R/get_fpbase_properties.R

In ec363/fpcountr: Fluorescent Protein Calibration For Plate Readers

#' Get properties of an FP from FPbase
#'
#' Gets properties of an FP from FPbase, including the maximal excitation
#' wavelength and extinction coefficient. Optionally saves these as a CSV.
#'
#' @param slug Name of FP, which is used to find the FP-relevant data lines in
#'   the FPbase datasets. This argument is called `slug` because for FPbase
#'   retrievals, this needs to be an exact match to the slug specified by
#'   FPbase. (To find this, navigate to the FPbase entry for your FP and copy
#'   the part after `https://www.fpbase.org/protein/` (without the trailing
#'   `/`).
#' @param verbose logical. Should the function print messages to allow the user
#'   to check its progress? Defaults to TRUE.
#' @param save_file logical. Should the function save the output as a CSV file?
#'   Defaults to FALSE.
#' @param outfolder path to folder where output files should be saved. Defaults
#'   to current working directory.
#' @param filename How to name the output CSV file. Requires `.csv` at the end.
#'   Defaults to `fp_properties.csv`.
#'
#' @export
#'
#' @importFrom dplyr %>%
#' @importFrom rlang .data :=
#'
#' @examples get_fpbase_properties("mcherry")
get_fpbase_properties <- function(slug, verbose = TRUE, save_file = FALSE, outfolder = ".", filename = "fp_properties.csv"){

  # Location for saved outputs ---------------------------------------------------------------------------------------------------

  # make folder if it doesn't exist already
  ifelse(test = !dir.exists(file.path(outfolder)), yes = dir.create(file.path(outfolder)), no = FALSE)

  ## Get FP properties -----------------------------------------------------------------------------------------------------------

  all_fp_df <- NULL ###
  source <- NULL

  # 1) fpbase version ---

  # In case of FPbase url error, wrap FPbase call in tryCatch
  tryCatch(
    expr = {

      # all_fp_df <- "empty" ###

      # All FP properties
      all_fp_df <- jsonlite::fromJSON("https://www.fpbase.org/api/proteins/?format=json")
      if(verbose){
        message("FP data retrieved from FPbase.")
      }
      source <- "fpbase"

    },
    error = function(e){
      # Do this if an error is caught...
      message('Error in call to FPbase:')
      print(e)
    },
    warning = function(w){
      # Do this if an warning is caught...
      message('Warning in call to FPbase:')
      print(w)
    },
    finally = {
      # do this at the end before quitting the tryCatch structure...
      # empty
    }
  )

  # If FPbase download fails, use package data instead:

  # 2) pre-downloaded version ---

  # if(all_fp_df == "empty"){ # ### causes persistent error Error in if (all_fp_df == "empty") { : the condition has length > 1
  if(is.null(all_fp_df)){ ###

    # All FP properties - from pre-downloaded data
    all_fp_df <- fpcountr::fpbase_data
    all_fp_df

    if(verbose){
      message("FP data retrieved from FPbase data stored in package.")
    }
    source <- "fpcountr"

  }

  # Get FP entry
  fp_entry <- all_fp_df %>%
    dplyr::filter(slug == {{slug}})
  fp_entry

  # Error message for slugs with no entries
  if(nrow(fp_entry)<1){
    return(message("Error: no entries matching slug in database."))
  }

  # FP properties
  if(source == "fpbase"){
    fp_properties <- fp_entry[[11]][[1]]
    fp_properties
  } else {
    fp_properties <- fp_entry
    fp_properties
  }

  # Warning mesg for proteins with multiple states
  if(nrow(fp_properties)>1){
    message("FP has multiple states:")
    print(fp_properties)
    message("..taking first:")
    fp_properties <- fp_properties[1,]
    print(fp_properties)
  }

  # Save and return ------------------------------

  if(isTRUE(save_file)){
    utils::write.csv(fp_properties, file.path(outfolder, filename), row.names = FALSE)
  }

  return(fp_properties)
}