots into seperate files
#' @param save_width With of exported plot (ggplot only)
#' @param save_height Height of exported plot in 'in' (ggplot only)
#' @param save_format Format of exported plot in 'in' (ggplot only)
#' @return cummeRbund cuff object
createHTMLReport <- function(cuffdiff_path, output_path, save_plots = FALSE, save_width = 7, save_height = 5, save_format = "pdf") {
  # https://stackoverflow.com/questions/30377213/how-to-include-rmarkdown-file-in-r-package
  path_to_report <- system.file("rmd/Report.Rmd", package = "seqc")
  # Render the document and put it into the output dir
  # render(path_to_report, intermediates_dir = output_path, params = list(
  render(path_to_report,
    params = list(
      cuffdiff_path = cuffdiff_path,
      save_plots_path = output_path,
      save_plots = save_plots,
      save_width = save_width,
      save_height = save_height,
      save_format = save_format
    ),
    # Change the intermediate path to the output to avoid write access errors
    intermediates_dir = output_path,
    knit_root_dir = output_path,
    # clean: TRUE to clean intermediate files created during rendering.
    clean = TRUE,
    output_dir = output_path,
    output_options = list(
      self_contained = TRUE
    )
  )
}

#' Save image and print it
#'
#' @export
#' @import magrittr ggplot2
#' @param plot ggplot2 plot object
#' @param plot_name name of ggplot file
#' @param output_path path to output
#' @param save_plot Save plot to disk
#' @param save_width With of exported plot (ggplot only)
#' @param save_height Height of exported plot in 'in' (ggplot only)
#' @param save_format Format of exported plot in 'in' (ggplot only)
#' @param is_ggplot Plot is ggplot object or not
saveReturnPlot <- function(
                           plot,
                           save_plot = TRUE,
                           plot_name = "",
                           output_path = "",
                           is_ggplot = TRUE,
                           save_width,
                           save_height,
                           save_format) {
  saveReturn <- function() {
    if (save_plot) {
      plot_filename <- paste0(output_path, "/", plot_name, ".", save_format)
      if (is_ggplot) {
        # Output the plot to the path
        ggplot2::ggsave(plot = plot, filename = plot_filename, width = save_width, height = save_height)
      } else {
        # Is base plot
        pdf(plot_filename)
        plot %>% print()
        dev.off()
      }
    }
    plot %>% print()
  }
  # Some plots may fail. To still get the whole document, wrap the print and saving into a tryCatch
  tryCatch({
    saveReturn()
  },
  error = function(cond) {
    print("Cannot generate plot")
    print(cond)
    NA %>% return()
  }
  )
}