Merge branch 'dev'

Docs/ChangeLog.md

@@ -1,3 +1,10 @@
+# Version: 1.110.0
+## Date: 2024-08-12
+### Changes:
+- Fix: 1. Fixed the group order was not correct in the title of the volcano plot. 2. col scale bug when plot the basic heatmap.
+- Change: 1. Enable alpha/beta divversity for all type of tables. 2. Only asiign peptide to one protein rather than sahre the intensity when sum peptide to protein by razor method.
+
+
 # Version: 1.109.12
 ## Date: 2024-08-10
 ### Changes:

metax/gui/main_gui.py

@@ -592,8 +592,11 @@ def get_list_by_df_type(self, df_type:str, remove_no_linked:bool=False, silent:b
         return res_list
 
     def change_event_checkBox_basic_plot_table(self):
-        taxa_only_button_list = [self.pushButton_plot_alpha_div, self.pushButton_plot_beta_div, 
-                                 self.pushButton_plot_sunburst, self.pushButton_plot_basic_treemap]
+        taxa_only_button_list = [
+                                # self.pushButton_plot_alpha_div, 
+                                # self.pushButton_plot_beta_div, 
+                                 self.pushButton_plot_sunburst, 
+                                 self.pushButton_plot_basic_treemap]
 
         taxa_func_button_list = [self.pushButton_plot_basic_sankey]
 
@@ -2984,6 +2987,8 @@ def enable_multi_button(self, state=True):
         self.pushButton_trends_clean_list,
         self.comboBox_trends_table,
         self.pushButton_plot_pca_js,
+        self.pushButton_plot_alpha_div, 
+        self.pushButton_plot_beta_div,
         self.pushButton_trends_add_a_list,
         self.pushButton_co_expr_add_a_list,
         self.pushButton_basic_heatmap_add_a_list,
@@ -4217,8 +4222,9 @@ def get_title_by_table_name(self, table_name):
                                                              width=width, height=height, font_size=font_size, 
                                                              plot_all_samples=plot_all_samples, theme=theme,
                                                              sub_meta = sub_meta, show_fliers = show_fliers,
-                                                             legend_col_num=legend_col_num, rename_sample = rename_sample)
-                self.update_table_dict('alpha_diversity', aplha_diversity_df)
+                                                             legend_col_num=legend_col_num, rename_sample = rename_sample, 
+                                                             df_type=table_name, title_name=title_name)
+                self.update_table_dict(f'alpha_diversity({title_name})', aplha_diversity_df)
             elif method == "beta_div":
                 self.show_message('Beta diversity is running, please wait...')
                 metric = self.comboBox_beta_div_method.currentText()
@@ -4227,8 +4233,8 @@ def get_title_by_table_name(self, table_name):
                                                             rename_sample = rename_sample,
                                                             show_label = show_label, adjust_label = adjust_label, 
                                                             theme=theme,sub_meta = sub_meta, legend_col_num=legend_col_num,
-                                                            dot_size = dot_size)
-                self.update_table_dict('beta_diversity_distance_matrix', beta_diversity_distance_matrix)
+                                                            dot_size = dot_size, df_type=table_name, title_name=title_name)
+                self.update_table_dict(f'beta_diversity_distance_matrix({title_name})', beta_diversity_distance_matrix)
 
 
             elif method == 'sunburst':
@@ -4926,7 +4932,7 @@ def plot_deseq2_volcano(self):
             height = self.spinBox_fc_plot_height.value()
             group1 = self.comboBox_deseq2_group1.currentText()
             group2 = self.comboBox_deseq2_group2.currentText()
-            title_name = f'{group1} vs {group2} of {table_name.split("(")[1].split(")")[0]}'
+            title_name = f'{group2} vs {group1} of {table_name.split("(")[1].split(")")[0]}'
             font_size = self.spinBox_deseq2_font_size.value()
             dot_size = self.spinBox_deseq2_dot_size.value()
             plot_js = self.checkBox_deseq2_js_volcano.isChecked()
@@ -5085,7 +5091,7 @@ def deseq2_plot_sankey(self):
             return None
         try:
             df = self.table_dict[table_name]
-            title_name = f'{group1} vs {group2} of {table_name.split("(")[1].split(")")[0]}'
+            title_name = f'{group2} vs {group1} of {table_name.split("(")[1].split(")")[0]}'
 
