From dcddaa24555360620ac8e6d7418bd2f376617436 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Thu, 9 Jan 2025 15:39:03 -0500
Subject: [PATCH] layout(visualizeNetworks): Set up cose layout for network viz

---
 R/visualizeNetworks.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/visualizeNetworks.R b/R/visualizeNetworks.R
index 1a04e24..b146986 100644
--- a/R/visualizeNetworks.R
+++ b/R/visualizeNetworks.R
@@ -30,7 +30,8 @@
 #'
 #'
 visualizeNetworks <- function(nodes, edges,
-                              pvalueCutoff = 0.05, logfcCutoff = 0.5) {
+                              pvalueCutoff = 0.05, 
+                              logfcCutoff = 0.5) {
     # Add additional columns for visualization
     nodes$logFC_color <- nodes$logFC
     nodes$logFC_color[nodes$pvalue > pvalueCutoff |
@@ -64,6 +65,7 @@ visualizeNetworks <- function(nodes, edges,
             VISUAL_STYLE_MAPPINGS
         )
         setVisualStyle(VISUAL_STYLE_NAME)
+        layoutNetwork("cose")
     } else {
         warning("Visualization is not available in non-interactive mode.")
     }