Merge branch 'dev'

byemaxx · Sep 12, 2024 · 6babbf7 · 6babbf7
2 parents 9f5378e + 893cdbd
commit 6babbf7
Show file tree

Hide file tree

Showing 15 changed files with 1,048 additions and 810 deletions.
diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,15 @@
+# Version: 1.112.0
+## Date: 2024-09-09
+### Changes:
+- New: Added sub_meta for taxa-func link part.
+- Change: Chnaged the [Get Table] of the taxa-func link part to get the table from the heatmap(values and order).
+
+# Version: 1.111.8
+## Date: 2024-09-08
+### Changes:
+- New: 1. Added Box-Cox method of Data Preprocessing. 2. Added an option to change number of cos of trends clusuter figure.
+
+
 # Version: 1.111.7
 ## Date: 2024-09-06
 ### Changes:

diff --git a/Docs/MetaX_Cookbook.assets/OTF_Structure.png b/Docs/MetaX_Cookbook.assets/OTF_Structure.png
diff --git a/README.md b/README.md
@@ -6,7 +6,15 @@ MetaX also features <u>statistical modules</u> and <u>plotting tools</u> for ana
 
 
 ![abstract](https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/abstract.png)
-## Taxa-Functions Linkage
+
+## Operational Taxon-Function (OTF)
+
+**Operational Taxon-Function (OTF) Unit**: An operational unit which represents the association between specific taxa and biological functions. 
+
+![OTF_Structure](https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/OTF_Structure.png)
+
+## OTFs Network
+
 Linking Taxa and Functions in different levels of the hierarchy, and different functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc.
 
 - ![OTF](https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/tf_link_net.png)

diff --git a/metax/gui/main_gui.py b/metax/gui/main_gui.py
@@ -361,6 +361,7 @@ def __init__(self, MainWindow):
         self.checkBox_create_protein_table.stateChanged.connect(self.change_event_checkBox_create_protein_table)
         self.comboBox_method_of_protein_inference.currentIndexChanged.connect(self.update_method_of_protein_inference)
         self.comboBox_3dbar_sub_meta.currentIndexChanged.connect(self.change_event_comboBox_3dbar_sub_meta)
+        self.comboBox_tflink_sub_meta.currentIndexChanged.connect(self.change_event_comboBox_tflink_sub_meta)
 
         ## Basic Stat
         self.pushButton_plot_pca_sns.clicked.connect(lambda: self.plot_basic_info_sns('pca'))
@@ -473,8 +474,8 @@ def __init__(self, MainWindow):
         self.comboBox_tfnet_select_list.add_all_searched.connect(self.add_all_searched_tfnet_to_focus_list)
 
         # Taxa-func link
-        self.pushButton_others_get_intensity_matrix.clicked.connect(self.get_tflink_intensity_matrix)
-        self.pushButton_others_plot_heatmap.clicked.connect(self.plot_tflink_heatmap)
+        self.pushButton_others_get_intensity_matrix.clicked.connect(lambda: self.plot_tflink_heatmap('table'))
+        self.pushButton_others_plot_heatmap.clicked.connect(lambda: self.plot_tflink_heatmap('fig'))
         self.pushButton_others_plot_line.clicked.connect(self.plot_tflink_bar)
         self.pushButton_others_show_linked_taxa.clicked.connect(self.show_others_linked_taxa)
         self.pushButton_others_show_linked_func.clicked.connect(self.show_others_linked_func)
@@ -671,7 +672,9 @@ def update_all_condition_meta(self):
             self.comboBox_sub_meta_pca.addItems(['None'] + meta_list)
             self.comboBox_3dbar_sub_meta.clear()
             self.comboBox_3dbar_sub_meta.addItems(['None'] + meta_list)
-
+            self.comboBox_tflink_sub_meta.clear()
+            self.comboBox_tflink_sub_meta.addItems(['None'] + meta_list)
+
         except Exception as e:
             print(e)
 