             pic = SankeyPlot(self.tfa, theme=self.html_theme).plot_fc_sankey(df, width=width, height=height, pvalue=pvalue, p_type = p_type,
                                                       log2fc_min=log2fc_min, log2fc_max=log2fc_max, title =title_name, font_size=font_size)

metax/gui/metax_gui/main_window.ui

@@ -46,7 +46,7 @@
            <enum>Qt::LeftToRight</enum>
           </property>
           <property name="currentIndex">
-           <number>4</number>
+           <number>3</number>
           </property>
           <property name="documentMode">
            <bool>false</bool>
@@ -245,8 +245,8 @@
                 <rect>
                  <x>0</x>
                  <y>0</y>
-                 <width>528</width>
-                 <height>573</height>
+                 <width>391</width>
+                 <height>80</height>
                 </rect>
                </property>
                <attribute name="label">
@@ -1400,7 +1400,7 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>1016</width>
+                        <width>660</width>
                         <height>232</height>
                        </rect>
                       </property>
@@ -2672,7 +2672,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>1016</width>
-                        <height>162</height>
+                        <height>158</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_50">
@@ -2808,7 +2808,7 @@
                              </item>
                              <item>
                               <property name="text">
-                               <string>column</string>
+                               <string>col</string>
                               </property>
                              </item>
                              <item>
@@ -3674,7 +3674,7 @@
                       <rect>
                        <x>0</x>
                        <y>0</y>
-                       <width>1003</width>
+                       <width>1020</width>
                        <height>126</height>
                       </rect>
                      </property>
@@ -5543,7 +5543,7 @@
                            <x>0</x>
                            <y>0</y>
                            <width>996</width>
-                           <height>146</height>
+                           <height>140</height>
                           </rect>
                          </property>
                          <layout class="QGridLayout" name="gridLayout_68">
@@ -6093,8 +6093,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>1016</width>
-                        <height>181</height>
+                        <width>493</width>
+                        <height>128</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_49">
@@ -7323,8 +7323,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>1016</width>
-                        <height>144</height>
+                        <width>538</width>
+                        <height>63</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_57">
@@ -8171,8 +8171,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>1016</width>
-                        <height>185</height>
+                        <width>775</width>
+                        <height>102</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_69">
@@ -9091,8 +9091,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>1016</width>
-                        <height>168</height>
+                        <width>383</width>
+                        <height>68</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_66">
@@ -10086,7 +10086,7 @@
      <x>0</x>
      <y>0</y>
      <width>1122</width>
-     <height>21</height>
+     <height>23</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuTools">

