Merge branch 'dev'

Docs/ChangeLog.md

@@ -1,3 +1,46 @@
+# Version: 1.109.11
+## Date: 2024-08-10
+### Changes:
+- Fix: Fixed the scale method and color bar of heatmap for Cross Test result table.
+
+# Version: 1.109.10
+## Date: 2024-08-9
+### Changes:
+- Fix: Fixed the of test result table, the t-statistic was reversed.
+- New: adde z-score for heatmap scale.
+
+
+# Version: 1.109.9
+## Date: 2024-08-7
+### Changes:
+- Fix: Fixed the bug when restore the object, some cross_test top table was added to the GUI by wrong.
+- Change: Changed the "pixel_ratio" from 2 to 3 for the HTML plot to make the plot more clear.
+
+
+# Version: 1.109.8
+## Date: 2024-08-1
+### Changes:
+- Fix: Fixed title of the static volcano plot.
+- New: added theme option for the static volcano plot.
+
+
+# Version: 1.109.7
+## Date: 2024-07-31
+### Changes:
+- Change: Optimized the volcano plot.
+
+# Version: 1.109.6
+## Date: 2024-07-31
+### Changes:
+- Change: Optimized the Sankey plot.
+
+
+# Version: 1.109.6
+## Date: 2024-07-31
+### Changes:
+- New: Added a checkbox to enable user to plot 2D or 3D bar plot for the baisc plot part with sub meta.
+
+
 # Version: 1.109.5
 ## Date: 2024-07-25
 ### Changes:

metax/gui/metax_gui/setting_window.ui

@@ -17,7 +17,7 @@
  <item row="0" column="0">
  <widget class="QToolBox" name="toolBox">
  <property name="currentIndex">
- <number>2</number>
+ <number>0</number>
  </property>
  <widget class="QWidget" name="page">
  <property name="geometry">
@@ -159,7 +159,7 @@
  <number>100000</number>
  </property>
  <property name="singleStep">
- <number>10</number>
+ <number>50</number>
  </property>
  <property name="value">
  <number>500</number>
@@ -316,7 +316,7 @@
  <double>1.000000000000000</double>
  </property>
  <property name="singleStep">
- <double>0.100000000000000</double>
+ <double>0.010000000000000</double>
  </property>
  <property name="value">
  <double>0.200000000000000</double>
@@ -673,6 +673,14 @@
  </layout>
  </widget>
  <widget class="QWidget" name="page_3">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>748</width>
+ <height>340</height>
+ </rect>
+ </property>
  <attribute name="label">
  <string>Others</string>
  </attribute>

metax/gui/metax_gui/ui_setting_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\utils\MetaX_GUI\Setting.ui'
+# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\setting_window.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -83,7 +83,7 @@ def setupUi(self, Settings):
  self.gridLayout_7.addWidget(self.label_18, 2, 0, 1, 1)
  self.spinBox_tf_link_net_repulsion = QtWidgets.QSpinBox(self.page_2)
  self.spinBox_tf_link_net_repulsion.setMaximum(100000)
- self.spinBox_tf_link_net_repulsion.setSingleStep(10)
+ self.spinBox_tf_link_net_repulsion.setSingleStep(50)
  self.spinBox_tf_link_net_repulsion.setProperty("value", 500)
  self.spinBox_tf_link_net_repulsion.setObjectName("spinBox_tf_link_net_repulsion")
  self.gridLayout_7.addWidget(self.spinBox_tf_link_net_repulsion, 1, 1, 1, 1)
@@ -145,7 +145,7 @@ def setupUi(self, Settings):
  self.gridLayout_7.addWidget(self.label_19, 1, 2, 1, 1)
  self.doubleSpinBox_tf_link_net_gravity = QtWidgets.QDoubleSpinBox(self.page_2)
  self.doubleSpinBox_tf_link_net_gravity.setMaximum(1.0)
- self.doubleSpinBox_tf_link_net_gravity.setSingleStep(0.1)
+ self.doubleSpinBox_tf_link_net_gravity.setSingleStep(0.01)
  self.doubleSpinBox_tf_link_net_gravity.setProperty("value", 0.2)
  self.doubleSpinBox_tf_link_net_gravity.setObjectName("doubleSpinBox_tf_link_net_gravity")
  self.gridLayout_7.addWidget(self.doubleSpinBox_tf_link_net_gravity, 1, 3, 1, 1)
@@ -275,6 +275,7 @@ def setupUi(self, Settings):
  self.gridLayout_4.addWidget(self.label, 1, 0, 1, 1)
  self.toolBox.addItem(self.page_2, "")
  self.page_3 = QtWidgets.QWidget()
+ self.page_3.setGeometry(QtCore.QRect(0, 0, 748, 340))
  self.page_3.setObjectName("page_3")
  self.gridLayout_11 = QtWidgets.QGridLayout(self.page_3)
  self.gridLayout_11.setObjectName("gridLayout_11")
@@ -296,7 +297,7 @@ def setupUi(self, Settings):
  self.gridLayout.addWidget(self.toolBox, 0, 0, 1, 1)
 
  self.retranslateUi(Settings)
- self.toolBox.setCurrentIndex(2)
+ self.toolBox.setCurrentIndex(0)
  QtCore.QMetaObject.connectSlotsByName(Settings)
 
  def retranslateUi(self, Settings):

metax/taxafunc_analyzer/analyzer_utils/cross_test.py

@@ -151,6 +151,10 @@ def get_stats_ttest(self, group_list: list = None, df_type: str = 'taxa-func', c
  res["t-statistic"].append(t)
 
  res = pd.DataFrame(res)
+
+ # print('reverse the t-statistic value due to the order of group_list is not correct')
+ res['t-statistic'] = -res['t-statistic']
+
  on_values = [primary]
  if df_type in ['taxa-func', 'func-taxa']:
  on_values.append(secondary)

metax/taxafunc_ploter/bar_plot_js.py

@@ -49,7 +49,7 @@ def plot_intensity_bar(self, taxon_name:str=None, sample_list:list = None,
  show_legend:bool=True, font_size:int=10,
  rename_sample:bool=True, plot_mean:bool=False,
  plot_percent:bool=False, sub_meta:str="None",
- show_all_labels:tuple = (False, False)
+ show_all_labels:tuple = (False, False), use_3d:bool=False
  ):
  if df is None:
  df = self.tfa.GetMatrix.get_intensity_matrix(taxon_name=taxon_name, func_name=func_name, peptide_seq=peptide_seq, sample_list= sample_list)
@@ -64,6 +64,11 @@ def plot_intensity_bar(self, taxon_name:str=None, sample_list:list = None,
 
  rename_sample = False
 
+ if use_3d:
+ if sub_meta == "None":
+ use_3d = False
+ print('sub_meta must be provided for 3D bar plot, use 2D bar plot instead')
+
  # rename taxa
  if rename_taxa:
  df = self.rename_taxa(df)
@@ -121,7 +126,7 @@ def plot_intensity_bar(self, taxon_name:str=None, sample_list:list = None,
  save_as_image=opts.ToolBoxFeatureSaveAsImageOpts(
  type_="png",
  background_color="black" if self.theme == 'dark' else "white",
- pixel_ratio=2,
+ pixel_ratio=3,
  title="Save as PNG",
  ),
  restore=opts.ToolBoxFeatureRestoreOpts(title="Restore"),
@@ -157,7 +162,9 @@ def plot_intensity_bar(self, taxon_name:str=None, sample_list:list = None,
  }
 
 
- if sub_meta == "None":
+ if not use_3d:
+ if sub_meta != "None":
+ df, _ = self.tfa.BasicStats.get_combined_sub_meta_df(df=df, sub_meta=sub_meta, rename_sample=rename_sample, plot_mean=plot_mean)
  colors = self.get_distinct_colors(col_num, convert=True)
 
  c = (
@@ -252,7 +259,7 @@ def plot_intensity_bar(self, taxon_name:str=None, sample_list:list = None,
  feature=opts.ToolBoxFeatureOpts( 
  save_as_image=opts.ToolBoxFeatureSaveAsImageOpts(type_="png", 
  background_color="black" if self.theme == 'dark' else "white", 
- pixel_ratio=2, 
+ pixel_ratio=3, 
  title="Save as PNG"),
  restore=opts.ToolBoxFeatureRestoreOpts(title="Restore"),
  data_zoom=opts.ToolBoxFeatureDataZoomOpts(zoom_title="Zoom",