@@ -781,6 +784,13 @@ def change_event_comboBox_3dbar_sub_meta(self):
         #     self.comboBox_3dbar_sub_meta.setEnabled(False)
         # else:
         #     self.comboBox_3dbar_sub_meta.setEnabled(True)
+    def change_event_comboBox_tflink_sub_meta(self):
+        # when the sub_meta comboBox is not None, the mean plot is not available
+        if self.comboBox_tflink_sub_meta.currentText() != 'None':
+            self.checkBox_tflink_plot_mean.setEnabled(False)
+
+        else:
+            self.checkBox_tflink_plot_mean.setEnabled(True)
 
     def hide_plot_setting_groupbox(self):
         groupbox_list = ["groupBox_basic_plot", "groupBox_basic_heatmap_plot_settings", 
@@ -2552,6 +2562,8 @@ def set_multi_table(self, restore_taxafunc=False,  saved_obj=None):
                     "Log 10 transformation": "log10",
                     "Square root transformation": "sqrt",
                     "Cube root transformation": "cube",
+                    "Box-Cox": "boxcox",
+
                 }
                 normalize_dict = {
                     "None": None,
@@ -3545,7 +3557,7 @@ def plot_basic_list(self, plot_type='heatmap'):
                                                          scale=scale, row_cluster=row_cluster, col_cluster=col_cluster, 
                                                          cmap=cmap, rename_taxa=rename_taxa, font_size=font_size,
                                                          show_all_labels=show_all_labels, rename_sample=rename_sample,
-                                                         plot_mean = plot_mean, sub_meta = sub_meta)
+                                                         plot_mean = plot_mean, sub_meta = sub_meta, return_type = 'fig')
 
 
             elif plot_type == 'bar':
@@ -3732,7 +3744,8 @@ def plot_trends_cluster(self):
         table_name = self.comboBox_trends_table.currentText()
         font_size = self.spinBox_trends_font_size.value()
 
-        title = f'{table_name.capitalize()} Cluster'
+        # title = f'{table_name.capitalize()} Cluster'
+        title = 'Cluster'
         num_cluster = self.spinBox_trends_num_cluster.value()
 
 
@@ -3786,15 +3799,20 @@ def plot_trends_cluster(self):
             df = dft.loc[self.trends_cluster_list]
 
         try:
+            num_col = self.spinBox_trends_num_col.value()
+            if num_col > num_cluster:
+                print(f'num_col: {num_col} > num_cluster: {num_cluster}. Reset num_col to num_cluster.')
+                num_col = num_cluster
+
             df = df.loc[(df!=0).any(axis=1)]
-            self.show_message(f'Plotting trends cluster...')
+            self.show_message('Plotting trends cluster...')
             # plot trends and get cluster table
             fig, cluster_df = TrendsPlot(self.tfa).plot_trends(df= df, num_cluster = num_cluster, 
                                                                width=width, height=height, title=title
-                                                               , font_size=font_size)
+                                                               , font_size=font_size, num_col=num_col)
             # create a dialog to show the figure
             # plt_dialog = PltDialog(self.MainWindow, fig)
-            plt_size= (width*50,height*num_cluster*50)
+            plt_size= (width*50, int(height*num_cluster*50/num_col) )
             plt_dialog = ExportablePlotDialog(self.MainWindow,fig, plt_size)
             #set title
             plt_dialog.setWindowTitle(title)
@@ -4431,7 +4449,7 @@ def plot_top_heatmap(self):
             self.logger.write_log(f'plot_top_heatmap error: {error_message}')
             self.logger.write_log(f'plot_top_heatmap: table_name: {table_name}, top_num: {top_num}, value_type: {value_type}, fig_size: {fig_size}, pvalue: {pvalue}, sort_by: {sort_by}, cmap: {cmap}, scale: {scale}', 'e')
             if 'No significant' in error_message:
-                QMessageBox.warning(self.MainWindow, 'Warning', f'No significant results.')
+                QMessageBox.warning(self.MainWindow, 'Warning', f'No significant results. \n\n{error_message}')
             else:
                 QMessageBox.warning(self.MainWindow, 'Error', f'{error_message}')
 
