risk-network 0.0.9b13__py3-none-any.whl → 0.0.9b14__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.13"
+__version__ = "0.0.9-beta.14"

risk/network/io.py

@@ -379,15 +379,17 @@ class NetworkIO:
         node_y_positions = {}
         for node in cyjs_data["elements"]["nodes"]:
             node_data = node["data"]
-            node_id = node_data["id_original"]
+            # Use the original node ID if available, otherwise use the default ID
+            node_id = node_data.get("id_original", node_data.get("id"))
             node_x_positions[node_id] = node["position"]["x"]
             node_y_positions[node_id] = node["position"]["y"]
 
         # Process edges and add them to the graph
         for edge in cyjs_data["elements"]["edges"]:
             edge_data = edge["data"]
-            source = edge_data[f"{source_label}_original"]
-            target = edge_data[f"{target_label}_original"]
+            # Use the original source and target labels if available, otherwise fall back to default labels
+            source = edge_data.get(f"{source_label}_original", edge_data.get(source_label))
+            target = edge_data.get(f"{target_label}_original", edge_data.get(target_label))
             # Add the edge to the graph, optionally including weights
             if self.weight_label is not None and self.weight_label in edge_data:
                 weight = float(edge_data[self.weight_label])

risk/network/plot/network.py

@@ -250,11 +250,11 @@ class Network:
         nonsignificant_color_rgba = to_rgba(
             color=nonsignificant_color, alpha=nonsignificant_alpha, num_repeats=1
         )  # num_repeats=1 for a single color
-        # Adjust node colors: replace any nodes where all three RGB values are equal and less than 0.1
+        # Adjust node colors: replace any nodes where all three RGB values are equal and less than or equal to 0.1
         # 0.1 is a predefined threshold for the minimum color intensity
         adjusted_network_colors = np.where(
             (
-                np.all(network_colors[:, :3] < 0.1, axis=1)
+                np.all(network_colors[:, :3] <= 0.1, axis=1)
                 & np.all(network_colors[:, :3] == network_colors[:, 0:1], axis=1)
             )[:, None],
             np.tile(

{risk_network-0.0.9b13.dist-info → risk_network-0.0.9b14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b13
+Version: 0.0.9b14
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b13.dist-info → risk_network-0.0.9b14.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=bXkN8xIF7g0uIiSoCAXatSRkI_KRTbjWye4l_trCCfk,113
+risk/__init__.py,sha256=Iidh958zzqC-3UdCs4vJpPixUJXUPBHxeQJYNHO4IHI,113
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=MXu8T93NUgMDl3NaZDbm0j9c4KWwzx-kmp9Rd1ax0N4,23534
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
@@ -13,7 +13,7 @@ risk/neighborhoods/domains.py,sha256=t91xSpx9Ty9hSlhRq2_XwyPpBP7sjKhovcPPvkwWtf0
 risk/neighborhoods/neighborhoods.py,sha256=XB2Gd0xghKKBNkwp1H-1138NegTlAiyOqAkv_vaLEZM,21150
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=gFtYUj9j9aul4paKq_qSGJn39Nazxu_MXv8m-tYYtrk,6840
-risk/network/io.py,sha256=AWSbZGLZHtl72KSlafQlcYoG00YLSznG7UYDi_wDT7M,22958
+risk/network/io.py,sha256=Dl-Xwv1gWdmvDkZ77581s_JYO5ujZjvmHG7wq_-ApZU,23239
 risk/network/graph/__init__.py,sha256=H0YEiwqZ02LBTkH4blPwUjQ-DOUnhaTTNHM0BcXii6U,81
 risk/network/graph/network.py,sha256=JzYbrgJLiNWFyPIR6_qNSjMtmXmfzRv2FwWSdyg8HjY,12205
 risk/network/graph/summary.py,sha256=h2bpUjfwI1NMflkKwplGQEGPswfAtunormdTIEQYbvs,8987
@@ -21,7 +21,7 @@ risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo
 risk/network/plot/canvas.py,sha256=W8dFv4XYTzCWXBchgsc0esOQRn4usM4LkwNGPSDMobE,13357
 risk/network/plot/contour.py,sha256=VONX9l6owrZvWtR0mWQ6z2GSd1YXIv5wV_sf5ROQLT4,15581
 risk/network/plot/labels.py,sha256=aU_ClDGVPHyQ3H5E_ygx8hsMhrpJB0i9Cn65PlLmw7s,45679
-risk/network/plot/network.py,sha256=_K8Am2y6zSGrm3fAgMbXxzgspbugJi3uK4_tG8qqGoI,14015
+risk/network/plot/network.py,sha256=0j7pAZgt9PBfFCnOz4QwXnYWTlnLjTrtMm-50I_1G8o,14028
 risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
 risk/network/plot/utils/colors.py,sha256=9zuU2O-Nkpljb1yVGUR_IjqD1y-wH6Bf6Vm1MMVB0Lo,18718
 risk/network/plot/utils/layout.py,sha256=6o7idoWQnyzujSWOFXQykUvyPy8NuRtJV04TnlbXXBo,3647
@@ -32,8 +32,8 @@ risk/stats/stats.py,sha256=z8NrhiVj4BzJ250bVLfytpmfC7RzYu7mBuIZD_l0aCA,7222
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=meBNSrbRa9P8WJ54n485l0H7VQJlMSfHqdN4aCKYCtQ,10105
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b13.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b13.dist-info/METADATA,sha256=tbqUuKfdv5QjAprQruLMmTk5wzGWrwVqg528BeWcynQ,47552
-risk_network-0.0.9b13.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b13.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b13.dist-info/RECORD,,
+risk_network-0.0.9b14.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b14.dist-info/METADATA,sha256=-H8Qrl5r36ZNGNJO3RHOzUOi_CzgplZf061rYGcIfJI,47552
+risk_network-0.0.9b14.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+risk_network-0.0.9b14.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b14.dist-info/RECORD,,