Update app.py

app.py

@@ -79,7 +79,7 @@ gene_names = []
 descriptions = []
     
 for gene_id in gene_ids:
-    try:    
+    try:
         TGME49_id = TGME49_transcript_annotations.loc[TGME49_transcript_annotations["gene_id"] == gene_id]["TGME49_id"].values[0]
         gene_name = TGME49_transcript_annotations.loc[TGME49_transcript_annotations["gene_id"] == gene_id]["gene_name"].values[0]
         description = TGME49_transcript_annotations.loc[TGME49_transcript_annotations["gene_id"] == gene_id]["description"].values[0]
@@ -92,14 +92,27 @@ for gene_id in gene_ids:
     TGME49_ids.append(TGME49_id)
     gene_names.append(gene_name)
     descriptions.append(description)
-    
+
 node_info = pd.DataFrame({
+    "gene_index": range(gene_ids),
     "gene_id" : gene_ids,
     "gene_type" : gene_types,
     "TGME49_id": TGME49_ids,
     "gene_name": gene_names,
     "description": description})
 
+neighbors = neighbors.merge(
+    right = node_info,
+    left_by = "gene_id_1",
+    right_by = "gene_id",
+    suffix = "_1")
+
+neighbors = neighbors.merge(
+    right = node_info,
+    left_by = "gene_id_2",
+    right_by = "gene_id",
+    suffix = "_2")
+
 ################################
 # Use NetworkX to layout graph #
 ################################
@@ -107,25 +120,17 @@ node_info = pd.DataFrame({
 # but I'm unsure how to do it through the streamlit-cytoscapejs interface :(
 
 
-st.write(f"gene_id_1: {neighbors.gene_id_1.to_list()}")
-st.write(f"gene_id_2: {neighbors.gene_id_2.to_list()}")
-st.write(f"coexp_score: {neighbors.coexp_score.to_list()}")
-st.write(f"gene_id_1: {len(neighbors.gene_id_1.to_list())}")
-st.write(f"gene_id_2: {len(neighbors.gene_id_2.to_list())}")
-st.write(f"coexp_score: {len(neighbors.coexp_score.to_list())}")
-
-
 G = nx.Graph()
 G.add_weighted_edges_from(
-    [neighbors.gene_id_1.to_list()[0:3],
-     neighbors.gene_id_2.to_list()[0:3],
-     neighbors.coexp_score.to_list()[0:3]])
+    [neighbors.gene_index_1.to_list(),
+     neighbors.gene_index_2.to_list(),
+     neighbors.coexp_score.to_list())
 layout = nx.spring_layout(G)
 
 
 
 elements = []
-for i in range(3):# range(len(gene_ids)):
+for i in range(len(gene_ids)):
     elements.append({
         "data": {
             "id": gene_ids[i],
@@ -133,7 +138,7 @@ for i in range(3):# range(len(gene_ids)):
         "position": {
             "x" : layout[gene_ids[i]][0],
             "y" : layout[gene_ids[i]][1]}})
-for i in range(3): #range(len(neighbors.index)):
+for i in range(len(neighbors.index)):
     edge = neighbors.iloc[i]
     elements.append({
         "data" : {