updates with revisions

SaniyaKhullar · May 7, 2024 · e861f4e · e861f4e
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Showing 13 changed files with 2,366 additions and 431 deletions.
diff --git a/NetREm_pipeline_figure.png b/NetREm_pipeline_figure.png
diff --git a/README.md b/README.md
diff --git a/code/Netrem_model_builder.py b/code/Netrem_model_builder.py
@@ -299,6 +299,8 @@ def updating_network_and_X_during_fitting(self, X, y):
         else:
             self.A_df = self.network.A_df
             self.A = self.network.A
+            self.W_df = self.network.W_df
+            self.final_input_W_df = self.W_df 
             self.nodes = self.A_df.columns.tolist()
         self.network_info = "fitted_network"
         self.M = y.shape[0]       
@@ -327,7 +329,8 @@ def organize_B_interaction_list(self): # TF-TF interactions to output :)
             max_other = np.max(np.abs(result)).max()
             coord_matrix = 100.0*result/max_other
             self.coord_score_df = coord_matrix
-        self.TF_interaction_df = self.coord_score_df
+            self.TF_interaction_df = self.coord_score_df
+            self.B_interaction_df = self.coord_score_df
         return self   
 
 
@@ -743,6 +746,7 @@ def updating_network_A_matrix_given_X(self) -> np.ndarray:
 
         self.W = W
         self.W_df = W_df
+        self.final_input_W_df = W_df
         # Feb 12, 2024
         edge_list = (
             W_df

diff --git a/code/previous_version/README.md b/code/previous_version/README.md
diff --git a/netrem_estimator.PNG → code/previous_version/netrem_estimator.PNG b/netrem_estimator.PNG → code/previous_version/netrem_estimator.PNG
diff --git a/code/previous_version/netrem_expression_demo.png b/code/previous_version/netrem_expression_demo.png
diff --git a/code/previous_version/netrem_final_demo.png b/code/previous_version/netrem_final_demo.png
diff --git a/output_3_1.png → code/previous_version/output_3_1.png b/output_3_1.png → code/previous_version/output_3_1.png
diff --git a/netrem_estimator_new.png b/netrem_estimator_new.png
diff --git a/netrem_expression_demo.png b/netrem_expression_demo.png
diff --git a/netrem_final_demo.png b/netrem_final_demo.png
diff --git a/netrem_pipeline.PNG b/netrem_pipeline.PNG
diff --git a/output_3_1_new.png b/output_3_1_new.png