- Change: Optimized the Data Overview section to make the layout more…

… clear.

- Update README.md

Docs/ChangeLog.md

@@ -1,3 +1,10 @@
+
+# Version: 1.119.7
+## Date: 2024-12-5
+### Changes:
+- Change: Optimized the Data Overview section to make the layout more clear.
+- Update README.md
+
 # Version: 1.119.6
 ## Date: 2024-12-5
 ### Changes:

README.md

@@ -43,7 +43,11 @@ Show all functions of a taxon
 
 - <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_bar.png" alt="tf_link_bar" style="zoom:50%;" />
 
+**OTF Heatmap**
 
+Show OTFS intensity in groups(samples), e.g., **Species-KO** OTF Heatmap
+
+<img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/otf_heatmap.png" alt="otf_heatmap" style="zoom:50%;" />
 
 ## Download & Installation
 - **Desktop Version** (Recommended)

metax/gui/main_gui.py

@@ -1045,7 +1045,7 @@ def change_theme(self, theme, silent=False):
                     padding: 5px;
                     margin: 2px;
                     height: 20px;
-                }}
+                    }}
 
                     '''
         current_app = QtWidgets.QApplication.instance()
@@ -4070,7 +4070,7 @@ def plot_trends_cluster(self):
                                                                width=width, height=height, title=title
                                                                , font_size=font_size, num_col=num_col)
             # create a dialog to show the figure
-            # plt_dialog = PltDialog(self.MainWindow, fig)
+            # plt_dialog = PltDialog(self.MainWindow, fig) #obsolete
             plt_size= (width*50, int(height*num_cluster*50/num_col) )
             plt_dialog = ExportablePlotDialog(self.MainWindow,fig, plt_size)
             #set title
@@ -4348,9 +4348,9 @@ def plot_taxa_stats(self):
         else:
             # BasicPlot(self.tfa).plot_taxa_stats()
             theme = self.comboBox_data_overiew_theme.currentText()
-            pic = BasicPlot(self.tfa).plot_taxa_stats_pie(theme=theme)
+            pic = BasicPlot(self.tfa).plot_taxa_stats_pie(theme=theme, font_size=8, width=5, height=4)
             # Add the new MatplotlibWidget
-            self.mat_widget_plot_peptide_num = MatplotlibWidget(pic)
+            self.mat_widget_plot_peptide_num = MatplotlibWidget(pic, width = 5, height = 4)
             self.verticalLayout_overview_plot.addWidget(self.mat_widget_plot_peptide_num)
 
     def plot_taxa_stats_new_window(self):
@@ -4369,9 +4369,10 @@ def plot_taxa_number(self):
             QMessageBox.warning(self.MainWindow, 'Warning', 'Please run OTF Analyzer first!')
         else:
             theme = self.comboBox_data_overiew_theme.currentText()
-            pic = BasicPlot(self.tfa).plot_taxa_number(theme = theme).get_figure()
+            pic = BasicPlot(self.tfa).plot_taxa_number(theme = theme, font_size = 8, width = 5,height = 4
+                                                       ).get_figure()
 
-            self.mat_widget_plot_taxa_num = MatplotlibWidget(pic)
+            self.mat_widget_plot_taxa_num = MatplotlibWidget(pic, width = 5, height = 4)
             self.verticalLayout_overview_plot.addWidget(self.mat_widget_plot_taxa_num)
 
     def plot_taxa_number_new_window(self):
@@ -4399,9 +4400,9 @@ def plot_peptide_num_in_func(self):
             self.show_message('Plotting peptide number in function...')
             BasicPlot(self.tfa).plot_prop_stats(func_name, theme=theme, res_type='show', font_size = font_size)
         else:
-            pic = BasicPlot(self.tfa).plot_prop_stats(func_name, theme=theme)
+            pic = BasicPlot(self.tfa).plot_prop_stats(func_name, theme=theme, font_size = 8, width=5, height=4)
 
-            self.mat_widget_plot_peptide_num_in_func = MatplotlibWidget(pic.get_figure())
+            self.mat_widget_plot_peptide_num_in_func = MatplotlibWidget(pic.get_figure(), width = 5, height = 4)
             self.verticalLayout_overview_func.addWidget(self.mat_widget_plot_peptide_num_in_func)
 
 

metax/gui/metax_gui/main_window.ui

@@ -46,7 +46,7 @@
            <enum>Qt::LeftToRight</enum>
           </property>
           <property name="currentIndex">
-           <number>3</number>
+           <number>1</number>
           </property>
           <property name="documentMode">
            <bool>false</bool>
@@ -186,7 +186,7 @@
             <item row="0" column="0">
              <widget class="QLabel" name="label_26">
               <property name="text">
-               <string>Operational Taxa-Functions (OTF) Table (head 200)</string>
+               <string>Operational Taxon-Function (OTF) Table (head 200)</string>
               </property>
              </widget>
             </item>
@@ -205,6 +205,9 @@
                 <verstretch>0</verstretch>
                </sizepolicy>
               </property>
+              <property name="sortingEnabled">
+               <bool>true</bool>
+              </property>
              </widget>
             </item>
             <item row="1" column="0">
@@ -215,6 +218,15 @@
                 <verstretch>0</verstretch>
                </sizepolicy>
               </property>
+              <property name="showGrid">
+               <bool>true</bool>
+              </property>
+              <property name="sortingEnabled">
+               <bool>true</bool>
+              </property>
+              <property name="wordWrap">
+               <bool>false</bool>
+              </property>
              </widget>
             </item>
             <item row="1" column="1" rowspan="3">
@@ -246,7 +258,7 @@
                  <x>0</x>
                  <y>0</y>
                  <width>462</width>
-                 <height>531</height>
+                 <height>527</height>
                 </rect>
                </property>
                <attribute name="label">
@@ -3248,8 +3260,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>885</width>
-                        <height>170</height>
+                        <width>665</width>
+                        <height>157</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_50">
@@ -6810,7 +6822,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>885</width>
-                        <height>170</height>
+                        <height>168</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_49">
@@ -7664,8 +7676,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>885</width>
-                        <height>123</height>
+                        <width>620</width>
+                        <height>65</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_57">
@@ -9600,7 +9612,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>885</width>
-                        <height>158</height>
+                        <height>155</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_66">
@@ -10869,7 +10881,7 @@
      <x>0</x>
      <y>0</y>
      <width>991</width>
-     <height>21</height>
+     <height>23</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuTools">

metax/gui/metax_gui/matplotlib_figure_canvas.py

@@ -3,14 +3,42 @@
 from matplotlib.figure import Figure
 
 class MatplotlibWidget(QWidget):
-    def __init__(self, figure=None, parent=None):
+    def __init__(self, figure=None, parent=None, width=6, height=4, dpi=100):
+        """
+        A QWidget that embeds a Matplotlib figure with fixed size to prevent deformation.
+        
+        :param figure: The Matplotlib Figure object. If None, a new Figure is created.
+        :param parent: The parent QWidget.
+        :param width: Width of the figure in inches.
+        :param height: Height of the figure in inches.
+        :param dpi: Dots per inch (resolution) of the figure.
+        """
         super(MatplotlibWidget, self).__init__(parent)
 
-        self.figure = figure if figure else Figure()
+        # Create or use the provided figure
+        self.figure = figure if figure else Figure(figsize=(width, height), dpi=dpi)
         self.figure.tight_layout()
 
+        # Create the canvas for rendering the figure
         self.canvas = FigureCanvas(self.figure)
         self.canvas.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
+
+        # Set fixed size for the canvas
+        self.canvas.setFixedSize(width * dpi, height * dpi)
 
+        # Create and set layout
         self.layout = QHBoxLayout(self)
-        self.layout.addWidget(self.canvas)
+        self.layout.addWidget(self.canvas)
+
+    def set_size(self, width, height, dpi=None):
+        """
+        Update the size of the Matplotlib figure and canvas.
+        
+        :param width: New width in inches.
+        :param height: New height in inches.
+        :param dpi: Optional new DPI. If not provided, the current DPI is used.
+        """
+        dpi = dpi if dpi else self.figure.get_dpi()
+        self.figure.set_size_inches(width, height, forward=True)
+        self.canvas.setFixedSize(width * dpi, height * dpi)
+        self.canvas.draw()

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
 #
@@ -133,6 +133,8 @@ def setupUi(self, metaX_main):
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.tableWidget_taxa_func_view.sizePolicy().hasHeightForWidth())
         self.tableWidget_taxa_func_view.setSizePolicy(sizePolicy)
+        self.tableWidget_taxa_func_view.setShowGrid(True)
+        self.tableWidget_taxa_func_view.setWordWrap(False)
         self.tableWidget_taxa_func_view.setObjectName("tableWidget_taxa_func_view")
         self.tableWidget_taxa_func_view.setColumnCount(0)
         self.tableWidget_taxa_func_view.setRowCount(0)
@@ -147,7 +149,7 @@ 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, 462, 531))
+        self.page_2.setGeometry(QtCore.QRect(0, 0, 462, 527))
         self.page_2.setObjectName("page_2")
         self.gridLayout_27 = QtWidgets.QGridLayout(self.page_2)
         self.gridLayout_27.setObjectName("gridLayout_27")
@@ -1652,7 +1654,7 @@ 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, 885, 170))
+        self.scrollAreaWidgetContents_2.setGeometry(QtCore.QRect(0, 0, 665, 157))
         self.scrollAreaWidgetContents_2.setObjectName("scrollAreaWidgetContents_2")
         self.gridLayout_50 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_2)
         self.gridLayout_50.setObjectName("gridLayout_50")
@@ -3524,7 +3526,7 @@ 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, 885, 170))
+        self.scrollAreaWidgetContents_5.setGeometry(QtCore.QRect(0, 0, 885, 168))
         self.scrollAreaWidgetContents_5.setObjectName("scrollAreaWidgetContents_5")
         self.gridLayout_49 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_5)
         self.gridLayout_49.setObjectName("gridLayout_49")
@@ -3986,7 +3988,7 @@ 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, 885, 123))
+        self.scrollAreaWidgetContents_6.setGeometry(QtCore.QRect(0, 0, 620, 65))
         self.scrollAreaWidgetContents_6.setObjectName("scrollAreaWidgetContents_6")
         self.gridLayout_57 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_6)
         self.gridLayout_57.setObjectName("gridLayout_57")
@@ -5029,7 +5031,7 @@ 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, 885, 158))
+        self.scrollAreaWidgetContents_8.setGeometry(QtCore.QRect(0, 0, 885, 155))
         self.scrollAreaWidgetContents_8.setObjectName("scrollAreaWidgetContents_8")
         self.gridLayout_66 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_8)
         self.gridLayout_66.setObjectName("gridLayout_66")
@@ -5683,7 +5685,7 @@ 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, 991, 21))
+        self.menuBar.setGeometry(QtCore.QRect(0, 0, 991, 23))
         self.menuBar.setObjectName("menuBar")
         self.menuTools = QtWidgets.QMenu(self.menuBar)
         self.menuTools.setObjectName("menuTools")
@@ -5749,7 +5751,7 @@ def setupUi(self, metaX_main):
 
         self.retranslateUi(metaX_main)
         self.stackedWidget.setCurrentIndex(0)
-        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(3)
+        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(1)
         self.toolBox_2.setCurrentIndex(0)
         self.tabWidget_4.setCurrentIndex(0)
         self.tabWidget_3.setCurrentIndex(3)
@@ -5802,8 +5804,10 @@ def retranslateUi(self, metaX_main):
         self.pushButton_load_example_for_analyzer.setText(_translate("metaX_main", "Load Example Data"))
         self.label_46.setText(_translate("metaX_main", "Operational Taxa-Functions (OTF) Analyzer"))
         self.tabWidget_TaxaFuncAnalyzer.setTabText(self.tabWidget_TaxaFuncAnalyzer.indexOf(self.tab), _translate("metaX_main", "Data Import"))
-        self.label_26.setText(_translate("metaX_main", "Operational Taxa-Functions (OTF) Table (head 200)"))
+        self.label_26.setText(_translate("metaX_main", "Operational Taxon-Function (OTF) Table (head 200)"))
         self.label_25.setText(_translate("metaX_main", "Meta Table"))
+        self.tableWidget_meta_view.setSortingEnabled(True)
+        self.tableWidget_taxa_func_view.setSortingEnabled(True)
         self.pushButton_overview_tax_plot_new_window.setText(_translate("metaX_main", "Plot taxa stats in new window"))
         self.pushButton_overview_peptide_plot_new_window.setText(_translate("metaX_main", "Plot peptide stats in new window"))
         self.label_154.setText(_translate("metaX_main", "Theme"))

metax/utils/version.py

@@ -1,2 +1,2 @@
-__version__ = '1.119.6'
+__version__ = '1.119.7'
 API_version = '4'

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MetaXTools"
-version = "1.119.6"
+version = "1.119.7"
 description = "MetaXTools is a novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics."
 readme = "README_PyPi.md"
 license = { text = "NorthOmics" }