risk-network 0.0.5b6__py3-none-any.whl → 0.0.6__py3-none-any.whl

risk/risk.py

@@ -3,7 +3,7 @@ risk/risk
 ~~~~~~~~~
 """
 
-from typing import Any, Dict
+from typing import Any, Dict, Tuple
 
 import networkx as nx
 import numpy as np
@@ -62,7 +62,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): The matrix of annotations associated with the network.
+            annotations (dict): The annotations associated with the network.
             distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "dijkstra".
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             edge_length_threshold (float, optional): Edge length threshold for neighborhood analysis. Defaults to 0.5.
@@ -114,6 +114,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_workers=max_workers,
         )
 
+        # Return the computed neighborhood significance
         return neighborhood_significance
 
     def load_neighborhoods_by_fisher_exact(
@@ -130,7 +131,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): The matrix of annotations associated with the network.
+            annotations (dict): The annotations associated with the network.
             distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "dijkstra".
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             edge_length_threshold (float, optional): Edge length threshold for neighborhood analysis. Defaults to 0.5.
@@ -169,6 +170,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_workers=max_workers,
         )
 
+        # Return the computed neighborhood significance
         return neighborhood_significance
 
     def load_neighborhoods_by_hypergeom(
@@ -185,7 +187,7 @@ class RISK(NetworkIO, AnnotationsIO):
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (pd.DataFrame): The matrix of annotations associated with the network.
+            annotations (dict): The annotations associated with the network.
             distance_metric (str, optional): Distance metric for neighborhood analysis. Defaults to "dijkstra".
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             edge_length_threshold (float, optional): Edge length threshold for neighborhood analysis. Defaults to 0.5.
@@ -224,6 +226,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_workers=max_workers,
         )
 
+        # Return the computed neighborhood significance
         return neighborhood_significance
 
     def load_graph(
@@ -340,19 +343,15 @@ class RISK(NetworkIO, AnnotationsIO):
             top_annotations=top_annotations,
             domains=domains,
             trimmed_domains=trimmed_domains,
-            node_label_to_id_map=node_label_to_id,
+            node_label_to_node_id_map=node_label_to_id,
             node_enrichment_sums=node_enrichment_sums,
         )
 
     def load_plotter(
         self,
         graph: NetworkGraph,
-        figsize: tuple = (10, 10),
+        figsize: Tuple = (10, 10),
         background_color: str = "white",
-        plot_outline: bool = True,
-        outline_color: str = "black",
-        outline_scale: float = 1.00,
-        linestyle: str = "dashed",
     ) -> NetworkPlotter:
         """Get a NetworkPlotter object for plotting.
 
@@ -360,10 +359,6 @@ class RISK(NetworkIO, AnnotationsIO):
             graph (NetworkGraph): The graph to plot.
             figsize (tuple, optional): Size of the figure. Defaults to (10, 10).
             background_color (str, optional): Background color of the plot. Defaults to "white".
-            plot_outline (bool, optional): Whether to plot the network outline. Defaults to True.
-            outline_color (str, optional): Color of the outline. Defaults to "black".
-            outline_scale (float, optional): Scaling factor for the outline. Defaults to 1.00.
-            linestyle (str): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "dashed".
 
         Returns:
             NetworkPlotter: A NetworkPlotter object configured with the given parameters.
