From 44a7a6b5aca49595e019749e00ab4313e8ad6d50 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Fri, 8 Nov 2024 16:26:50 -0500
Subject: [PATCH 1/8] feat: Add Compound Nodes to Cytoscape Graph

Clusters Drugs (for gene searchs) and Genes (for drug searchs) will be put into a unique parent node based on the connected gene/drug all the nodes in the cluster share. Doing this makes it much easier to visually distinguish one cluster from another, and also allows a user to move clusters around without having to move each node individually.
---
 src/dgipy/graph_app.py     |  2 +-
 src/dgipy/network_graph.py | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/dgipy/graph_app.py b/src/dgipy/graph_app.py
index b94836f..2793848 100644
--- a/src/dgipy/graph_app.py
+++ b/src/dgipy/graph_app.py
@@ -197,7 +197,7 @@ def _update_cytoscape(app: dash.Dash) -> None:
     def update(terms: list | None, search_mode: str) -> dict:
         if len(terms) != 0:
             interactions = dgidb.get_interactions(terms, search_mode)
-            network_graph = ng.initalize_network(interactions, terms, search_mode)
+            network_graph = ng.create_network(interactions, terms, search_mode)
             return ng.generate_cytoscape(network_graph)
         return {}
 
diff --git a/src/dgipy/network_graph.py b/src/dgipy/network_graph.py
index 43d5a4a..d273759 100644
--- a/src/dgipy/network_graph.py
+++ b/src/dgipy/network_graph.py
@@ -97,6 +97,14 @@ def _add_node_attributes(interactions_graph: nx.Graph, search_mode: str) -> None
         interactions_graph.nodes[node]["node_color"] = set_color
         interactions_graph.nodes[node]["node_size"] = set_size
 
+        if (search_mode == "genes" and (not is_gene)) or (
+            search_mode == "drugs" and is_gene
+        ):
+            neighbors = "Group: " + "-".join(list(interactions_graph.neighbors(node)))
+            interactions_graph.nodes[node]["group"] = neighbors
+        else:
+            interactions_graph.nodes[node]["group"] = None
+
 
 def create_network(
     interactions: pd.DataFrame, terms: list, search_mode: str
@@ -129,4 +137,14 @@ def generate_cytoscape(graph: nx.Graph) -> dict:
             "position": {"x": int(node_pos[0].item()), "y": int(node_pos[1].item())}
         }
         cytoscape_node_data[node].update(node_pos)
+        if "group" in cytoscape_node_data[node]["data"]:
+            cytoscape_node_data[node]["data"]["parent"] = cytoscape_node_data[node][
+                "data"
+            ].pop("group")
+    groups = set()
+    for node in graph.nodes:
+        if ("group" in graph.nodes[node]) and (graph.nodes[node]["group"] is not None):
+            groups.add(graph.nodes[node]["group"])
+    for group in groups:
+        cytoscape_node_data.append({"data": {"id": group}})
     return cytoscape_node_data + cytoscape_edge_data

From f3c34cf9511787d1bba7293a3815809c0d85aaea Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Sat, 23 Nov 2024 10:12:40 -0500
Subject: [PATCH 2/8] test: Add tests for network_graph.py

Added barebone tests for network_graph, to be expanded/formalized in the future.
---
 pyproject.toml              |  2 +-
 src/dgipy/__init__.py       |  3 +++
 tests/test_network_graph.py | 18 ++++++++++++++++++
 3 files changed, 22 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_network_graph.py

diff --git a/pyproject.toml b/pyproject.toml
index f84e33c..601608b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,7 +75,7 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
-exclude = ["docs/source/conf.py", "tests/test_graph_app.py"]
+exclude = ["docs/source/conf.py", "tests/test_graph_app.py", "tests/test_network_graph.py"]
 lint.select = [
     "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
     "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
diff --git a/src/dgipy/__init__.py b/src/dgipy/__init__.py
index 11fa409..2d24363 100644
--- a/src/dgipy/__init__.py
+++ b/src/dgipy/__init__.py
@@ -12,6 +12,7 @@
     get_sources,
 )
 from .graph_app import generate_app
+from .network_graph import create_network, generate_cytoscape
 
