From f678da0eb6dcb8396a7b0613f31645d5cfd99d19 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 2 Oct 2025 15:14:20 -0400
Subject: [PATCH 1/2] increase edge font size

---
 R/visualizeNetworksWithHTML.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/visualizeNetworksWithHTML.R b/R/visualizeNetworksWithHTML.R
index d10eb33..c244d98 100644
--- a/R/visualizeNetworksWithHTML.R
+++ b/R/visualizeNetworksWithHTML.R
@@ -462,7 +462,7 @@ generateCytoscapeConfig <- function(nodes, edges,
                 `edge-text-rotation` = "autorotate",
                 `text-margin-y` = -12,
                 `text-halign` = "center",
-                `font-size` = "9px",
+                `font-size` = "12px",
                 `font-weight` = "bold",
                 color = "data(color)",
                 `text-background-color` = "#ffffff",

From 2657daf4215213703ccf24342b7762d035a3e814 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 2 Oct 2025 17:15:20 -0400
Subject: [PATCH 2/2] reorder node and edge tables columns

---
 R/utils_getSubnetworkFromIndra.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index f3b8bce..eda9444 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -245,6 +245,9 @@
         target = vapply(keys(res), function(x) {
             query(res, x)$target_uniprot_id
         }, ""),
+        site = vapply(keys(res), function(x) {
+            query(res, x)$site
+        }, ""),
         interaction = vapply(keys(res), function(x) {
             query(res, x)$data$stmt_type
         }, ""),
@@ -260,9 +263,6 @@
         sourceCounts = vapply(keys(res), function(x) {
             query(res, x)$data$source_counts
         }, ""),
-        site = vapply(keys(res), function(x) {
-            query(res, x)$site
-        }, ""),
         stringsAsFactors = FALSE
     )
     # add correlation - maybe create a separate function
@@ -289,8 +289,8 @@
 #' @keywords internal
 #' @noRd
 .constructNodesDataFrame <- function(input, edges) {
-    nodes = input[, c("Protein", "log2FC", "adj.pvalue", "HgncName", "Site")]
-    colnames(nodes) = c("id", "logFC", "adj.pvalue", "hgncName", "Site")
+    nodes = input[, c("Protein", "HgncName", "Site", "log2FC", "adj.pvalue")]
+    colnames(nodes) = c("id", "hgncName", "Site", "logFC", "adj.pvalue")
     
     nodes = nodes[nodes$id %in% c(edges$source, edges$target), ]
     nodes$hgncName = ifelse(is.na(nodes$hgncName), nodes$id, nodes$hgncName)