Merge branch 'dev'

byemaxx · Aug 20, 2024 · efb80e3 · efb80e3
2 parents 44756c9 + e715dec
commit efb80e3
Show file tree

Hide file tree

Showing 7 changed files with 48 additions and 40 deletions.
diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,10 @@
+# Version: 1.110.1
+## Date: 2024-08-20
+### Changes:
+- Fix: Fixed the bug of sum protein by anti-razor method.
+- Change: Changed the default color of the heatmap plot to make the color more clear.
+
+
 # Version: 1.110.0
 ## Date: 2024-08-12
 ### Changes:

diff --git a/metax/gui/metax_gui/main_window.ui b/metax/gui/metax_gui/main_window.ui
@@ -46,7 +46,7 @@
            <enum>Qt::LeftToRight</enum>
           </property>
           <property name="currentIndex">
-           <number>3</number>
+           <number>6</number>
           </property>
           <property name="documentMode">
            <bool>false</bool>
@@ -2803,22 +2803,22 @@
                              </property>
                              <item>
                               <property name="text">
-                               <string>row</string>
+                               <string>None</string>
                               </property>
                              </item>
                              <item>
                               <property name="text">
-                               <string>col</string>
+                               <string>row</string>
                               </property>
                              </item>
                              <item>
                               <property name="text">
-                               <string>all</string>
+                               <string>col</string>
                               </property>
                              </item>
                              <item>
                               <property name="text">
-                               <string>None</string>
+                               <string>all</string>
                               </property>
                              </item>
                             </widget>
@@ -3674,7 +3674,7 @@
                       <rect>
                        <x>0</x>
                        <y>0</y>
-                       <width>1020</width>
+                       <width>929</width>
                        <height>126</height>
                       </rect>
                      </property>
@@ -5542,8 +5542,8 @@
                           <rect>
                            <x>0</x>
                            <y>0</y>
-                           <width>996</width>
-                           <height>140</height>
+                           <width>535</width>
+                           <height>94</height>
                           </rect>
                          </property>
                          <layout class="QGridLayout" name="gridLayout_68">
@@ -8171,8 +8171,8 @@
                        <rect>
                         <x>0</x>
                         <y>0</y>
-                        <width>775</width>
-                        <height>102</height>
+                        <width>1016</width>
+                        <height>185</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_69">
@@ -8550,22 +8550,22 @@
                              </property>
                              <item>
                               <property name="text">
-                               <string>row</string>
+                               <string>None</string>
                               </property>
                              </item>
                              <item>
                               <property name="text">
-                               <string>column</string>
+                               <string>row</string>
                               </property>
                              </item>
                              <item>
                               <property name="text">
-                               <string>all</string>
+                               <string>column</string>
                               </property>
                              </item>
                              <item>
                               <property name="text">
-                               <string>None</string>
+                               <string>all</string>
                               </property>
                              </item>
                             </widget>

diff --git a/metax/gui/metax_gui/ui_main_window.py b/metax/gui/metax_gui/ui_main_window.py
@@ -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, 1020, 126))
+        self.scrollAreaWidgetContents_3.setGeometry(QtCore.QRect(0, 0, 929, 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, 140))
+        self.scrollAreaWidgetContents_4.setGeometry(QtCore.QRect(0, 0, 535, 94))
         self.scrollAreaWidgetContents_4.setObjectName("scrollAreaWidgetContents_4")
         self.gridLayout_68 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_4)
         self.gridLayout_68.setObjectName("gridLayout_68")
@@ -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, 775, 102))
+        self.scrollAreaWidgetContents_7.setGeometry(QtCore.QRect(0, 0, 1016, 185))
         self.scrollAreaWidgetContents_7.setObjectName("scrollAreaWidgetContents_7")
         self.gridLayout_69 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_7)
         self.gridLayout_69.setObjectName("gridLayout_69")
@@ -5336,7 +5336,7 @@ def setupUi(self, metaX_main):
 
         self.retranslateUi(metaX_main)
         self.stackedWidget.setCurrentIndex(0)
-        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(3)
+        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(6)
         self.toolBox_2.setCurrentIndex(0)
         self.tabWidget_4.setCurrentIndex(1)
         self.tabWidget_3.setCurrentIndex(3)
@@ -5615,10 +5615,10 @@ def retranslateUi(self, metaX_main):
         self.label_185.setText(_translate("metaX_main", "Bar"))
         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", "col"))
-        self.comboBox_basic_hetatmap_scale.setItemText(2, _translate("metaX_main", "all"))
-        self.comboBox_basic_hetatmap_scale.setItemText(3, _translate("metaX_main", "None"))
+        self.comboBox_basic_hetatmap_scale.setItemText(0, _translate("metaX_main", "None"))
+        self.comboBox_basic_hetatmap_scale.setItemText(1, _translate("metaX_main", "row"))
+        self.comboBox_basic_hetatmap_scale.setItemText(2, _translate("metaX_main", "col"))
+        self.comboBox_basic_hetatmap_scale.setItemText(3, _translate("metaX_main", "all"))
         self.label_13.setText(_translate("metaX_main", "Theme"))
         self.checkBox_basic_hetatmap_row_cluster.setText(_translate("metaX_main", "Row Cluster"))
         self.label_183.setText(_translate("metaX_main", "General"))
@@ -5952,10 +5952,10 @@ def retranslateUi(self, metaX_main):
         self.checkBox_tflink_bar_show_legend.setText(_translate("metaX_main", "Show Legend"))
         self.checkBox_tflink_hetatmap_row_cluster.setText(_translate("metaX_main", "Row Cluster"))
         self.label_23.setText(_translate("metaX_main", "Scale"))
-        self.comboBox_tflink_hetatmap_scale.setItemText(0, _translate("metaX_main", "row"))
-        self.comboBox_tflink_hetatmap_scale.setItemText(1, _translate("metaX_main", "column"))
-        self.comboBox_tflink_hetatmap_scale.setItemText(2, _translate("metaX_main", "all"))
-        self.comboBox_tflink_hetatmap_scale.setItemText(3, _translate("metaX_main", "None"))
+        self.comboBox_tflink_hetatmap_scale.setItemText(0, _translate("metaX_main", "None"))
+        self.comboBox_tflink_hetatmap_scale.setItemText(1, _translate("metaX_main", "row"))
+        self.comboBox_tflink_hetatmap_scale.setItemText(2, _translate("metaX_main", "column"))
+        self.comboBox_tflink_hetatmap_scale.setItemText(3, _translate("metaX_main", "all"))
         self.label_61.setText(_translate("metaX_main", "Theme"))
         self.tabWidget_2.setTabText(self.tabWidget_2.indexOf(self.tab_8), _translate("metaX_main", "Taxa-Func Link"))
         self.radioButton_network_bysample.setText(_translate("metaX_main", "Sample"))