 __all__ = [
     "get_drugs",
@@ -24,4 +25,6 @@
     "get_drug_applications",
     "generate_app",
     "get_clinical_trials",
+    "create_network",
+    "generate_cytoscape",
 ]
diff --git a/tests/test_network_graph.py b/tests/test_network_graph.py
new file mode 100644
index 0000000..1bec2c5
--- /dev/null
+++ b/tests/test_network_graph.py
@@ -0,0 +1,18 @@
+import pytest
+
+from dgipy.dgidb import get_interactions
+from dgipy.network_graph import create_network, generate_cytoscape
+
+
+def test_create_network():
+    interactions = get_interactions("BRAF")
+    terms = ["BRAF"]
+    search_mode = "genes"
+    assert create_network(interactions, terms, search_mode)
+
+def test_generate_cytoscape():
+    interactions = get_interactions("BRAF")
+    terms = ["BRAF"]
+    search_mode = "genes"
+    network = create_network(interactions, terms, search_mode)
+    assert generate_cytoscape(network)
\ No newline at end of file

From 3a028b952f841b3315e790b75a470a3a5b80d640 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Sat, 23 Nov 2024 10:15:18 -0500
Subject: [PATCH 3/8] fix: fix node selection bug

Fixed bug in which selecting a compound node caused an error. The error was due to the fact compound nodes lack a node_degree attribute (which node selection checks for). Problem was fixed by checking whether the node has a node_degree attribute
---
 src/dgipy/graph_app.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/dgipy/graph_app.py b/src/dgipy/graph_app.py
index 2793848..1c7b8ae 100644
--- a/src/dgipy/graph_app.py
+++ b/src/dgipy/graph_app.py
@@ -262,6 +262,7 @@ def update(selected_element: str | dict) -> tuple[list, None]:
         if (
             selected_element != ""
             and selected_element["group"] == "nodes"
+            and "node_degree" in selected_element["data"]
             and selected_element["data"]["node_degree"] != 1
         ):
             neighbor_set = set()

From f7857830abfa199d5a0c1328fd922dc31f60f6f7 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Sat, 23 Nov 2024 10:18:00 -0500
Subject: [PATCH 4/8] refactor: refactor network_graph.py

Made numerous changes to improve the readability of network_graph.py, and to remove redundant code (left over from the shift to cytoscape):
- Removed pandas dependency (Redundant, as functions were using dict)
- Modified dict iteration in initalize_network() to improve readability
- Privated initalize_network() (initalize_network serves as only one part of the overall create_network() function (which is public). initalize_network() should not be directly run itself)
- Removed node color/size assignment from add_node_attributes() (With the shift to cytoscape, Node color/size assignment is now done in graph_app.py)
- Moved node_degree attribute assignment to add_node_attributes()
---
 src/dgipy/network_graph.py | 93 ++++++++++----------------------------
 1 file changed, 23 insertions(+), 70 deletions(-)

diff --git a/src/dgipy/network_graph.py b/src/dgipy/network_graph.py
index d273759..3804033 100644
--- a/src/dgipy/network_graph.py
+++ b/src/dgipy/network_graph.py
@@ -1,50 +1,38 @@
 """Provides functionality to create networkx graphs and pltoly figures for network visualization"""
 
 import networkx as nx
-import pandas as pd
 
 LAYOUT_SEED = 7
 
 
-def initalize_network(
-    interactions: pd.DataFrame, terms: list, search_mode: str
-) -> nx.Graph:
-    """Create a networkx graph representing interactions between genes and drugs
-
-    :param interactions: DataFrame containing drug-gene interaction data
-    :param terms: List containing terms used to query interaction data
-    :param search_mode: String indicating whether query was gene-focused or drug-focused
-    :return: a networkx graph of drug-gene interactions
-    """
+def _initalize_network(interactions: dict, terms: list, search_mode: str) -> nx.Graph:
     interactions_graph = nx.Graph()
     graphed_terms = set()
-
-    for index in range(len(interactions["gene_name"]) - 1):
+    for row in zip(*interactions.values(), strict=True):
+        row_dict = dict(zip(interactions.keys(), row, strict=True))
         if search_mode == "genes":
-            graphed_terms.add(interactions["gene_name"][index])
+            graphed_terms.add(row_dict["gene_name"])
         if search_mode == "drugs":
-            graphed_terms.add(interactions["drug_name"][index])
+            graphed_terms.add(row_dict["drug_name"])
         interactions_graph.add_node(
-            interactions["gene_name"][index],
-            label=interactions["gene_name"][index],
+            row_dict["gene_name"],
+            label=row_dict["gene_name"],
             isGene=True,
         )
         interactions_graph.add_node(
-            interactions["drug_name"][index],
-            label=interactions["drug_name"][index],
+            row_dict["drug_name"],
+            label=row_dict["drug_name"],
             isGene=False,
         )
         interactions_graph.add_edge(
-            interactions["gene_name"][index],
-            interactions["drug_name"][index],
-            id=interactions["gene_name"][index]
-            + " - "
-            + interactions["drug_name"][index],
-            approval=interactions["drug_approved"][index],
-            score=interactions["interaction_score"][index],
-            attributes=interactions["interaction_attributes"][index],
-            sourcedata=interactions["interaction_sources"][index],
-            pmid=interactions["interaction_pmids"][index],
+            row_dict["gene_name"],
+            row_dict["drug_name"],
+            id=row_dict["gene_name"] + " - " + row_dict["drug_name"],
+            approval=row_dict["drug_approved"],
+            score=row_dict["interaction_score"],
+            attributes=row_dict["interaction_attributes"],
+            sourcedata=row_dict["interaction_sources"],
+            pmid=row_dict["interaction_pmids"],
         )
 
