R/loadMetadata.R

In microresearcher/MicroVis: Microbiome Analysis and Visualization

#' Load metadata file
#'
#' @param path_to_metadata (Optional) full path to metadata csv file
#'
#' @return Loaded metadata dataframe
#'
loadMDFile <- function(path_to_metadata=NA) {
  cat(paste0('\n\n|~~~~~~~~ LOADING metadata FILE ~~~~~~~~|\n'))
  mdfile <- NULL

  if(!is.null(path_to_metadata)) if(!file.exists(as.character(path_to_metadata))) {
    path_to_metadata <- NA

    message('\nSelect metadata table (csv format)')
    Sys.sleep(0.1) # To make sure it displays the above message before opening the dialogue box

    mdfile <- rstudioapi::selectFile(caption='Select metadata table (csv format)',
                                     path=get('project_dir',envir = mvEnv),
                                     filter="Comma-Separated Value (*.csv)")

  } else mdfile <- path_to_metadata

  if(is.null(mdfile)) {
    message('\nERROR: No metadata file selected. No comparative analysis can be run !!!\n')
    return(NULL)
  } else cat('\nmetadata loading from:\n',mdfile)

  metadata <- read.csv(file.path(mdfile))

  # Sample name must be in first column of metadata file!!
  if(length(unique(metadata[[1]])) != length(metadata[[1]])) {
    assign('.loading',FALSE,envir = mvEnv)
    return(message('\nERROR: First column of metadata must have sample names which should all be unique'))
  }

  colnames(metadata)[1] <- 'sample'

  cat(paste0('\n\n>>> METADATA FILE LOADED SUCCESSFULLY <<<\n'))

  return(metadata)
}