@@ -4495,14 +4513,15 @@ def get_top_cross_table(self):
                                                                        rename_taxa=rename_taxa, sort_by = sort_by, scale_method = scale_method, return_type = 'table')
 
 
-        except ValueError as e:
-            QMessageBox.warning(self.MainWindow, 'Warning', f'No significant results.\n\n{e}')
-            return None
         except Exception as e:
             error_message = traceback.format_exc()
             self.logger.write_log(f'get_top_cross_table error: {error_message}', 'e')
             self.logger.write_log(f'get_top_cross_table: table_name: {table_name}, top_num: {top_num}, value_type: {value_type}, pvalue: {pvalue}, sort_by: {sort_by}', 'e')
-            QMessageBox.warning(self.MainWindow, 'Erro', error_message)
+            if 'No significant' in error_message:
+                QMessageBox.warning(self.MainWindow, 'Warning', f'No significant results.\n\n{error_message}')
+            else:
+                QMessageBox.warning(self.MainWindow, 'Error', f'{error_message}')
+
             return None
 
         try:
@@ -5318,39 +5337,7 @@ def plot_network(self):
             self.logger.write_log(f'plot_network error: {error_message}', 'e')
             self.logger.write_log(f'plot_network: sample_list:{sample_list}, focus_list:{focus_list}, plot_list_only:{plot_list_only}', 'e')
             QMessageBox.warning(self.MainWindow, 'Error', f'{error_message}')
-
-    # link
-    def get_tflink_intensity_matrix(self):
-        taxa = self.remove_pep_num_str_and_strip(self.comboBox_others_taxa.currentText())
-        func = self.remove_pep_num_str_and_strip(self.comboBox_others_func.currentText())
-
-        if not taxa and not func:
-            QMessageBox.warning(self.MainWindow, 'Warning', 'Please select taxa or function!')
-            return None
-
-        params = {}
-
-        # extract sample list
-        sample_list = self.get_sample_list_tflink()
-
-        params['sample_list'] = sample_list
-
-        if taxa:
-            params['taxon_name'] = taxa
-        if func:
-            params['func_name'] = func
-
-        df = self.tfa.GetMatrix.get_intensity_matrix(**params)
-
-        if not df.empty:
-            if self.checkBox_tflink_hetatmap_rename_taxa.isChecked():
-                df = self.tfa.rename_taxa(df)
-            if self.checkBox_tflink_plot_mean.isChecked():
-                df = self.tfa.BasicStats.get_stats_mean_df_by_group(df)
-            self.show_table(df, title=f'{taxa} [ {func} ]')
-        else:
-            QMessageBox.warning(self.MainWindow, 'Warning', 'No data!, please reselect!')
-
+
 
     def get_sample_list_tflink(self):
         # get sample list
@@ -5432,7 +5419,7 @@ def filter_tflink(self):
 
         pass
     # Plot Heatmap
-    def plot_tflink_heatmap(self):
+    def plot_tflink_heatmap(self, return_type = 'fig'):
         taxa = self.remove_pep_num_str_and_strip(self.comboBox_others_taxa.currentText())
         func = self.remove_pep_num_str_and_strip(self.comboBox_others_func.currentText())
         width = self.spinBox_tflink_width.value()
@@ -5443,21 +5430,14 @@ def plot_tflink_heatmap(self):
         rename_taxa = self.checkBox_tflink_hetatmap_rename_taxa.isChecked()
         show_all_labels = (self.checkBox_tflink_bar_show_all_labels_x.isChecked(), self.checkBox_tflink_bar_show_all_labels_y.isChecked())
         plot_mean = self.checkBox_tflink_plot_mean.isChecked()
+        rename_sample=self.checkBox_tflink_hetatmap_rename_sample.isChecked()
+        row_cluster = True if self.checkBox_tflink_hetatmap_row_cluster.isChecked() else False
+        col_cluster = True if self.checkBox_tflink_hetatmap_col_cluster.isChecked() else False
+        sub_meta = self.comboBox_tflink_sub_meta.currentText()
 
