improved connect_nodes, minor fix to yfiles visualizer

sysbio-curie · Jun 28, 2024 · 0049046 · 0049046
1 parent 4157eba
commit 0049046
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Showing 2 changed files with 25 additions and 20 deletions.
diff --git a/neko/_visual/visualize_network.py b/neko/_visual/visualize_network.py
@@ -139,8 +139,7 @@ def render(self, output_file='network', view=False, highlight_nodes=None, highli
             display(self.graph)  # Display the graph directly in the Jupyter Notebook
 
     def yfiles_visual(
-        #       self,
-        network,
+        self,
         graph_layout,
         directed,
     ):
@@ -149,10 +148,10 @@ def yfiles_visual(
 
         # filling w with nodes
         objects = []
-        for idx, item in network.nodes.iterrows():
+        for idx, item in self.dataframe_nodes.iterrows():
             obj = {
-                "id": network.nodes["Uniprot"].loc[idx],
-                "properties": {"label": network.nodes["Genesymbol"].loc[idx]},
+                "id": self.dataframe_nodes["Uniprot"].loc[idx],
+                "properties": {"label": self.dataframe_nodes["Genesymbol"].loc[idx]},
                 "color": "#ffffff",
                 "styles": {"backgroundColor": "#ffffff"}
             }
@@ -161,12 +160,12 @@ def yfiles_visual(
 
         # filling w with edges
         objects = []
-        for index, row in network.edges.iterrows():
+        for index, row in self.dataframe_edges.iterrows():
             obj = {
-                "id": network.edges["Effect"].loc[index],
-                "start": network.edges["source"].loc[index],
-                "end": network.edges["target"].loc[index],
-                "properties": {"references": network.edges["References"].loc[index]}}
+                "id": self.dataframe_edges["Effect"].loc[index],
+                "start": self.dataframe_edges["source"].loc[index],
+                "end": self.dataframe_edges["target"].loc[index],
+                "properties": {"references": self.dataframe_edges["References"].loc[index]}}
             objects.append(obj)
         w.edges = objects
 
@@ -206,6 +205,7 @@ def custom_label_styles_mapping(node: Dict):
         display(w)
 
     def vis_comparison(
+        self,
         int_comparison,
         node_comparison,
         graph_layout,

diff --git a/neko/core/network.py b/neko/core/network.py
@@ -717,9 +717,9 @@ def connect_nodes(self,
         The only_signed flag makes sure that just signed interaction will be added to the network, while "consensus_only"
         makes sure that just signed interaction with consensus among references will be included.
 
-        Parameters:
-        - only_signed: A boolean flag indicating whether to only add signed interactions to the network.
-        - consensus_only: A boolean flag indicating whether to only add signed interactions with consensus among references to the network.
+        Parameters: - only_signed: A boolean flag indicating whether to only add signed interactions to the network.
+        - consensus_only: A boolean flag indicating whether to only add signed interactions with consensus among
+        references to the network.
 
         Returns:
         None. The function modifies the network object in-place.
@@ -731,7 +731,8 @@ def connect_nodes(self,
 
         def add_edge_if_not_empty_and_signed(node1, node2):
             """
-            Helper function to add an edge to the network if the interaction is not empty and, if the `only_signed` flag is set, the interaction is signed.
+            Helper function to add an edge to the network if the interaction is not empty and, if the `only_signed`
+            flag is set, the interaction is signed.
 
             Parameters:
             - node1: The source node of the interaction.
@@ -740,10 +741,12 @@ def add_edge_if_not_empty_and_signed(node1, node2):
             Returns:
             None. The function modifies the network object in-place.
             """
-            interaction = self.resources.loc[(self.resources["source"] == node1) &
-                                             (self.resources["target"] == node2)]
-            if not interaction.empty and (not only_signed or check_sign(interaction, consensus_only) != "undefined"):
-                self.add_edge(interaction)
+            if node2 in self.connect.find_all_neighbours(node1):
+                interaction = self.resources.loc[(self.resources["source"] == node1) &
+                                                 (self.resources["target"] == node2)]
+                if not interaction.empty and (
+                    not only_signed or check_sign(interaction, consensus_only) != "undefined"):
+                    self.add_edge(interaction)
 
         for node1, node2 in combinations(self.nodes["Uniprot"], 2):
             add_edge_if_not_empty_and_signed(node1, node2)
@@ -889,9 +892,10 @@ def dfs_algorithm(self,
 
         """
 
-        i = 0
+        i = 1
+        min_len = 1
         while i <= maxlen:
-            paths = self.connect.find_paths(node2, node1, maxlen=i)
+            paths = self.connect.find_paths(node2, node1, maxlen=i, minlen=min_len)
             if only_signed:
                 paths = self.filter_unsigned_paths(paths, consensus)
             if paths:
@@ -902,6 +906,7 @@ def dfs_algorithm(self,
                 break
             else:
                 i += 1
+                min_len += 1
 
     def bfs_algorithm(self,
                       node1: str,