     graphed_terms = set(terms).difference(graphed_terms)
@@ -54,48 +42,15 @@ def initalize_network(
         if search_mode == "drugs":
             interactions_graph.add_node(term, label=term, isGene=False)
 
-    nx.set_node_attributes(
-        interactions_graph, dict(interactions_graph.degree()), "node_degree"
-    )
     return interactions_graph
 
 
 def _add_node_attributes(interactions_graph: nx.Graph, search_mode: str) -> None:
+    nx.set_node_attributes(
+        interactions_graph, dict(interactions_graph.degree()), "node_degree"
+    )
     for node in interactions_graph.nodes:
         is_gene = interactions_graph.nodes[node]["isGene"]
-        degree = interactions_graph.degree[node]
-        if search_mode == "genes":
-            if is_gene:
-                if degree > 1:
-                    set_color = "cyan"
-                    set_size = 10
-                else:
-                    set_color = "blue"
-                    set_size = 10
-            else:
-                if degree > 1:
-                    set_color = "orange"
-                    set_size = 7
-                else:
-                    set_color = "red"
-                    set_size = 7
-        if search_mode == "drugs":
-            if is_gene:
-                if degree > 1:
-                    set_color = "cyan"
-                    set_size = 7
-                else:
-                    set_color = "blue"
-                    set_size = 7
-            else:
-                if degree > 1:
-                    set_color = "orange"
-                    set_size = 10
-                else:
-                    set_color = "red"
-                    set_size = 10
-        interactions_graph.nodes[node]["node_color"] = set_color
-        interactions_graph.nodes[node]["node_size"] = set_size
 
         if (search_mode == "genes" and (not is_gene)) or (
             search_mode == "drugs" and is_gene
@@ -106,17 +61,15 @@ def _add_node_attributes(interactions_graph: nx.Graph, search_mode: str) -> None
             interactions_graph.nodes[node]["group"] = None
 
 
-def create_network(
-    interactions: pd.DataFrame, terms: list, search_mode: str
-) -> nx.Graph:
+def create_network(interactions: dict, terms: list, search_mode: str) -> nx.Graph:
     """Create a networkx graph representing interactions between genes and drugs
 
-    :param interactions: DataFrame containing drug-gene interaction data
+    :param interactions: Dictionary containing drug-gene interaction data
     :param terms: List containing terms used to query interaction data
     :param search_mode: String indicating whether query was gene-focused or drug-focused
     :return: a networkx graph of drug-gene interactions
     """
-    interactions_graph = initalize_network(interactions, terms, search_mode)
+    interactions_graph = _initalize_network(interactions, terms, search_mode)
     _add_node_attributes(interactions_graph, search_mode)
     return interactions_graph
 

From 65aed7617b07eb703212d82a7ba91ab878bc4e61 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Sat, 23 Nov 2024 10:36:10 -0500
Subject: [PATCH 5/8] style(test_network_graph): add newline at end of file

---
 tests/test_network_graph.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_network_graph.py b/tests/test_network_graph.py
index 1bec2c5..087bafd 100644
--- a/tests/test_network_graph.py
+++ b/tests/test_network_graph.py
@@ -15,4 +15,4 @@ def test_generate_cytoscape():
     terms = ["BRAF"]
     search_mode = "genes"
     network = create_network(interactions, terms, search_mode)
-    assert generate_cytoscape(network)
\ No newline at end of file
+    assert generate_cytoscape(network)

From b6c26aca5fcafb261c137eef0b236b5df940f6c3 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Sat, 23 Nov 2024 13:47:52 -0500
Subject: [PATCH 6/8] refactor: refactor generate_cytoscape()