metax/gui/metax_gui/ui_main_window.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\main_window.ui'
+# Form implementation generated from reading ui file 'c:\Users\max\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\main_window.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -147,7 +147,7 @@ def setupUi(self, metaX_main):
         self.toolBox_2.setMaximumSize(QtCore.QSize(1677, 16777215))
         self.toolBox_2.setObjectName("toolBox_2")
         self.page_2 = QtWidgets.QWidget()
-        self.page_2.setGeometry(QtCore.QRect(0, 0, 528, 573))
+        self.page_2.setGeometry(QtCore.QRect(0, 0, 391, 80))
         self.page_2.setObjectName("page_2")
         self.gridLayout_27 = QtWidgets.QGridLayout(self.page_2)
         self.gridLayout_27.setObjectName("gridLayout_27")
@@ -706,7 +706,7 @@ def setupUi(self, metaX_main):
         self.scrollArea.setWidgetResizable(True)
         self.scrollArea.setObjectName("scrollArea")
         self.scrollAreaWidgetContents = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents.setGeometry(QtCore.QRect(0, 0, 1016, 232))
+        self.scrollAreaWidgetContents.setGeometry(QtCore.QRect(0, 0, 660, 232))
         self.scrollAreaWidgetContents.setObjectName("scrollAreaWidgetContents")
         self.gridLayout_34 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents)
         self.gridLayout_34.setObjectName("gridLayout_34")
@@ -1370,7 +1370,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_2.setWidgetResizable(True)
         self.scrollArea_2.setObjectName("scrollArea_2")
         self.scrollAreaWidgetContents_2 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_2.setGeometry(QtCore.QRect(0, 0, 1016, 162))
+        self.scrollAreaWidgetContents_2.setGeometry(QtCore.QRect(0, 0, 1016, 158))
         self.scrollAreaWidgetContents_2.setObjectName("scrollAreaWidgetContents_2")
         self.gridLayout_50 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_2)
         self.gridLayout_50.setObjectName("gridLayout_50")
@@ -1919,7 +1919,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_cross_heatmap_settings.setWidgetResizable(True)
         self.scrollArea_cross_heatmap_settings.setObjectName("scrollArea_cross_heatmap_settings")
         self.scrollAreaWidgetContents_3 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_3.setGeometry(QtCore.QRect(0, 0, 1003, 126))
+        self.scrollAreaWidgetContents_3.setGeometry(QtCore.QRect(0, 0, 1020, 126))
         self.scrollAreaWidgetContents_3.setObjectName("scrollAreaWidgetContents_3")
         self.gridLayout_38 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_3)
         self.gridLayout_38.setObjectName("gridLayout_38")
@@ -2844,7 +2844,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_3.setWidgetResizable(True)
         self.scrollArea_3.setObjectName("scrollArea_3")
         self.scrollAreaWidgetContents_4 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_4.setGeometry(QtCore.QRect(0, 0, 996, 146))
+        self.scrollAreaWidgetContents_4.setGeometry(QtCore.QRect(0, 0, 996, 140))
         self.scrollAreaWidgetContents_4.setObjectName("scrollAreaWidgetContents_4")
         self.gridLayout_68 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_4)
         self.gridLayout_68.setObjectName("gridLayout_68")
@@ -3145,7 +3145,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_4.setWidgetResizable(True)
         self.scrollArea_4.setObjectName("scrollArea_4")
         self.scrollAreaWidgetContents_5 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_5.setGeometry(QtCore.QRect(0, 0, 1016, 181))
+        self.scrollAreaWidgetContents_5.setGeometry(QtCore.QRect(0, 0, 493, 128))
         self.scrollAreaWidgetContents_5.setObjectName("scrollAreaWidgetContents_5")
         self.gridLayout_49 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_5)
         self.gridLayout_49.setObjectName("gridLayout_49")
@@ -3790,7 +3790,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_5.setWidgetResizable(True)
         self.scrollArea_5.setObjectName("scrollArea_5")
         self.scrollAreaWidgetContents_6 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_6.setGeometry(QtCore.QRect(0, 0, 1016, 144))
+        self.scrollAreaWidgetContents_6.setGeometry(QtCore.QRect(0, 0, 538, 63))
         self.scrollAreaWidgetContents_6.setObjectName("scrollAreaWidgetContents_6")
         self.gridLayout_57 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_6)
         self.gridLayout_57.setObjectName("gridLayout_57")
@@ -4261,7 +4261,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_6.setWidgetResizable(True)
         self.scrollArea_6.setObjectName("scrollArea_6")
         self.scrollAreaWidgetContents_7 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_7.setGeometry(QtCore.QRect(0, 0, 1016, 185))
+        self.scrollAreaWidgetContents_7.setGeometry(QtCore.QRect(0, 0, 775, 102))
         self.scrollAreaWidgetContents_7.setObjectName("scrollAreaWidgetContents_7")
         self.gridLayout_69 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_7)
         self.gridLayout_69.setObjectName("gridLayout_69")
@@ -4765,7 +4765,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_7.setWidgetResizable(True)
         self.scrollArea_7.setObjectName("scrollArea_7")
         self.scrollAreaWidgetContents_8 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_8.setGeometry(QtCore.QRect(0, 0, 1016, 168))
+        self.scrollAreaWidgetContents_8.setGeometry(QtCore.QRect(0, 0, 383, 68))
         self.scrollAreaWidgetContents_8.setObjectName("scrollAreaWidgetContents_8")
         self.gridLayout_66 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_8)
         self.gridLayout_66.setObjectName("gridLayout_66")
@@ -5276,7 +5276,7 @@ def setupUi(self, metaX_main):
         self.statusbar.setObjectName("statusbar")
         metaX_main.setStatusBar(self.statusbar)
         self.menuBar = QtWidgets.QMenuBar(metaX_main)
-        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1122, 21))
+        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1122, 23))
         self.menuBar.setObjectName("menuBar")
         self.menuTools = QtWidgets.QMenu(self.menuBar)
         self.menuTools.setObjectName("menuTools")
@@ -5336,7 +5336,7 @@ def setupUi(self, metaX_main):
 
