R/check_metadata_rownames.R

In bschilder/scKirby: Automated ingestion and conversion of various single-cell data formats.

check_metadata_rownames <- function(d,
                                    rownames_col=NULL,
                                    verbose=TRUE){
  #### Recursion ####
  if(is_list(d)){
    d <- lapply(d, check_metadata_rownames, verbose=verbose)
    return(d)
  }
  if(is.null(rownames(d)) ||
     methods::is(d,"data.table")){
    valid_rn <- sapply(d,function(x){length(unique(x))==nrow(d)})
    if(sum(valid_rn)>0){
      if(!is.null(rownames_col) &&
         rownames_col %in% valid_rn){
        rn_col <- rownames_col
      } else {
        rn_col <- names(valid_rn)[[1]]
      }
      messager("Assigning column",shQuote(rn_col),
               "as metadata row names.",v=verbose)
      d <- data.frame(d, row.names = d[[rn_col]])
    } else {
      wrn <- paste(
        "No columns could be identified as metadata row names.",
        "Please assign this manually."
      )
      warning(wrn)
    }
  }
  return(d)
}