reorder.column.R

#' Remove small factor levels  and reorder
#' @description This function removes factor levels with counts less than a set value. Additionally, it reorders the factor levels depending on the counts.
#' This may be necessary later on to get ordered labels when plotting.
#' @param cancer_data A large list created prior by multimodalR.
#' @param column Character - column name
#' @param remove Integer - threshold of counts; any factor level with equal or less counts are discarded
#' @importFrom magrittr %>%
#' @examples
#' lungMeta <- reorder.colums(lungMeta, "primary_diagnosis", 10) #keeps factor levels with >= 10 counts.
#' @return Returns the same large list with changed column names of the expressionmatrix.


reorder.column <- function(cancer_metadata, column, remove = 0) {
  if(is.factor(cancer_metadata[[column]])) {
  arrangedCounts <- cancer_metadata %>% dplyr::group_by_(column) %>% dplyr::summarize(n = n())
  arrangedCounts <- dplyr::arrange(arrangedCounts, desc(n))                                              #order by descending counts
  cancer_metadata[[column]] <- factor(cancer_metadata[[column]], levels = arrangedCounts[[column]])        #reorder factor in data frame

  factorCount <- plyr::count(cancer_metadata[[column]]) %>% dplyr::filter(freq >= remove)                 #removes counts less than the value of removes
  factorCount  <- factorCount[,1]
  columnSymbol <- rlang::sym(column)
  cancer_metadata <- dplyr::filter(cancer_metadata, !!(columnSymbol) %in% factorCount)                     # !! is the newer version of rlang::UQ() which unquotes the variable
  cancer_metadata[[column]] <- factor(cancer_metadata[[column]])
} else {
  warning(column, " is no factor, no changes applied")
}
  return(cancer_metadata)
}