risk-network 0.0.5b0__py3-none-any.whl → 0.0.5b2__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.0"
+__version__ = "0.0.5-beta.2"

risk/network/graph.py

@@ -11,7 +11,6 @@ import networkx as nx
 import numpy as np
 import pandas as pd
 import matplotlib
-import matplotlib.cm as cm
 
 
 class NetworkGraph:
@@ -270,7 +269,7 @@ def _get_colors(
         rgba = matplotlib.colors.to_rgba(kwargs["color"])
         rgbas = [rgba] * num_colors_to_generate
     else:
-        colormap = cm.get_cmap(cmap)
+        colormap = matplotlib.colormaps.get_cmap(cmap)
         # Generate evenly distributed color positions
         color_positions = np.linspace(0, 1, num_colors_to_generate)
         random.shuffle(color_positions)  # Shuffle the positions to randomize colors

risk/network/plot.py

@@ -33,7 +33,7 @@ class NetworkPlotter:
         plot_outline: bool = True,
         outline_color: str = "black",
         outline_scale: float = 1.0,
-        linestyle: str = "--",
+        linestyle: str = "dashed",
     ) -> None:
         """Initialize the NetworkPlotter with a NetworkGraph object and plotting parameters.
 
@@ -44,7 +44,7 @@ class NetworkPlotter:
             plot_outline (bool, optional): Whether to plot the network perimeter circle. Defaults to True.
             outline_color (str, optional): Color of the network perimeter circle. Defaults to "black".
             outline_scale (float, optional): Outline scaling factor for the perimeter diameter. Defaults to 1.0.
-            linestyle (str): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "--".
+            linestyle (str): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "dashed".
         """
         self.graph = graph
         # Initialize the plot with the specified parameters
@@ -499,10 +499,6 @@ class NetworkPlotter:
             fontcolor = fontcolor[selected_indices]
             arrow_color = arrow_color[selected_indices]
 
-        # Update the terms in the graph after omitting words and filtering
-        for domain, terms in filtered_domain_terms.items():
-            self.graph.trimmed_domain_to_term[domain] = terms
-
         # Calculate the bounding box around the network
         center, radius = _calculate_bounding_box(
             self.graph.node_coordinates, radius_margin=perimeter_scale
@@ -514,7 +510,7 @@ class NetworkPlotter:
         # Annotate the network with labels
         for idx, (domain, pos) in enumerate(best_label_positions.items()):
             centroid = filtered_domain_centroids[domain]
-            annotations = self.graph.trimmed_domain_to_term[domain].split(" ")[:max_words]
+            annotations = filtered_domain_terms[domain].split(" ")[:max_words]
             self.ax.annotate(
                 "\n".join(annotations),
                 xy=centroid,

risk/risk.py

@@ -352,6 +352,7 @@ class RISK(NetworkIO, AnnotationsIO):
         plot_outline: bool = True,
         outline_color: str = "black",
         outline_scale: float = 1.00,
+        linestyle: str = "dashed",
     ) -> NetworkPlotter:
         """Get a NetworkPlotter object for plotting.
 
@@ -362,6 +363,7 @@ class RISK(NetworkIO, AnnotationsIO):
             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.
@@ -374,6 +376,7 @@ class RISK(NetworkIO, AnnotationsIO):
             plot_outline=plot_outline,
             outline_color=outline_color,
             outline_scale=outline_scale,
+            linestyle=linestyle,
         )
 
         # Initialize and return a NetworkPlotter object
@@ -384,6 +387,7 @@ class RISK(NetworkIO, AnnotationsIO):
             plot_outline=plot_outline,
             outline_color=outline_color,
             outline_scale=outline_scale,
+            linestyle=linestyle,
         )
 
     def _load_neighborhoods(

{risk_network-0.0.5b0.dist-info → risk_network-0.0.5b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b0
+Version: 0.0.5b2
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.5b0.dist-info → risk_network-0.0.5b2.dist-info}/RECORD

@@ -1,6 +1,6 @@
-risk/__init__.py,sha256=BeaJc2vCPQfWsDq_X0WgE8j297o7o4mNWJXOR7oAvQw,112
+risk/__init__.py,sha256=g5Fqdi0t7DMMUt-AIDs34tPprO6samWzfE57y5gp5Tg,112
 risk/constants.py,sha256=AICk3x5qRQhls_ijTb4VdbdxU6mZ1aLGbAjLEdBwfJI,550
-risk/risk.py,sha256=4Y-fViqdK9gvxEjJRYsV_7gbN0kh7eiTwD8eesd_M6o,21109
+risk/risk.py,sha256=UYM_Pf2Db-lbf4O5T2v5zKutz_GLXK-f43PgYT6xRyY,21328
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=t4aLwROCFHcqk8g-viuwkFG--HqVpVN_2yVVcjhg6wI,10534
 risk/annotations/io.py,sha256=TMicRACfY8bNtmbvVrxHoh8zkOVLOIhZwWrpxUlR28Q,7988
@@ -13,9 +13,9 @@ risk/neighborhoods/domains.py,sha256=HwuChmZH0RGD9eQOvk2-ezQDJRUHHn93vhVgHb-kX6I
 risk/neighborhoods/neighborhoods.py,sha256=SqYJaT49rUj77ts0XsPXb9cURM11aGh2Teks0nBH_4s,13939
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
-risk/network/graph.py,sha256=m3bFWU5528OEm246LPG5XP3l_30vaBiJv4AO4iq0pSA,11552
+risk/network/graph.py,sha256=F_SY7nZev6XZuHwkJnVdeow-oMSmR4u8AUiFCrh6yvk,11543
 risk/network/io.py,sha256=otiRG6uT6HLgbbJql7X2wjYxab8OFJSgRoWJlcDoyu4,20291
-risk/network/plot.py,sha256=kjQYWJawYnKRau1JL68L3LUn1MROuue0fdYWEoN7ct4,40469
+risk/network/plot.py,sha256=HBF8uQVNddU6v_vLWHDvhw2YeKQ1zkNR1SINd-KGk3Q,40267
 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-0.0.5b0.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.5b0.dist-info/METADATA,sha256=DgS8QL4IrzTqHgrz7hnJRnmQZETqzi6L-b5PLaGYOJI,43236
-risk_network-0.0.5b0.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-risk_network-0.0.5b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.5b0.dist-info/RECORD,,
+risk_network-0.0.5b2.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.5b2.dist-info/METADATA,sha256=YYcItoAoouEEdFmBo8DsvAw3gmp2M22RfNNSYaSYjWs,43236
+risk_network-0.0.5b2.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+risk_network-0.0.5b2.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.5b2.dist-info/RECORD,,