         if cmap == 'Auto':
             cmap = None
 
-        row_cluster = False
-        col_cluster = False
-
-        if self.checkBox_tflink_hetatmap_row_cluster.isChecked():
-            row_cluster = True
-
-        if self.checkBox_tflink_hetatmap_col_cluster.isChecked():
-            col_cluster = True
-
-
-
         if not taxa and not func:
             QMessageBox.warning(self.MainWindow, 'Warning', 'Please select taxa or function!')
             return None
@@ -5468,10 +5448,18 @@ def plot_tflink_heatmap(self):
 
         if taxa:
             params['taxon_name'] = taxa
-            title = taxa
+            if rename_taxa:
+                short_taxa = taxa.split('|')[-1]
+            else:
+                short_taxa = taxa
+            title = short_taxa
+
         if func:
             params['func_name'] = func
-            title = func if not title else f"{taxa} [ {func} ]"
+            title = func
+
+        if taxa and func:    
+            title = f"{short_taxa}\n{func}"
 
 
         df = self.tfa.GetMatrix.get_intensity_matrix(**params)
@@ -5488,12 +5476,17 @@ def plot_tflink_heatmap(self):
             df = self.delete_zero_columns(df)
 
         try:
-            self.show_message('Plotting heatmap, please wait...')
-            HeatmapPlot(self.tfa, **self.heatmap_params_dict).plot_basic_heatmap(df=df, title=title, fig_size=(int(width), int(height)), 
+            self.show_message('Plotting heatmap, please wait...') if return_type == 'fig' else self.show_message('Calculating data, please wait...')
+            fig_res = HeatmapPlot(self.tfa, **self.heatmap_params_dict).plot_basic_heatmap(df=df, title=title, fig_size=(int(width), int(height)), 
                                   scale=scale, row_cluster=row_cluster, col_cluster=col_cluster,
                                   cmap=cmap, rename_taxa=rename_taxa, font_size=font_size, show_all_labels=show_all_labels,
-                                  rename_sample=self.checkBox_tflink_hetatmap_rename_sample.isChecked(), plot_mean=plot_mean
+                                  rename_sample=rename_sample,  sub_meta=sub_meta,
+                                  plot_mean=plot_mean, return_type = return_type
                                   )
+
+            if return_type == 'table':
+                self.show_table(fig_res, title=title.replace('\n', '-'))
+
         except Exception as e:
             error_message = traceback.format_exc()
             self.logger.write_log(f'plot_others_heatmap error: {error_message}', 'e')
@@ -5545,7 +5538,8 @@ def plot_tflink_bar(self):
         show_legend = self.checkBox_tflink_bar_show_legend.isChecked()
         plot_mean = self.checkBox_tflink_plot_mean.isChecked()
         show_all_labels = (self.checkBox_tflink_bar_show_all_labels_x.isChecked(), self.checkBox_tflink_bar_show_all_labels_y.isChecked())
-
+        sub_meta = self.comboBox_tflink_sub_meta.currentText()
+
         if not taxa and not func:
             QMessageBox.warning(self.MainWindow, 'Warning', 'Please select taxa or function!')
 
@@ -5586,6 +5580,7 @@ def plot_tflink_bar(self):
             params['font_size'] = font_size
             params['plot_mean'] = plot_mean
             params['show_all_labels'] = show_all_labels
+            params['sub_meta'] = sub_meta
 
             self.show_message('Plotting bar plot, please wait...')
             pic = BarPlot_js(self.tfa, theme=self.html_theme).plot_intensity_bar(**params)