diff --git a/metax/taxafunc_analyzer/analyzer_utils/sum_protein_intensity.py b/metax/taxafunc_analyzer/analyzer_utils/sum_protein_intensity.py
@@ -317,7 +317,8 @@ def _sum_protein_rank(self, sample_name:str, by_sample=False):
     def _sum_protein_anti_razor(self, sample_name:str):
         print(f'Creating protein intensity dict for [{sample_name}]', end='\r')
         df = self.df.loc[:,[ self.tfa.protein_col_name, sample_name]]
-
+        self.share_intensity = True
+
         for row in df.itertuples():
             proteins = row[1].split(';')
             intensity = row[2]

diff --git a/metax/taxafunc_ploter/heatmap_plot.py b/metax/taxafunc_ploter/heatmap_plot.py
@@ -101,8 +101,8 @@ def plot_top_taxa_func_heatmap_of_test_res(self, df, top_number:int|str= 100,
             sns_params = {
                 'center': 0 if data_include_negative_and_positive else None,
                 "cmap": cmap,
-                "linewidths": 0.5, 
-                "linecolor": 'gray',
+                "linewidths": 0.01, 
+                "linecolor": (0 ,0 ,0 ,0.1),
                 "dendrogram_ratio": (0.1, 0.2),
                 "figsize": fig_size if return_type == 'fig' else None,
                 "col_cluster": col_cluster,
@@ -255,8 +255,8 @@ def plot_basic_heatmap_of_test_res(self, df, top_number:int = 100, value_type:st
             sns_params = {
                 "center": 0 if data_include_negative_and_positive else None,
                 "cmap": cmap,
-                "linewidths": 0.5, 
-                "linecolor": 'gray',
+                "linewidths": 0.01, 
+                "linecolor": (0 ,0 ,0 ,0.01),
                 "figsize": fig_size if return_type == 'fig' else None,
                 "cbar_kws": {"label": "Intensity", "shrink": 0.5},
                 "col_cluster": col_cluster,
@@ -341,7 +341,7 @@ def plot_basic_heatmap(self,  df, title = 'Heatmap',fig_size:tuple|None = None,
             mat = self.rename_taxa(mat)
 
         if cmap is None:
-            cmap = 'Spectral_r'
+            cmap = 'YlOrRd'
         if fig_size is None:
             fig_size = (30,30)
 
@@ -357,11 +357,11 @@ def plot_basic_heatmap(self,  df, title = 'Heatmap',fig_size:tuple|None = None,
 
 
         sns_params = {
-            "center": 0,
+            # "center": 0,
             "cmap": cmap,
             "figsize": fig_size,
             "linewidths": 0.01,
-            "linecolor": (0 / 255, 0 / 255, 0 / 255, 0.01),
+            "linecolor": (0 ,0 ,0 ,0.01),
             "dendrogram_ratio": (0.1, 0.2),
             "cbar_kws": {"label": "Intensity", "shrink": 0.5},
             "col_cluster": col_cluster,
@@ -504,8 +504,8 @@ def plot_heatmap_of_all_condition_res(self, df,  pvalue:float = 0.05,scale:str|N
                 "cmap": cmap,
                 "figsize": fig_size,
                 "norm": norm,
-                "linewidths": 0.01,
-                "linecolor": (0 / 255, 0 / 255, 0 / 255, 0.01),
+                "linewidths": 0.01, 
+                "linecolor": (0 ,0 ,0 ,0.01),
                 "dendrogram_ratio": (0.1, 0.2),
                 "col_cluster": col_cluster,
                 "row_cluster": row_cluster,
@@ -638,8 +638,8 @@ def plot_heatmap_of_dunnett_test_res(self, df,  pvalue:float = 0.05,scale:str|No
                 "cmap": cmap,
                 "figsize": fig_size,
                 "norm": norm,
-                "linewidths": 0.01,
-                "linecolor": (0 / 255, 0 / 255, 0 / 255, 0.01),
+                "linewidths": 0.01, 
+                "linecolor": (0 ,0 ,0 ,0.01),
                 "dendrogram_ratio": (0.1, 0.2),
                 "cbar_kws": {"label": "t-statistic", "shrink": 0.5},
                 "col_cluster": col_cluster,

diff --git a/metax/utils/version.py b/metax/utils/version.py
@@ -1,2 +1,2 @@
-__version__ = '1.110.0'
+__version__ = '1.110.1'
 API_version = '2'
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MetaXTools"
-version = "1.110.0"
+version = "1.110.1"
 description = "MetaXTools is a novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics."
 readme = "README_PyPi.md"
 license = { text = "NorthOmics" }