@@ -373,10 +368,6 @@ class RISK(NetworkIO, AnnotationsIO):
         params.log_plotter(
             figsize=figsize,
             background_color=background_color,
-            plot_outline=plot_outline,
-            outline_color=outline_color,
-            outline_scale=outline_scale,
-            linestyle=linestyle,
         )
 
         # Initialize and return a NetworkPlotter object
@@ -384,10 +375,6 @@ class RISK(NetworkIO, AnnotationsIO):
             graph,
             figsize=figsize,
             background_color=background_color,
-            plot_outline=plot_outline,
-            outline_color=outline_color,
-            outline_scale=outline_scale,
-            linestyle=linestyle,
         )
 
     def _load_neighborhoods(
@@ -430,6 +417,7 @@ class RISK(NetworkIO, AnnotationsIO):
             random_seed=random_seed,
         )
 
+        # Return the computed neighborhoods
         return neighborhoods
 
     def _define_top_annotations(

{risk_network-0.0.5b6.dist-info → risk_network-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b6
+Version: 0.0.6
 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-0.0.5b6.dist-info → risk_network-0.0.6.dist-info}/RECORD

@@ -1,21 +1,21 @@
-risk/__init__.py,sha256=UDR_mfSH0Yt17WiBlUHBj2-WkPQBIs6qKklXCo37n74,112
+risk/__init__.py,sha256=is0cU74uqxLBDA8RBSAV8DgntPYa1peA9P3Jf3uoPlM,105
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=UYM_Pf2Db-lbf4O5T2v5zKutz_GLXK-f43PgYT6xRyY,21328
+risk/risk.py,sha256=CKDIzVo9Jvl-fgzIlk5ZtJL9pIBMma24WK6EYdVu5po,20648
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=DRUTdGzMdqo62NWSapBUksbvPr9CrzD76qtOcxeNKmo,10554
-risk/annotations/io.py,sha256=TMicRACfY8bNtmbvVrxHoh8zkOVLOIhZwWrpxUlR28Q,7988
+risk/annotations/io.py,sha256=lo7NKqOVkeeBp58JBxWJHtA0xjL5Yoxqe9Ox0daKlZk,9457
 risk/log/__init__.py,sha256=xuLImfxFlKpnVhzi_gDYlr2_c9cLkrw2c_3iEsXb1as,107
 risk/log/console.py,sha256=im9DRExwf6wHlcn9fewoDcKIpo3vPcorZIaNAl-0csY,355
-risk/log/params.py,sha256=Tbb-sovFTptGBqPDKafUA8KOpby4zFObutAT_Iti1hE,6302
+risk/log/params.py,sha256=Rfdg5UcGCrG80m6V79FyORERWUqIzHFO7tGiY4zAImM,6347
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
-risk/neighborhoods/community.py,sha256=eL2IGT-8sbiJIyfyb_FGngev7pEMxw7tZb8YzbzOYw8,6512
-risk/neighborhoods/domains.py,sha256=HwuChmZH0RGD9eQOvk2-ezQDJRUHHn93vhVgHb-kX6I,10192
-risk/neighborhoods/neighborhoods.py,sha256=SqYJaT49rUj77ts0XsPXb9cURM11aGh2Teks0nBH_4s,13939
+risk/neighborhoods/community.py,sha256=7ebo1Q5KokSQISnxZIh2SQxsKXdXm8aVkp-h_DiQ3K0,6818
+risk/neighborhoods/domains.py,sha256=5V--Nj-TrSdubhD_2PI57ffcn_PMSEgpX_iY5OjT6R8,10626
+risk/neighborhoods/neighborhoods.py,sha256=sHmjFFl2U5qV9YbQCRbpbI36j7dS7IFfFwwRb1_-AuM,13945
 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=XB-fH67SqIm3bonFj_UvbO85725Zp1z0Ug6LblDEUYo,41062
+risk/network/graph.py,sha256=7haHu4M3fleqbrIzs6HC9jnKizSERzmmAYSmUwdoSXA,13953
+risk/network/io.py,sha256=gG50kOknO-D3HkW1HsbHMkTMvjUtn3l4W4Jwd-rXNr8,21202
+risk/network/plot.py,sha256=_g5xHolMTAfZCBvYYEX1CYME4s4zA2hTHtN-utaMPik,61978
 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-0.0.5b6.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.5b6.dist-info/METADATA,sha256=QbGxhcKULWkZ064qoWmSI43caZIrvaXostHJqCnezwc,43236
-risk_network-0.0.5b6.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-risk_network-0.0.5b6.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.5b6.dist-info/RECORD,,
+risk_network-0.0.6.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.6.dist-info/METADATA,sha256=L5ITD9hXoxsmiKIr6q1yOgDQRtdKmOCCi8Clt2mxAEs,43140
+risk_network-0.0.6.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+risk_network-0.0.6.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.6.dist-info/RECORD,,

{risk_network-0.0.5b6.dist-info → risk_network-0.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.1.2)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any