#' Gather graph nodes from a data frame

#' Please note that this function is from the 'ggraph' package and has not been altered in functionality,

#' but it has been optimized and iterated.

#' It is not original content of 'TransProR'.

#' However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR',

#' the author directly referenced the involved functions in 'TransProR'.

#' This is not the author's original creation. All users please be aware!

#' @inheritParams gather_graph_edge

#' @param value Column name used for summarizing node size, defaults to the last column

#' @return a tibble of graph nodes

#' @export

#' @importFrom dplyr group_by summarise mutate bind_rows n all_of across

#' @importFrom tidyr unite

#' @importFrom tibble as_tibble

#' @importFrom utils tail

gather_graph_node <- function(df, index = NULL, value = utils::tail(colnames(df), 1), root = NULL) {

  if (length(index) < 2) {

    stop("Please specify at least two index columns.")

  } else {

    nodes_list <- lapply(seq_along(index), function(i) {

      dots <- index[1:i]

      df %>%

        dplyr::group_by(dplyr::across(dplyr::all_of(dots))) %>%

        dplyr::summarise(node.size = sum(.data[[value]], na.rm = TRUE),

                         node.level = index[i],

                         node.count = dplyr::n(), .groups = 'drop') %>%

        dplyr::mutate(node.short_name = as.character(.data[[dots[length(dots)]]]),

                      node.branch = as.character(.data[[dots[1]]])) %>%

        tidyr::unite(col = "node.name", all_of(dots), sep = "/")

    })

    nodes <- dplyr::bind_rows(nodes_list) %>%

      tibble::as_tibble()

    nodes$node.level <- factor(nodes$node.level, levels = index)

    if (!is.null(root)) {

      root_data <- data.frame(

        node.name = root,

        node.size = sum(df[[value]], na.rm = TRUE),

        node.level = root,

        node.count = 1,

        node.short_name = root,

        node.branch = root,

        stringsAsFactors = FALSE

      )

      nodes <- dplyr::bind_rows(root_data, nodes)

      nodes$node.level <- factor(nodes$node.level, levels = c(root, index))

    }

    return(nodes)

  }

}