From dc6c5ec46d7a5cb9075d8c217d76b3bc166285ad Mon Sep 17 00:00:00 2001
From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com>
Date: Fri, 15 Mar 2024 20:58:30 +0000
Subject: [PATCH] Fix get_ontology. add plot_graph_visnetwork opt for arrows

---
 R/get_ontology.R          | 9 ++++++---
 R/plot_graph_visnetwork.R | 2 ++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/R/get_ontology.R b/R/get_ontology.R
index 4f434a9..dee016b 100644
--- a/R/get_ontology.R
+++ b/R/get_ontology.R
@@ -52,6 +52,9 @@ get_ontology <- function(name=c("mondo",
   if(isFALSE(force_new) && file.exists(save_path)){
     messager("Loading cached ontology:",save_path)
     ont <- readRDS(save_path)
+    #### Subset ontology ####
+    ont <- filter_ontology(ont = ont, 
+                           terms = terms)
     return(ont)
   } 
   ol <- rols::Ontologies()
@@ -115,15 +118,15 @@ get_ontology <- function(name=c("mondo",
                                  add_ancestors=add_ancestors, 
                                  add_ontology_levels=add_ontology_levels)
   }
-  #### Subset ontology ####
-  ont <- filter_ontology(ont = ont, 
-                         terms = terms)
   #### Cache RDS object ####
   if(!is.null(save_dir)){
     dir.create(save_dir, recursive=TRUE, showWarnings = FALSE)
     messager("Saving ontology -->",save_path)
     saveRDS(ont, save_path)
   }
+  #### Subset ontology ####
+  ont <- filter_ontology(ont = ont, 
+                         terms = terms)
   #### Return ####
   return(ont)
 }
\ No newline at end of file
diff --git a/R/plot_graph_visnetwork.R b/R/plot_graph_visnetwork.R
index c917940..1b6a55f 100644
--- a/R/plot_graph_visnetwork.R
+++ b/R/plot_graph_visnetwork.R
@@ -30,6 +30,7 @@ plot_graph_visnetwork <- function(g,
                                     avoidOverlap = 0.5, 
                                     gravitationalConstant = -50),
                                   scaling = NULL,
+                                  arrows = "from",
                                   smooth = list(enabled = TRUE, 
                                                 type = "cubicBezier", 
                                                 roundness = 0.5),
@@ -111,6 +112,7 @@ plot_graph_visnetwork <- function(g,
     ) |>
     visNetwork::visEdges(shadow = list(enabled=FALSE),
                          smooth = smooth,
+                         arrows = arrows,
                          color = list(opacity = 0.5)) |>
     # visNetwork::visLegend() |>
     # visNetwork::visClusteringByConnection(nodes = unique(top_targets[[group_var]])) |>