R/file_manipulation.R

In ArthurPERE/RNASeqDE:

#' Read the parameter file
#'
#' @param name_file path to the file we went to read
#'
#' @return
#' @export
#'
#' @importFrom jsonlite read_json
#' @importFrom data.table as.data.table
#'
#' @examples
read_parameter_file <- function(name_file) {
  data_parameters <- read_json(name_file, simplifyVector = T)

  data_parameters$contrast <- as.data.table(data_parameters$contrast)

  return(data_parameters)
}


#' Write the parameter file
#'
#' @param param param we want to write
#' @param name_file the name of the file
#'
#' @return
#' @export
#'
#' @importFrom jsonlite write_json
#'
#' @examples
write_parameter_file <- function(param, name_file) {
  write_json(param, name_file, dataframe = "columns", pretty = T)
}



#' put list of ggplot in a directory by names
#'
#' @param plot_list the plot list
#' @param path the path you want to save the plot
#'
#' @return nothing
#' @export
#'
#' @importFrom ggplot2 ggsave is.ggplot
#' @importFrom purrr pwalk
#'
plot_list_save <- function(plot_list, path) {
  if (is.null(plot_list)) {
    return(invisible())
  }
  if (missing(path)) path <- tempdir()

  dir.create(path, showWarnings = F, recursive = T)

  plot_list <- Filter(is.ggplot, plot_list)
  names_plot <- paste0(names(plot_list), ".svg")
  pwalk(list(filename = names_plot, plot = plot_list), ggsave, path = path)

  invisible()
}



#' save the pca
#'
#' @param pca
#' @param radius
#' @param path
#'
#' @return the result of the analysis
#' @export
#'
#' @importFrom ggplot2 ggsave
pca_save <- function(pca = NULL, radius = 0, path) {
  if (is.null(pca)) {
    return(NULL)
  }
  dir.create(path, showWarnings = F, recursive = T)

  as.data.frame(t(combn(1:pca$nf, 2))) %>% pwalk(~ {
    title_partial <- paste(.x, .y, sep = "_")
    tmp <- pca_analysis(pca, .x, .y, radius)
    ggsave(paste0("pca_corcircle_axis_", title_partial, ".svg"), tmp$plot$corcircle, path = path)
    ggsave(paste0("pca_axis_", title_partial, ".svg"), tmp$plot$axis, path = path)
  })

  return(NULL)
}