R/pgs.subnetwork.R

In oacar/pgsNetwork: This package is used for ref

#' This function is helper to create a 1st degree neighborhood for the genes given
#'@param allnet full network
#'@param pgs.name subset of genes that will be queried for first degree neighborhood
#'
#'@return subnetwork of all genes in pgs.names and first degree neighbors color and category reflect the given set
#'
pgs.subnetwork <- function(allnet, pgs.names,order= 1) {
  nn <- neighborhood(allnet,order=order,pgs.names[pgs.names%in%V(allnet)$name]) %>% unlist %>% induced_subgraph(allnet,.,impl='copy_and_delete')
  V(nn)$size <- 1
  V(nn)$color <- ifelse(V(nn)$name%in%pgs.names,'red','blue')
  V(nn)$cat <- ifelse(V(nn)$name%in%pgs.names,'proto-gene','gene')
  #plot(nn,vertex.label=NA,edge.arrow.size=0.1)
  nn
}