R/file_templates.R

In bennyyclo/Cytofin: Integrate CyTOF Datasets From Heterogeneous Sources

#' Generate a template for a cytofin metadata file
#' 
#' `cytofin_generate_metadata_template` creates a template metadata .csv file 
#' (with the correct columns and dummy example data) in a specified location. 
#'
#' @param file_name A string representing the name of the .csv file to be 
#' saved in the directory specified by `template_path`. Defaults to 
#' "template_metadata.csv"
#'
#' @param template_path A file path or connection where the template file should be 
#' written. Defaults to the current working directory
#'
#' 
#' @export
#'
#' @examples
#' # specify the path where you'd like to store the template file
#' my_name <- "metadata_template.csv"
#' my_path <- file.path("~", "Desktop", "template_folder")
#'     
#' 
#' # generate the template file, which then can be edited manually 
#' cytofin_generate_metadata_template(
#'    file_name = my_name, 
#'    template_path = my_path
#' )
#' 
cytofin_generate_metadata_template <- 
  function(
    file_name = "template_metadata.csv", 
    template_path = getwd()
  ) { 
    
    # create template_path if needed
    if(!dir.exists(template_path)) { 
      dir.create(template_path, showWarnings = FALSE, recursive = TRUE)
    }
    
    #create output data.frame
    output_frame <- 
      data.frame(
        filename = c("file_1.fcs", "file_2.fcs", "file_3.fcs", "file_4.fcs"), 
        cohort = c("cohort_1", "cohort_1", "cohort_2", "cohort_2"),
        plate_number = c("plate_1", "plate_1", "plate_2", "plate_2"), 
        patient_id = c("patient_1", "patient_2", "patient_a", "patient_b"), 
        condition = c("basal", "basal", "stimulation_1", "stimulation_2"), 
        is_anchor = c(0, 1, 0, 1), 
        validation = 
          paste0(
            "validation_", 
            c("file_1.fcs", "file_2.fcs", "file_3.fcs", "file_4.fcs")
          )
      )
    
    readr::write_csv(
      x = output_frame, 
      file = file.path(template_path, file_name)
    )
    
  }


#' Generate a template for a cytofin reference panel file
#' 
#' `cytofin_generate_panel_template` creates a template reference panel .csv file 
#' (with the correct columns and dummy example data) in a specified location. 
#'
#' @param file_name A string representing the name of the .csv file to be 
#' saved in the directory specified by `template_path`. Defaults to 
#' "template_panel_info.csv"
#'
#' @param template_path File path or connection where the template file should be 
#' written. Defaults to the current working directory
#'
#' 
#' @export
#'
#' @examples
#' 
#' # specify the path where you'd like to store the template file
#' my_name <- "panel_template.csv"
#' my_path <- file.path("~", "Desktop", "template_folder")
#' 
#' # generate the template file, which then can be edited manually 
#' cytofin_generate_panel_template(
#'    file_name = my_name, 
#'    template_path = my_path
#' )
#' 
cytofin_generate_panel_template <- 
  function(
    file_name = "template_panel_info.csv", 
    template_path = getwd()
  ) { 
    
    # create template_path if needed
    if(!dir.exists(template_path)) { 
      dir.create(template_path, showWarnings = FALSE, recursive = TRUE)
    }
    
    #create output data.frame
    output_frame <- 
      data.frame(
        metal_name = c("Time", "Event_length", "(Pd102)Di", "(Pd104)Di"), 
        antigen_name = c("Time", "Event_length", "marker_name_1", "marker_name_2"),
        antigen_pattern = c("", "", "", ""),
        lineage = c(0, 0, 1, 1), 
        functional = c(0, 0, 0, 1), 
        general = c(0, 1, 1, 1)
      )
    
    readr::write_csv(
      x = output_frame, 
      file = file.path(template_path, file_name)
    )
    
  }