Closing plots

Author: niklases

README.md

@@ -33,8 +33,6 @@ a framework written in Python 3 for performing sequence-based machine learning-a
 - Direct coupling analysis (amino acid coevolution based on multiple sequence alignments) encoding
 - LLM embeddings (currently, [ESM1v](https://github.com/facebookresearch/esm) and [ProSST](https://github.com/ai4protein/ProSST))
 
-Written by Niklas Siedhoff and Alexander-Maurice Illig.
-
 <p align="center">
     <img src=".github/imgs/ML_Model_Performance_DCA_GREMLIN.png" alt="drawing" width="500"/>
 </p>
@@ -68,12 +66,16 @@ pypef --help
 <a name="gui"></a>
 ### GUI
 
+```
+pip install -U pypef[gui]
+```
+
 After installation, a rudimentary graphical user interface (GUI) can be invoked using the command
 
 ```bash
 pypef-gui      # loading takes some seconds
 # or
-pypef-gui-cli  # command for keeping background debug/tqdm progress information in terminal on Windows
+pypef-gui-cli  # command for keeping background debug/tqdm progress information in terminal (only Windows OS-specific)
 ```
 
 <p align="center">

pypef/dca/gremlin_inference.py

@@ -84,7 +84,7 @@ def __init__(
                 else "cpu"
             )
         self.device = device    
-        logger.info(f'Using {self.device.upper()} for GREMLIN computations...')   
+        logger.info(f'Using {self.device.upper()} device for GREMLIN computations...')   
         self.char_alphabet = char_alphabet
         self.allowed_chars = "ARNDCQEGHILKMFPSTWYV-"
         self.allowed_chars += self.allowed_chars.lower()
@@ -734,6 +734,8 @@ def plot_predicted_ssm(gremlin: GREMLIN):
     ax.set_yticks(range(len(aas)), aas, size=6)
     plt.tight_layout()
     plt.savefig('SSM_landscape.png', dpi=500)
+    plt.clf()
+    plt.close('all')
     pd.DataFrame(
         {
             'Variant': np.array(variantss).flatten(),

pypef/gui/qt_window.py

@@ -119,19 +119,12 @@ def work(self):
         from such long working thread job during run, e.g., 
         every trained epoch from the executed imported function. 
         """
-        thread_name = QThread.currentThread().objectName()
-        #self.sig_msg.emit(
-        #    f'Running worker #{self.__id} from thread "{thread_name}" '
-        #    f'executing command: "{self.cmd}"'
-        #)
         print(f"Executing command: {self.cmd}")
-
         run_main(argv=self.cmd)
         self.sig_done.emit(f"Done: {self.__id}")
 
     def abort(self):
         self.sig_msg.emit(f'Worker #{self.__id} notified to abort')
-        #self.__abort = True
 
 
 class SecondWindow(QWidget):
@@ -162,7 +155,6 @@ def __init__(self):
         # Texts #########################################################################
         layout = QGridLayout(self)  # MAIN LAYOUT: QGridLayout
         self.version_text = QLabel(f"PyPEF v. {__version__}", alignment=Qt.AlignRight)
-        #self.ncores_text = QLabel("Single-/multiprocessing")
         self.llm_text = QLabel("LLM")
         self.regression_model_text =  QLabel("Regression model")
         self.utils_text = QLabel("Utilities")

pypef/utils/directed_evolution.py

@@ -377,6 +377,7 @@ def plot_trajectories(self):
         plt.tight_layout()
         plt.savefig(str(self.model) + '_DE_trajectories.png', dpi=500)
         plt.clf()
+        plt.close('all')
 
         with open(os.path.join('EvoTraj', 'Trajectories.csv'), 'w') as file:
             file.write('Trajectory;Variant;Sequence;Fitness\n')

pypef/utils/low_n_mutation_extrapolation.py

@@ -58,6 +58,7 @@ def plot_low_n(
 
     plt.savefig(plt_name.split(os.sep)[-1] + '.png', dpi=500)
     plt.clf()
+    plt.close('all')
 
 
 def low_n(
@@ -386,3 +387,4 @@ def plot_extrapolation(
     name = name.split(os.sep)[-1] + '_extrapolation.png'
     plt.savefig(name, dpi=500)
     plt.clf()
+    plt.close('all')

pypef/utils/plot.py

@@ -42,12 +42,13 @@ def plot_y_true_vs_y_pred(
             y_true=y_true, y_pred=y_pred
         )
         plt.scatter(
-            y_true, y_pred, marker='o', s=20, linewidths=0.5, edgecolor='black', alpha=0.7, c=y_true, vmin=min(y_true), vmax=max(y_true),
-            label=r'$R^2$' + f' = {r_squared:.3f}' + f'\nRMSE = {rmse:.3f}' + f'\nNRMSE = {nrmse:.3f}' 
-                  + f'\nPearson\'s ' + r'$r$'+f' = {pearson_r:.3f}' 
-                  + f'\nSpearman\'s ' + fr'$\rho$ = {spearman_rho:.3f}' + '\n' 
-                  + r'Recall$_\mathrm{top 10 \%}$' + f' = {rec:.3f}\n'
-                  + fr'($N$ = {len(y_true)})'
+            y_true, y_pred, marker='o', s=20, linewidths=0.5, 
+            edgecolor='black', alpha=0.7, c=y_true, 
+            vmin=min(y_true), vmax=max(y_true),
+            label=r'$R^2$' + f' = {r_squared:.3f}' + f'\nRMSE = {rmse:.3f}' + f'\nNRMSE = {nrmse:.3f}'
+                  + f'\nPearson\'s ' + r'$r$'+f' = {pearson_r:.3f}' + f'\nSpearman\'s ' 
+                  + fr'$\rho$ = {spearman_rho:.3f}' + '\n' + r'Recall$_\mathrm{top 10 \%}$'
+                  + f' = {rec:.3f}\n' + fr'($N$ = {len(y_true)})'
         )
         if name != '':
             file_name = f'ML_Model_Performance_{name}.png'
@@ -77,5 +78,6 @@ def plot_y_true_vs_y_pred(
     #     file_name = f'DCA_Hybrid_Model_LS_TS_Performance({i}).png'
     plt.colorbar()
     plt.savefig(file_name, dpi=500)
+    plt.clf()
     plt.close('all')
     logger.info(f'Saved plot as {os.path.abspath(file_name)}...')