         self.retranslateUi(metaX_main)
         self.stackedWidget.setCurrentIndex(0)
-        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(4)
+        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(3)
         self.toolBox_2.setCurrentIndex(0)
         self.tabWidget_4.setCurrentIndex(1)
         self.tabWidget_3.setCurrentIndex(3)
@@ -5616,7 +5616,7 @@ def retranslateUi(self, metaX_main):
         self.label_186.setText(_translate("metaX_main", "Sankey"))
         self.label_31.setText(_translate("metaX_main", "Scale"))
         self.comboBox_basic_hetatmap_scale.setItemText(0, _translate("metaX_main", "row"))
-        self.comboBox_basic_hetatmap_scale.setItemText(1, _translate("metaX_main", "column"))
+        self.comboBox_basic_hetatmap_scale.setItemText(1, _translate("metaX_main", "col"))
         self.comboBox_basic_hetatmap_scale.setItemText(2, _translate("metaX_main", "all"))
         self.comboBox_basic_hetatmap_scale.setItemText(3, _translate("metaX_main", "None"))
         self.label_13.setText(_translate("metaX_main", "Theme"))

metax/peptide_annotator/convert_id_to_name.py

@@ -177,15 +177,18 @@ def lookup_and_join(ec_nums, column_name):
     print("Add EC columns to df successfully!")
     return df
 
-def add_pathway_name_to_df(df: pd.DataFrame) -> pd.DataFrame:
-    def query_kegg(id_str, pathway_dict):
+def add_pathway_name_to_df(df: pd.DataFrame, kppe_id:bool = False) -> pd.DataFrame:
+    def query_kegg(id_str, pathway_dict, kppe_id=False):
         id_list = id_str.split(',')
         if id_list[0] == 'not_found':
             return 'not_found'
         pathway_list = []
         for id in id_list:
             if id in pathway_dict:
-                pathway_list.append(pathway_dict[id])
+                if kppe_id:
+                    pathway_list.append(f'{id}:{pathway_dict[id]}')
+                else:
+                    pathway_list.append(pathway_dict[id])
         # remove duplicates
         pathway_list = list(dict.fromkeys(pathway_list))
         if len(pathway_list) == 0:
@@ -199,9 +202,12 @@ def query_kegg(id_str, pathway_dict):
     if 'KEGG_Pathway' not in df.columns:
         print('KEGG_Pathway column does not exist!, return the original dataframe')
         return df
+
+    #! fill the missing pathway names if necessary
+    # df['KEGG_Pathway'] = df['KEGG_Pathway'].fillna('not_found')
 
     pathway_dict = get_pathway_dict()
-    df.loc[:, 'KEGG_Pathway_name'] = df['KEGG_Pathway'].apply(lambda x: query_kegg(x, pathway_dict))
+    df.loc[:, 'KEGG_Pathway_name'] = df['KEGG_Pathway'].apply(lambda x: query_kegg(x, pathway_dict, kppe_id))
     df.loc[:, 'KEGG_Pathway_name_prop'] = df['KEGG_Pathway_prop']    
     print("Add KEGG_Pathway_name to df successfully!")
     return df
@@ -250,7 +256,7 @@ def query_ko(id_str, ko_dict):
 # if __name__ == '__main__':
 #     df_path = "MetaX/data/example_data/Example_OTF.tsv"
 #     df = pd.read_csv(df_path, sep='\t')
-#     df = add_pathway_name_to_df(df)
+#     df = add_pathway_name_to_df(df, kppe_id=True)
 #     df = add_ec_name_to_df(df)
 #     df = add_ko_name_to_df(df)
 #     df.to_csv("11.tsv", sep='\t', index=False)

metax/taxafunc_analyzer/analyzer.py

@@ -791,6 +791,7 @@ def get_df(self, table_name:str = 'taxa'):
             "proteins": "protein_df",
 
         }
+        table_name = table_name.lower()
         dft = getattr(self, name_dict[table_name])
         # remove peptide_num column if exists
         if "peptide_num" in dft.columns: