edited plot visuals for seed_var

cami_src/cami.py

@@ -295,9 +295,12 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
         #PLOT
 
         # Create a figure instance
-        plt.figure(figsize=(48,12))
+        fig, axs = plt.subplots(2, 1, figsize=(20,15))
+        plt.subplots_adjust(left=0.2)
+        
+        ax1 = axs[0]
+        ax5 = axs[1]
         # Extract Figure and Axes instance
-        ax1 = plt.subplot(1,2,1, label='ax1')
 
         # Create a plot
         violins1 = ax1.violinplot(redisc_rates, showmeans=True, showextrema=True)
@@ -313,7 +316,8 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
         ax1.set_xticklabels(tool_labels)
         ax1.tick_params(axis='x', labelsize=11)
 
-        ax1.set_ylabel('Rediscovery rate (<rediscovered seeds>/<removed seeds>)', wrap=True)
+        ax1.set_ylabel('Rediscovery rate (<rediscovered seeds>/<removed seeds>)', wrap=True, fontsize=14)
+
         
         # ax4 = plt.subplot(1,3,2, label='ax4')
         # violins2 = ax4.violinplot([tp_rate_dict[tool] for tool in tools], showmeans=True, showextrema=True)
@@ -329,7 +333,6 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
 
         # ax4.set_ylabel('Sensitivity (TP/TP + FN)', wrap=True)
 
-        ax5 = plt.subplot(1,2,2)
         violins3 = ax5.violinplot([module_size_dict[tool] for tool in tools], showmeans=True, showextrema=True)
         # Add title
         for violinpart in list(violins3.keys())[2:]:
@@ -342,10 +345,10 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
         ax5.set_xticks(list(range(1,len(tools)+1)))
         ax5.set_xticklabels(tool_labels)
         
-        ax5.set_ylabel('(<rediscovered seeds>/<module size>)')
+        ax5.set_ylabel('(<rediscovered seeds>/<module size>)', fontsize=14)
         ax5.tick_params(axis='x', labelsize=11)
-        plt.tight_layout
-        plt.savefig(f'{output_dir}/00_{identifier}_seed_variation_result.png')
+        plt.tight_layout()
+        fig.savefig(f'{output_dir}/00_{identifier}_seed_variation_result.png', bbox_inches="tight")
         
         print(f'Violin plot saved under: 00_{identifier}_seed_variation_result.png')
         

cami_src/cami_suite.py

@@ -184,6 +184,7 @@ class cami():
         inputparams = tool.prepare_input()
         print(f'running {tool.name}...')
         preds = set(tool.run_algorithm(inputparams))
+        if self.debug:
             print(f'{tool.name} predicted {len(preds)} active vertices (seeds not excluded):')
             print(preds)
         return preds
@@ -361,7 +362,7 @@ class cami():
                 for vertex in cami_vlist:
                     print(f'{gene_name_map[vertex]}\t{cami_scores[vertex]}\t{codes2tools[vertex]}')
             else:
-                print(f'With the {len(seed_genes)} seed genes CAMI ({cami_method_name}) proposes {len(seed_genes)} to add to the Active Module')
+                print(f'With the {len(seed_genes)} seed genes CAMI ({cami_method_name}) proposes {len(cami_vlist)} to add to the Active Module')
                 
             # for visualization with nvenn
             self.result_gene_sets[cami_method_name] = cami_genes
@@ -450,7 +451,7 @@ class cami():
             degradome_sets = {tool:self.result_gene_sets[tool] 
                               for tool in self.result_gene_sets 
                               if len(self.result_gene_sets[tool])>0}
-            url = degradome.send_request(degradome_sets, {self.ppi_vertex2gene[seed] for seed in self.seed_lst})
+            url = degradome.send_request(degradome_sets)
             with open(f'{self.output_dir}/venn_link_{self.uid}.txt', 'w') as f:
                 f.write(url)
             return url
@@ -463,6 +464,7 @@ class cami():
         #     webbrowser.open(url)
         else:
             print('Cannot use degradome to create venn diagrams of 6 or more tools')
+            return None
 
     def download_diagram(self, url):
         venn_name = f'{self.output_dir}/vdiagram_{self.uid}'