risk-network 0.0.5b5__py3-none-any.whl → 0.0.6b0__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.5-beta.5"
+__version__ = "0.0.6-beta.0"

risk/constants.py

@@ -3,6 +3,8 @@ risk/constants
 ~~~~~~~~~~~~~~
 """
 
+GROUP_LINKAGE_METHODS = ["single", "complete", "average", "weighted", "centroid", "median", "ward"]
+
 GROUP_DISTANCE_METRICS = [
     "braycurtis",
     "canberra",
@@ -27,5 +29,3 @@ GROUP_DISTANCE_METRICS = [
     "sqeuclidean",
     "yule",
 ]
-
-GROUP_LINKAGE_METHODS = ["single", "complete", "average", "weighted", "centroid", "median", "ward"]

risk/network/io.py

@@ -418,29 +418,37 @@ class NetworkIO:
         return G
 
     def _remove_invalid_graph_properties(self, G: nx.Graph) -> None:
-        """Remove invalid properties from the graph.
+        """Remove invalid properties from the graph, including self-loops, nodes with fewer edges than
+        the threshold, and isolated nodes.
 
         Args:
             G (nx.Graph): A NetworkX graph object.
         """
-        # First, Remove self-loop edges to ensure correct edge count
+        # Count number of nodes and edges before cleaning
+        num_initial_nodes = G.number_of_nodes()
+        num_initial_edges = G.number_of_edges()
+        # Remove self-loops to ensure correct edge count
         G.remove_edges_from(list(nx.selfloop_edges(G)))
-        # Then, iteratively remove nodes with fewer edges than the specified threshold
+        # Iteratively remove nodes with fewer edges than the threshold
         while True:
-            nodes_to_remove = [
-                node for node in G.nodes() if G.degree(node) < self.min_edges_per_node
-            ]
+            nodes_to_remove = [node for node in G.nodes if G.degree(node) < self.min_edges_per_node]
             if not nodes_to_remove:
-                break  # Exit loop if no more nodes to remove
-
-            # Remove the nodes and their associated edges
+                break  # Exit loop if no more nodes need removal
             G.remove_nodes_from(nodes_to_remove)
 
-        # Optionally: Remove any isolated nodes if needed
+        # Remove isolated nodes
         isolated_nodes = list(nx.isolates(G))
         if isolated_nodes:
             G.remove_nodes_from(isolated_nodes)
 
+        # Log the number of nodes and edges before and after cleaning
+        num_final_nodes = G.number_of_nodes()
+        num_final_edges = G.number_of_edges()
+        print(f"Initial node count: {num_initial_nodes}")
+        print(f"Final node count: {num_final_nodes}")
+        print(f"Initial edge count: {num_initial_edges}")
+        print(f"Final edge count: {num_final_edges}")
+
     def _assign_edge_weights(self, G: nx.Graph) -> None:
         """Assign weights to the edges in the graph.
 
@@ -502,6 +510,7 @@ class NetworkIO:
         print(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
         if self.include_edge_weight:
             print(f"Weight label: {self.weight_label}")
+        print(f"Minimum edges per node: {self.min_edges_per_node}")
         print(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
         if self.compute_sphere:
             print(f"Surface depth: {self.surface_depth}")

risk/network/plot.py

@@ -494,6 +494,7 @@ class NetworkPlotter:
         if max_labels is not None and max_labels < len(filtered_domain_centroids):
             step = len(filtered_domain_centroids) / max_labels
             selected_indices = [int(i * step) for i in range(max_labels)]
+            # Filter the centroids, terms, and valid_indices to only use the selected indices
             filtered_domain_centroids = {
                 k: v
                 for i, (k, v) in enumerate(filtered_domain_centroids.items())
@@ -504,8 +505,8 @@ class NetworkPlotter:
                 for i, (k, v) in enumerate(filtered_domain_terms.items())
                 if i in selected_indices
             }
-            fontcolor = fontcolor[selected_indices]
-            arrow_color = arrow_color[selected_indices]
+            # Update valid_indices to match selected indices
+            valid_indices = [valid_indices[i] for i in selected_indices]
 
         # Calculate the bounding box around the network
         center, radius = _calculate_bounding_box(
@@ -629,12 +630,16 @@ class NetworkPlotter:
         return domain_central_node
 
     def get_annotated_node_colors(
-        self, nonenriched_color: str = "white", random_seed: int = 888, **kwargs
+        self,
+        nonenriched_color: Union[str, List, Tuple, np.ndarray] = "white",
+        random_seed: int = 888,
+        **kwargs,
     ) -> np.ndarray:
         """Adjust the colors of nodes in the network graph based on enrichment.
 
         Args:
-            nonenriched_color (str, optional): Color for non-enriched nodes. Defaults to "white".
+            nonenriched_color (str, list, tuple, or np.ndarray, optional): Color for non-enriched nodes.
+                Defaults to "white". If an alpha channel is provided, it will be used to darken the RGB values.
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
             **kwargs: Additional keyword arguments for `get_domain_colors`.
 
@@ -647,12 +652,23 @@ class NetworkPlotter:
             # Convert the non-enriched color from string to RGBA
             nonenriched_color = mcolors.to_rgba(nonenriched_color)
 
+        # Ensure nonenriched_color is a NumPy array
+        nonenriched_color = np.array(nonenriched_color)
+        # If alpha is provided (4th value), darken the RGB values based on alpha
+        if len(nonenriched_color) == 4 and nonenriched_color[3] < 1.0:
+            alpha = nonenriched_color[3]
+            # Adjust RGB based on alpha (darken)
+            nonenriched_color[:3] = nonenriched_color[:3] * alpha
+            # Set alpha to 1.0 after darkening the color
+            nonenriched_color[3] = 1.0
+
         # Adjust node colors: replace any fully transparent nodes (enriched) with the non-enriched color
         adjusted_network_colors = np.where(
-            np.all(network_colors == 0, axis=1, keepdims=True),
-            np.array([nonenriched_color]),
-            network_colors,
+            np.all(network_colors[:, :3] == 0, axis=1, keepdims=True),  # Check RGB values only
+            np.array([nonenriched_color]),  # Apply the non-enriched color (with adjusted alpha)
+            network_colors,  # Keep the original colors
         )
+
         return adjusted_network_colors
 
     def get_annotated_node_sizes(

{risk_network-0.0.5b5.dist-info → risk_network-0.0.6b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b5
+Version: 0.0.6b0
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -710,8 +710,7 @@ Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
 <p align="center">
-  <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="400" />
-  <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="400" />
+  <img src="https://i.imgur.com/Fo9EmnK.png" width="400" />
 </p>
 
 <p align="center">
@@ -736,7 +735,7 @@ RISK is a software tool for visualizing spatial relationships in networks. It ai
 
 *Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
 
-![PPI Network Demo](./docs/github/network.png)
+![PPI Network Demo](https://i.imgur.com/NnyK6nO.png)
 
 ## Installation
 

{risk_network-0.0.5b5.dist-info → risk_network-0.0.6b0.dist-info}/RECORD

@@ -1,5 +1,5 @@
-risk/__init__.py,sha256=zGjRj03AbzDx0VGLJyR7TPzNLA1XQ5eLF7gbAKK507o,112
-risk/constants.py,sha256=AICk3x5qRQhls_ijTb4VdbdxU6mZ1aLGbAjLEdBwfJI,550
+risk/__init__.py,sha256=IF4pnbb0hT2Ku49jwIG1EpkhgqUxp5qnolYAmF2ujds,112
+risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=UYM_Pf2Db-lbf4O5T2v5zKutz_GLXK-f43PgYT6xRyY,21328
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=DRUTdGzMdqo62NWSapBUksbvPr9CrzD76qtOcxeNKmo,10554
@@ -14,8 +14,8 @@ risk/neighborhoods/neighborhoods.py,sha256=SqYJaT49rUj77ts0XsPXb9cURM11aGh2Teks0
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
 risk/network/graph.py,sha256=DTjNRQwgQbt6jJYDBHm7sgrdbZUDLL4HiZpdixkSI7Y,12433
-risk/network/io.py,sha256=otiRG6uT6HLgbbJql7X2wjYxab8OFJSgRoWJlcDoyu4,20291
-risk/network/plot.py,sha256=rg4pB0sndOnoayeNZSu4sU3sQ2P8x9ksE4XRTRP2HPM,40942
+risk/network/io.py,sha256=8oncBfUaE-uDqWOr4OOWhR3ouhuOOzhnGlTUVxst3hs,20851
+risk/network/plot.py,sha256=SXbHSBPNzrRw0m9xoENyRSgR6qHm2YoWMQat3PrFkI8,41866
 risk/stats/__init__.py,sha256=e-BE_Dr_jgiK6hKM-T-tlG4yvHnId8e5qjnM0pdwNVc,230
 risk/stats/fisher_exact.py,sha256=-bPwzu76-ob0HzrTV20mXUTot7v-MLuqFaAoab-QxPg,4966
 risk/stats/hypergeom.py,sha256=lrIFdhCWRjvM4apYw1MlOKqT_IY5OjtCwrjdtJdt6Tg,4954
@@ -23,8 +23,8 @@ risk/stats/stats.py,sha256=kvShov-94W6ffgDUTb522vB9hDJQSyTsYif_UIaFfSM,7059
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=qLWdwxEY6nmkYPxpM8HLDcd2mbqYv9Qr7CKtJvhLqIM,9220
 risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.5b5.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.5b5.dist-info/METADATA,sha256=qSRqHP8c46IzvZU--rO7eUeir3LErWx98mPIbh0Q_c4,43236
-risk_network-0.0.5b5.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-risk_network-0.0.5b5.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.5b5.dist-info/RECORD,,
+risk_network-0.0.6b0.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.6b0.dist-info/METADATA,sha256=TWOChIBPVrDKpp8wPEoCXayEWSp8M3uwdSQQw18rdMQ,43142
+risk_network-0.0.6b0.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+risk_network-0.0.6b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.6b0.dist-info/RECORD,,