R/find_node_perturbation.R

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

#' Calculates average expression changes of all (or specified)
#' nodes except trigger and finds the perturbed node count for
#' all (or specified) nodes in system.
#'
#'
#' @importFrom furrr future_map future_map_dfr
#' @importFrom future plan
#' @importFrom rlang set_names
#' @importFrom igraph gsize degree V 'V<-'
#' @importFrom purrr map_dbl map
#' @importFrom tidyr unnest
#'
#' @return It gives a tibble form dataset that includes node names,
#' perturbation efficiency and perturbed count of nodes.
#'
#' @details find_node_perturbation calculates mean expression changes
#' of elements after the change in the network in terms of percentage.
#' It also calculates the number of nodes that have expression changes
#' after the change occur in the network. The outputs of the function
#' are the perturbation efficiency and perturbed count of nodes for
#' each nodes.
#'
#' @param input_graph The graph object that was processed with priming_graph function.
#' @param how The change of count (expression) of the given node in terms of fold change.
#' @param cycle The iteration of simulation.
#' @param limit The minimum fold change which can be taken into account for
#' perturbation calculation on all nodes in terms of percentage.
#' @param fast specifies percentage of affected target in target expression.
#' For example, if fast = 1, the nodes that are affected from miRNA repression
#' activity more than one percent of their expression is determined as subgraph.
#'
#' @examples
#'
#' data('minsamp')
#' data('midsamp')
#'
#'  minsamp%>%
#'   priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression)%>%
#'   find_node_perturbation()%>%
#'   select(name, perturbation_efficiency, perturbed_count)
#'
#'
#'  minsamp%>%
#'   priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression,
#'     aff_factor = c(energy,seed_type), deg_factor = region)%>%
#'   find_node_perturbation(how = 3, cycle = 4)%>%
#'   select(name, perturbation_efficiency, perturbed_count)
#'
#'  midsamp%>%
#'   priming_graph(competing_count = Gene_expression, miRNA_count = miRNA_expression)%>%
#'   find_node_perturbation(how = 2, cycle= 3, limit=1, fast = 5)%>%
#'   select(name, perturbation_efficiency, perturbed_count)
#'
#'
#' @export

find_node_perturbation <- function(input_graph, how = 2, cycle = 1, limit = 0, fast = 0) {
  
  if (fast == 0) {
    
    result <- input_graph %>% 
      activate(nodes) %>% 
      tidygraph::mutate(eff_count = future_map(V(input_graph)$name, ~calc_perturbation(input_graph, .x, how, cycle, limit))) %>%
      tibble::as_tibble() %>% 
      unnest(eff_count)
  }
  
  if (fast != 0) {
    
    input_graph %>% 
      tidygraph::activate(edges) -> main_graph
    
    main_graph %>% 
      tidygraph::mutate(fast = ifelse(100*effect_current/comp_count_current > fast, TRUE, FALSE)) %>%
      tidygraph::filter(fast) %>%
      tidygraph::activate(nodes) %>%
      tidygraph::mutate(degree = tidygraph::centrality_degree(mode = "all")) %>%
      tidygraph::filter(degree > 0) -> fast_graph
    
    fast_graph %>% 
      tidygraph::mutate(eff_count = purrr::map(name, ~calc_perturbation(fast_graph, .x,  how, cycle, limit))) %>% 
      activate(nodes) %>% 
      as_tibble() %>% 
      unnest() %>% 
      dplyr::select(name, perturbation_efficiency, perturbed_count)-> res_calc_per
    
    result<- main_graph %>% 
      activate(nodes) %>% 
      as_tibble() %>% 
      left_join(res_calc_per, by = "name")
    
  }

  
  return(result)
  
}