Merge branch 'dev'

byemaxx · Aug 26, 2024 · 99ce6ce · 99ce6ce
2 parents efb80e3 + 5dfc08b
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diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,43 @@
+# Version: 1.111.6
+## Date: 2024-08-21
+### Changes:
+- Fix: Fixed the bug of extrcting the peptides of taxa, funcs or taxa-funcs, when split the function items.
+
+
+# Version: 1.111.5
+## Date: 2024-08-21
+### Changes:
+- Change: Optimized the x-axis and y-axis labels of the heatmap plot to make the labels more clear.
+
+# Version: 1.111.4
+## Date: 2024-08-21
+### Changes:
+- New: Added rotation option for the x-axis and y-axis of the heatmap plot.
+
+# Version: 1.111.3
+## Date: 2024-08-21
+### Changes:
+- New: Added protein_id as a function to the OTF table, only keep the first protein_id as the function.
+
+# Version: 1.111.2
+## Date: 2024-08-21
+### Changes:
+- Fix: Fixed the bug when restore the object, the seetings was not restored completely.
+
+
+# Version: 1.111.1
+## Date: 2024-08-21
+### Changes:
+- Fix: Fixed the bug of spliting the function items, the redundant items were not sumed.
+
+
+
+# Version: 1.111.0
+## Date: 2024-08-20
+### Changes:
+- New: Added a option to split the items contain multiple functions to multiple items when set OTF table.
+
+
 # Version: 1.110.1
 ## Date: 2024-08-20
 ### Changes:

diff --git a/Docs/MetaX_Cookbook.md b/Docs/MetaX_Cookbook.md
@@ -4,7 +4,7 @@ This is the guidebook for the MetaX **GUI Version**. If you are using the CLI to
 
 # Overview
 
-**[MetaX](https://github.com/byemaxx/MetaX)** is a novel tool for linking peptide sequences with taxonomic and functional information in **Metaproteomics**. We introduce the ***Operational Taxa-Functions (OTF)*** concept to explore microbial roles and interactions ("**who is doing what and how**") within ecosystems. 
+**[MetaX](https://github.com/byemaxx/MetaX)** is a novel tool for linking peptide sequences with taxonomic and functional information in **Metaproteomics**. We introduce the ***Operational Taxon-Function (OTF)*** concept to explore microbial roles and interactions ("**who is doing what and how**") within ecosystems. 
 
 MetaX also features <u>statistical modules</u> and <u>plotting tools</u> for analyzing peptides, taxa, functions, proteins, and taxon-function contributions across groups.
 

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # MetaX
 
-**MetaX** is a novel tool for linking peptide sequences with taxonomic and functional information in **Metaproteomics**. We introduce the ***Operational Taxa-Functions (OTF)*** concept to explore microbial roles and interactions ("**who is doing what and how**") within ecosystems. 
+**MetaX** is a novel tool for linking peptide sequences with taxonomic and functional information in **Metaproteomics**. We introduce the ***Operational Taxon-Function (OTF)*** concept to explore microbial roles and interactions ("**who is doing what and how**") within ecosystems. 
 
 MetaX also features <u>statistical modules</u> and <u>plotting tools</u> for analyzing peptides, taxa, functions, proteins, and taxon-function contributions across groups.
 

diff --git a/metax/data/example_data/Example_OTF.tsv b/metax/data/example_data/Example_OTF.tsv
diff --git a/metax/gui/main_gui.py b/metax/gui/main_gui.py
@@ -207,8 +207,13 @@ def __init__(self, MainWindow):
         # ploting parameters
         # set the default theme mode
         self.html_theme = 'white'
-
-        self.heatmap_params_dict = {'linkage_method': 'average', 'distance_metric': 'euclidean'}
+
+        self.heatmap_params_dict = {
+            "linkage_method": "average",
+            "distance_metric": "euclidean",
+            "x_labels_rotation": 90,
+            "y_labels_rotation": 0,
+        }
 
         self.tf_link_net_params_dict = {'taxa_shape': 'circle', 'func_shape': 'rect', 
                                         'taxa_color': '#374E55','taxa_focus_color': '#6A6599', 
@@ -1175,6 +1180,12 @@ def save_set_multi_table_settings(self):
 
             elif isinstance(widget, QtWidgets.QSpinBox):
                 self.settings.setValue(f"{settings_key}/value", widget.value())
+
+            elif isinstance(widget, QtWidgets.QCheckBox):
+                self.settings.setValue(f"{settings_key}/isChecked", widget.isChecked())
+
+            elif isinstance(widget, QtWidgets.QLineEdit):
+                self.settings.setValue(f"{settings_key}/text", widget.text())
 
 
     def export_log_file(self):
@@ -1251,6 +1262,17 @@ def restore_settings_after_load_taxafunc_obj(self):
             elif isinstance(widget, QtWidgets.QSpinBox):
                 value = self.settings.value(f"{settings_key}/value", 0, type=int)
                 widget.setValue(value)
+            elif isinstance(widget, QtWidgets.QCheckBox):
+                checked = self.settings.value(f"{settings_key}/isChecked", False, type=bool)
+                widget.setChecked(checked)
+                if widget.objectName() == 'checkBox_set_taxa_func_split_func':
+                    enable_list = [self.lineEdit_set_taxa_func_split_func_sep, self.checkBox_set_taxa_func_split_func_share_intensity]
+                    for w in enable_list:
+                        w.setEnabled(checked)
+
+            elif isinstance(widget, QtWidgets.QLineEdit):
+                text = self.settings.value(f"{settings_key}/text", "", type=str)
+                widget.setText(text)
 
 
         # enable button after multi table is set  
@@ -2452,6 +2474,10 @@ def set_multi_table(self, restore_taxafunc=False,  saved_obj=None):
             func_threshold = self.doubleSpinBox_func_threshold.value()
             func_threshold = round(func_threshold, 3)
 
+            split_func = self.checkBox_set_taxa_func_split_func.isChecked()
+            split_func_params: dict = {'split_by': self.lineEdit_set_taxa_func_split_func_sep.text(),
+                                       'share_intensity': self.checkBox_set_taxa_func_split_func_share_intensity.isChecked()}
+
             peptide_num_threshold = {
                 'taxa': self.spinBox_peptide_num_threshold_taxa.value(),
                 'func': self.spinBox_peptide_num_threshold_func.value(),
@@ -2602,7 +2628,8 @@ def set_multi_table(self, restore_taxafunc=False,  saved_obj=None):
                                         'processing_after_sum': processing_after_sum, 
                                         'peptide_num_threshold': peptide_num_threshold, 
                                         'sum_protein': sum_protein, 'sum_protein_params': sum_protein_params,
-                                        'keep_unknow_func': False}
+                                        'keep_unknow_func': False,
+                                        'split_func': split_func, 'split_func_params': split_func_params}
 
                 def callback_after_set_multi_tables(result, success):
                     if success:
@@ -3452,28 +3479,19 @@ def plot_basic_list(self, plot_type='heatmap'):
                 df = self.tfa.peptide_df.copy()
 
             else:
+                peptides_list = []
+
                 if table_name == 'Taxa':
-                    df = self.tfa.clean_df.loc[self.tfa.clean_df['Taxon'].isin(self.basic_heatmap_list)]
-                    df.index = df[self.tfa.peptide_col_name]
+                    for i in self.basic_heatmap_list:
+                        peptides_list.extend(self.tfa.peptides_linked_dict['taxa'][i])
 
                 elif table_name == 'Functions':
-                    df = self.tfa.clean_df.loc[self.tfa.clean_df[self.tfa.func_name].isin(self.basic_heatmap_list)]
-                    df.index = df[self.tfa.peptide_col_name]
+                    for i in self.basic_heatmap_list:
+                        peptides_list.extend(self.tfa.peptides_linked_dict['func'][i])
 
                 elif table_name == 'Taxa-Functions':
-                    df_list = [] 
                     for i in self.basic_heatmap_list:
-                        taxon, func = i.split(' <')
-                        func = func[:-1] 
-                        dft = self.tfa.clean_df.loc[(self.tfa.clean_df['Taxon'] == taxon) & (self.tfa.clean_df[self.tfa.func_name] == func)]
-                        df_list.append(dft)
-
-                    if df_list:  
-                        df_all = pd.concat(df_list)
-                        df_all.index = df_all[self.tfa.peptide_col_name] 
-                        df = df_all
-                    else:
-                        raise ValueError('No valid taxa-function belongs to the selected taxa-function!')
+                        peptides_list.extend(self.tfa.peptides_linked_dict['taxa_func'][i])
 
                 elif table_name == 'Proteins':
                     QMessageBox.warning(self.MainWindow, 'Warning',
@@ -3484,9 +3502,9 @@ def plot_basic_list(self, plot_type='heatmap'):
                     return
 
                 else: # Peptide
-                    df = self.tfa.peptide_df.copy()
-                    df = df.loc[self.basic_heatmap_list]
+                    peptides_list = self.basic_heatmap_list
 
+                df = self.tfa.peptide_df.loc[peptides_list]
                 df = df[sample_list]
 
         else: