dcscope 2.22.1__py3-none-any.whl

dcscope/gui/compute/comp_lme4_dataset.ui

@@ -0,0 +1,92 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Form</class>
+ <widget class="QWidget" name="Form">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>563</width>
+    <height>26</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QHBoxLayout" name="horizontalLayout">
+   <property name="leftMargin">
+    <number>0</number>
+   </property>
+   <property name="topMargin">
+    <number>0</number>
+   </property>
+   <property name="rightMargin">
+    <number>0</number>
+   </property>
+   <property name="bottomMargin">
+    <number>0</number>
+   </property>
+   <item>
+    <widget class="QCheckBox" name="checkBox_dataset">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="text">
+      <string>CheckBox</string>
+     </property>
+     <property name="checked">
+      <bool>true</bool>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QLabel" name="label_region">
+     <property name="text">
+      <string>pxm</string>
+     </property>
+     <property name="alignment">
+      <set>Qt::AlignCenter</set>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QComboBox" name="comboBox_group">
+     <property name="toolTip">
+      <string>group</string>
+     </property>
+     <item>
+      <property name="text">
+       <string>control</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>treatment</string>
+      </property>
+     </item>
+    </widget>
+   </item>
+   <item>
+    <widget class="QSpinBox" name="spinBox_repeat">
+     <property name="toolTip">
+      <string>repetition</string>
+     </property>
+     <property name="prefix">
+      <string>rep. </string>
+     </property>
+     <property name="minimum">
+      <number>1</number>
+     </property>
+     <property name="maximum">
+      <number>42</number>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

dcscope/gui/compute/comp_lme4_results.py

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+import pathlib
+import importlib.resources
+
+import dclab
+import numpy as np
+from PyQt6 import uic, QtCore, QtGui, QtWidgets
+
+
+class Rlme4ResultsDialog(QtWidgets.QDialog):
+    def __init__(self, parent, rlme4_results, *args, **kwargs):
+        super(Rlme4ResultsDialog, self).__init__(parent, *args, **kwargs)
+        ref = importlib.resources.files(
+            "dcscope.gui.compute") / "comp_lme4_results.ui"
+        with importlib.resources.as_file(ref) as path_ui:
+            uic.loadUi(path_ui, self)
+
+        res = rlme4_results
+
+        # parameters
+        self.label_model.setText(res["model"])
+        self.label_feature.setText(dclab.dfn.get_feature_label(res["feature"]))
+        if res["is differential"]:
+            self.label_differential.setText("Yes")
+        else:
+            self.label_differential.setText("No")
+
+        # results
+        if res["model converged"]:
+            self.label_yes.show()
+            self.label_no.hide()
+        else:
+            self.label_yes.hide()
+            self.label_no.show()
+        self.lineEdit_pvalue.setText(format_float(res["anova p-value"]))
+        self.lineEdit_intercept.setText(
+            format_float(res["fixed effects intercept"]))
+        self.lineEdit_treatment.setText(
+            format_float(res["fixed effects treatment"]))
+
+        # summary text
+        summary = []
+        if res["lme4 messages"]:
+            summary += ["lme4 messages"]
+            summary += ["-------------"]
+            summary += str(res["lme4 messages"]).split("\n")
+            summary += "\n"
+        summary += ["Model summary"]
+        summary += ["-------------"]
+        summary += self.parse_r_model_summary(
+            str(res["r model summary"]).split("\n"))
+        summary += "\n"
+        summary += ["Coefficient table"]
+        summary += ["-----------------"]
+        summary += str(res["r model coefficients"]).split("\n")
+        summary += "\n"
+        summary += ["Anova test"]
+        summary += ["----------"]
+        summary += str(res["r anova"]).split("\n")
+        excludelines = [
+            "$repetition",
+            'attr(,"clas',
+            '[1] "coef.m',
+            "Data: struc",
+        ]
+        summary = [ll for ll in summary if not ll[:11] in excludelines]
+
+        self.summary = summary
+        font = QtGui.QFont("Courier")
+        self.plainTextEdit.setFont(font)
+        self.plainTextEdit.setPlainText("\n".join(summary))
+
+        # button signals
+        btn_close = self.buttonBox.button(
+            QtWidgets.QDialogButtonBox.StandardButton.Close)
+        btn_close.clicked.connect(self.on_close)
+        btn_close.setToolTip("Close this dialog")
+        closeicon = QtGui.QIcon.fromTheme("dialog-close")
+        btn_close.setIcon(closeicon)
+        btn_openlme4 = self.buttonBox.button(
+            QtWidgets.QDialogButtonBox.StandardButton.Apply)
+        btn_openlme4.clicked.connect(self.on_save)
+        btn_openlme4.setToolTip("Save report as text file")
+        btn_openlme4.setText("Save report (.txt)")
+
+    @staticmethod
+    def parse_r_model_summary(slist):
+        """Parse model summary from R (remove data lines)"""
+        use = []
+        just_data = False
+        for line in slist:
+            if line.startswith("   Data: "):
+                just_data = True
+            elif line.startswith("REML criterion "):
+                just_data = False
+            if not just_data:
+                use.append(line)
+        return use
+
+    @QtCore.pyqtSlot()
+    def on_close(self):
+        """Close window"""
+        self.close()
+
+    @QtCore.pyqtSlot()
+    def on_save(self):
+        """Save summary text as .txt file"""
+        path, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, "Save summary", ".", "*.txt (*.txt files)")
+        if path:
+            path = pathlib.Path(path)
+            if path.suffix != ".txt":
+                path = path.with_name(path.name + ".txt")
+            path.write_text("\n".join(self.summary))
+
+
+def format_float(value):
+    return np.format_float_positional(value,
+                                      precision=5,
+                                      fractional=False,
+                                      trim="0")

dcscope/gui/compute/comp_lme4_results.ui

@@ -0,0 +1,268 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Dialog</class>
+ <widget class="QDialog" name="Dialog">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>684</width>
+    <height>573</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>R-lme4 results</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_2">
+     <item>
+      <widget class="QGroupBox" name="groupBox">
+       <property name="title">
+        <string>Parameters</string>
+       </property>
+       <layout class="QGridLayout" name="gridLayout">
+        <item row="2" column="1">
+         <widget class="QLabel" name="label_differential">
+          <property name="text">
+           <string>Yes/No</string>
+          </property>
+         </widget>
+        </item>
+        <item row="0" column="1">
+         <widget class="QLabel" name="label_model">
+          <property name="text">
+           <string>model</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="1">
+         <widget class="QLabel" name="label_feature">
+          <property name="text">
+           <string>feat</string>
+          </property>
+         </widget>
+        </item>
+        <item row="0" column="0">
+         <widget class="QLabel" name="label_5">
+          <property name="text">
+           <string>Model</string>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="0">
+         <widget class="QLabel" name="label_7">
+          <property name="text">
+           <string>Differential</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="0">
+         <widget class="QLabel" name="label_6">
+          <property name="text">
+           <string>Feature</string>
+          </property>
+         </widget>
+        </item>
+        <item row="3" column="0">
+         <spacer name="spacer_parms">
+          <property name="orientation">
+           <enum>Qt::Vertical</enum>
+          </property>
+          <property name="sizeType">
+           <enum>QSizePolicy::Fixed</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>20</width>
+            <height>30</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </widget>
+     </item>
+     <item>
+      <widget class="QGroupBox" name="groupBox_2">
+       <property name="title">
+        <string>Results</string>
+       </property>
+       <layout class="QGridLayout" name="gridLayout_2">
+        <item row="3" column="0">
+         <widget class="QLabel" name="label_3">
+          <property name="toolTip">
+           <string>The effect size of the parameter chosen between the mean of all controls and the mean of all treatments</string>
+          </property>
+          <property name="text">
+           <string>Fixed effect treatment</string>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="1">
+         <widget class="QLineEdit" name="lineEdit_intercept">
+          <property name="toolTip">
+           <string>The mean of the parameter chosen for all controls</string>
+          </property>
+          <property name="text">
+           <string>nan</string>
+          </property>
+          <property name="readOnly">
+           <bool>true</bool>
+          </property>
+         </widget>
+        </item>
+        <item row="3" column="1">
+         <widget class="QLineEdit" name="lineEdit_treatment">
+          <property name="toolTip">
+           <string>The effect size of the parameter chosen between the mean of all controls and the mean of all treatments</string>
+          </property>
+          <property name="text">
+           <string>nan</string>
+          </property>
+          <property name="readOnly">
+           <bool>true</bool>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="0">
+         <widget class="QLabel" name="label_2">
+          <property name="toolTip">
+           <string>The p-value of the ANOVA test</string>
+          </property>
+          <property name="text">
+           <string>Anova p-value</string>
+          </property>
+         </widget>
+        </item>
+        <item row="2" column="0">
+         <widget class="QLabel" name="label_4">
+          <property name="toolTip">
+           <string>The mean of the parameter chosen for all controls</string>
+          </property>
+          <property name="text">
+           <string>Fixed effect intercept</string>
+          </property>
+         </widget>
+        </item>
+        <item row="0" column="0">
+         <widget class="QLabel" name="label">
+          <property name="text">
+           <string>Model converged</string>
+          </property>
+         </widget>
+        </item>
+        <item row="0" column="1">
+         <layout class="QHBoxLayout" name="horizontalLayout">
+          <item>
+           <widget class="QLabel" name="label_yes">
+            <property name="styleSheet">
+             <string notr="true">QLabel {
+color: green;
+font-weight:600}</string>
+            </property>
+            <property name="text">
+             <string>Yes</string>
+            </property>
+           </widget>
+          </item>
+          <item>
+           <widget class="QLabel" name="label_no">
+            <property name="styleSheet">
+             <string notr="true">QLabel {
+color: red;
+font-weight:600}</string>
+            </property>
+            <property name="text">
+             <string>No</string>
+            </property>
+           </widget>
+          </item>
+          <item>
+           <spacer name="horizontalSpacer">
+            <property name="orientation">
+             <enum>Qt::Horizontal</enum>
+            </property>
+            <property name="sizeHint" stdset="0">
+             <size>
+              <width>0</width>
+              <height>0</height>
+             </size>
+            </property>
+           </spacer>
+          </item>
+         </layout>
+        </item>
+        <item row="1" column="1">
+         <widget class="QLineEdit" name="lineEdit_pvalue">
+          <property name="toolTip">
+           <string>The p-value of the ANOVA test</string>
+          </property>
+          <property name="text">
+           <string>nan</string>
+          </property>
+          <property name="readOnly">
+           <bool>true</bool>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <widget class="QPlainTextEdit" name="plainTextEdit">
+     <property name="readOnly">
+      <bool>true</bool>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Apply|QDialogButtonBox::Close</set>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>accepted()</signal>
+   <receiver>Dialog</receiver>
+   <slot>accept()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>227</x>
+     <y>553</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>157</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>rejected()</signal>
+   <receiver>Dialog</receiver>
+   <slot>reject()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>295</x>
+     <y>559</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>