R/cAMARETTO_InformationTable.R

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

#' @title cAMARETTO_InformationTable
#'
#' @param cAMARETTOnetworkM The output of the Module Network function.
#' @param cAMARETTOnetworkC The output of the Identify Communities function.
#'
#' @return an information table about the communities containing the included nodes and overlapping genes per community.
#' 
#' @import igraph
#' @importFrom tibble add_row tibble
#' 
#' @examples 
#' 
#' cAMARETTO_InformationTable(cAMARETTOnetworkM, cAMARETTOnetworkC)
#' 
#' @export
cAMARETTO_InformationTable <- function(cAMARETTOnetworkM, cAMARETTOnetworkC) {
  Nodes_Cnetwork <- igraph::as_data_frame(cAMARETTOnetworkC$CommGraph, what="vertices")
  Edges_Cnetwork <- igraph::as_data_frame(cAMARETTOnetworkC$CommGraph, what="edges")
  Comm_Info <- tibble::tibble(community_numb = as.numeric(), included_nodes = as.character(), overlapping_genes = as.character())
  i=1
  for (comm in cAMARETTOnetworkC$community_list) {
    Edges_Cnetwork_comm <- Edges_Cnetwork %>% 
      filter(from %in% comm & to %in% comm)
    all_overlapping_genes <- unique(unlist(strsplit(Edges_Cnetwork_comm$Overlapping_genes,", ")))
    Comm_Info <- add_row(Comm_Info, community_numb = as.numeric(names(cAMARETTOnetworkC$community_list[i])), included_nodes = paste(comm,collapse=", "), overlapping_genes = paste(all_overlapping_genes,collapse=", "))
    i = i + 1
  }
  return(Comm_Info)
}