minor updates

associations/extend_network/get_extended_network.R

@@ -75,11 +75,9 @@ retrieve_stringdb_net <- function(finput, fn, fscore) {
                             score = json[[1]]$scores$`stringdb::score`,
                             stringsAsFactors = F)
   
-  ppi_network <- ppi_network[ppi_network$score >= fscore,]
+  ppi_network <- unique(ppi_network[ppi_network$score >= fscore,])
   ppi_network$source <- gsub('9606.', "", ppi_network$source)
   ppi_network$target <- gsub('9606.', "", ppi_network$target)
-  ppi_network
-  ppi_network <- unique(ppi_network)
   message("after pruning by score, the network contains ", dim(ppi_network)[1], " interactions ")
   return(ppi_network)
 }
@@ -146,6 +144,9 @@ if (dbsource == "stringdb" | dbsource == "text_mining") {
   }
 } 
 
+### if PPI network is either null (no text mining requested) or empty
+### fall back completely to OmniPathDB network
+### else use OmniPathDB to filter out the text mining results
 if(length(ppi_network) == 0) {
   message("No text mining network, relying only on OmniPathDB")
   ppi_network <- retrieve_omnipath(input)