Code was refactored so as to remove redundant iteration and variable instantiation
---
 src/dgipy/network_graph.py | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/src/dgipy/network_graph.py b/src/dgipy/network_graph.py
index 3804033..40add63 100644
--- a/src/dgipy/network_graph.py
+++ b/src/dgipy/network_graph.py
@@ -84,20 +84,14 @@ def generate_cytoscape(graph: nx.Graph) -> dict:
     cytoscape_data = nx.cytoscape_data(graph)["elements"]
     cytoscape_node_data = cytoscape_data["nodes"]
     cytoscape_edge_data = cytoscape_data["edges"]
-    for node in range(len(cytoscape_node_data)):
-        node_pos = pos[cytoscape_node_data[node]["data"]["id"]]
-        node_pos = {
-            "position": {"x": int(node_pos[0].item()), "y": int(node_pos[1].item())}
-        }
-        cytoscape_node_data[node].update(node_pos)
-        if "group" in cytoscape_node_data[node]["data"]:
-            cytoscape_node_data[node]["data"]["parent"] = cytoscape_node_data[node][
-                "data"
-            ].pop("group")
     groups = set()
-    for node in graph.nodes:
-        if ("group" in graph.nodes[node]) and (graph.nodes[node]["group"] is not None):
-            groups.add(graph.nodes[node]["group"])
+    for node in cytoscape_node_data:
+        node_pos = pos[node["data"]["id"]]
+        node.update({"position": {"x": node_pos[0], "y": node_pos[1]}})
+        if "group" in node["data"]:
+            group = node["data"].pop("group")
+            groups.add(group)
+            node["data"]["parent"] = group
     for group in groups:
         cytoscape_node_data.append({"data": {"id": group}})
     return cytoscape_node_data + cytoscape_edge_data

From 1ea0d5beab1a3cef765bade3b1ff6939b3185e07 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Sat, 23 Nov 2024 14:05:25 -0500
Subject: [PATCH 7/8] style(ruff): Apply ruff style to graph_app and
 network_graph tests

---
 pyproject.toml              | 2 +-
 tests/test_graph_app.py     | 2 --
 tests/test_network_graph.py | 3 +--
 3 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 601608b..328b84a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,7 +75,7 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
-exclude = ["docs/source/conf.py", "tests/test_graph_app.py", "tests/test_network_graph.py"]
+exclude = ["docs/source/conf.py"]
 lint.select = [
     "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
     "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
diff --git a/tests/test_graph_app.py b/tests/test_graph_app.py
index 7607b01..58f38d9 100644
--- a/tests/test_graph_app.py
+++ b/tests/test_graph_app.py
@@ -1,5 +1,3 @@
-import pytest
-
 from dgipy.graph_app import generate_app
 
 
diff --git a/tests/test_network_graph.py b/tests/test_network_graph.py
index 087bafd..812b17d 100644
--- a/tests/test_network_graph.py
+++ b/tests/test_network_graph.py
@@ -1,5 +1,3 @@
-import pytest
-
 from dgipy.dgidb import get_interactions
 from dgipy.network_graph import create_network, generate_cytoscape
 
@@ -10,6 +8,7 @@ def test_create_network():
     search_mode = "genes"
     assert create_network(interactions, terms, search_mode)
 
+
 def test_generate_cytoscape():
     interactions = get_interactions("BRAF")
     terms = ["BRAF"]

From cc1a47aa60584ce33d2ab988da18e3532db74c00 Mon Sep 17 00:00:00 2001
From: Rohit Basu <107427918+rbasu101@users.noreply.github.com>
Date: Fri, 29 Nov 2024 14:38:20 -0500
Subject: [PATCH 8/8] fix: remove unused group

Previously, any nodes without a group would create an additoinal 'None' group, which would result in the addition of a single unlabeled node in the graph. This has been fixed by removing the 'None' group.
---
 src/dgipy/network_graph.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/dgipy/network_graph.py b/src/dgipy/network_graph.py
index 40add63..873e2f6 100644
--- a/src/dgipy/network_graph.py
+++ b/src/dgipy/network_graph.py
@@ -92,6 +92,7 @@ def generate_cytoscape(graph: nx.Graph) -> dict:
             group = node["data"].pop("group")
             groups.add(group)
             node["data"]["parent"] = group
+    groups.remove(None)
     for group in groups:
         cytoscape_node_data.append({"data": {"id": group}})
     return cytoscape_node_data + cytoscape_edge_data