R/update_nodes.R

In ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

#' Carries the variables from edge to node.
#'
#' Carries the variables from edge to node.
#'
#' @details The function is a helper function for
#' processing of graph object with update_nodes function.
#'
#' @param input_graph Processed graph object in previous step.
#' @return tibble object
#' @keywords internal
#'


prepare_rhs_once <- function(input_graph) {

  dplyr::bind_rows((tidygraph::as_tibble(input_graph %>% tidygraph::activate(edges) %>%
                                           tidygraph::select(Competing_name, comp_count_current, comp_count_pre)) %>%
                      tidygraph::mutate(initial_count = comp_count_pre) %>% tidygraph::select(id = Competing_name,
                                                                                              initial_count, count_pre = comp_count_pre, count_current = comp_count_current) %>%
                      tidygraph::distinct()), (tidygraph::as_tibble(input_graph %>% tidygraph::activate(edges) %>%
                                                                      tidygraph::select(miRNA_name, mirna_count_current, mirna_count_pre)) %>%
                                                 tidygraph::mutate(initial_count = mirna_count_pre) %>% tidygraph::select(id = miRNA_name,
                                                                                                                          initial_count, count_pre = mirna_count_pre, count_current = mirna_count_current) %>%
                                                 tidygraph::distinct()))


}

#' Carries the variables from edge to node
#'
#' Carries the variables from edge to node.
#'
#' @details The function is a helper function for
#' processing of graph object with update_nodes function.
#'
#' @param input_graph Processed graph object in previous step.
#' @return tibble object
#' @keywords internal
#'


prepare_rhs <- function(input_graph) {

  dplyr::bind_rows((tidygraph::as_tibble(input_graph %>% tidygraph::activate(edges)) %>%
                      dplyr::select(id = Competing_name, count_current = comp_count_current) %>%
                      dplyr::distinct()), (tidygraph::as_tibble(input_graph %>% tidygraph::activate(edges)) %>%
                                             dplyr::select(id = miRNA_name, count_current = mirna_count_current) %>%
                                             dplyr::distinct()))
}

#' Carries variables from edge to node.
#'
#' This function carries variables from edge to node and should be used
#' after `update_how` or `update_variables` functions
#'
#' @return the graph object.
#'
#' @param input_graph Processed graph object in previous step.
#' @param once The argument is about when the carrying process
#' runs (internal use only)
#' @param limit absolute minimum amount of change required to
#' be considered as up/down regulated element
#'
#' @details If the carrying process performs after priming_graph
#' function, the argument must be TRUE. The function helps to
#' visualisation of processed graph object, especially that
#' includes too many nodes.This step makes it easily to follow
#' the processes.
#'
#' @examples
#'
#' data('minsamp')
#'
#' minsamp %>%
#'   priming_graph(Competing_expression, miRNA_expression) %>%
#'   update_how('Gene2',2)
#'
#' @export

update_nodes <- function(input_graph, once = FALSE, limit = 0) {
  if (once) {
    rhs_table <- prepare_rhs_once(input_graph)
  } else {
    rhs_table <- prepare_rhs(input_graph)
  }
  if (!once) {
    input_graph <- input_graph %>% tidygraph::activate(nodes) %>% tidygraph::select(-count_pre) %>%
      tidygraph::select(name, type, node_id, initial_count, count_pre = count_current)
  }

  input_graph <- input_graph %>% tidygraph::activate(nodes) %>% tidygraph::left_join(rhs_table,
                                                                                     by = c(name = "id")) %>% tidygraph::mutate(changes_variable = ifelse(count_current -
                                                                                                                                                            count_pre < -limit, "Down", type), changes_variable = ifelse(count_current -
                                                                                                                                                                                                                           count_pre > limit, "Up", changes_variable))

  input_graph
}