def __init__(self, parent=None): widget.OWWidget.__init__(self, parent) self.min_value, self.max_value = \ self.thresholds.get(self.Scores[self.score_index][0], (1, 0)) #: Input data set self.data = None #: Current target group selection self.targets = [] #: The computed scores self.scores = None #: The computed scores from label permutations self.nulldist = None self.__scores_future = self.__scores_state = None self.__in_progress = False self.test_f = { OWFeatureSelection.LowTail: test_low, OWFeatureSelection.HighTail: test_high, OWFeatureSelection.TwoTail: test_two_tail, } self.histogram = Histogram(enableMouse=False, enableMenu=False, background="w") self.histogram.enableAutoRange(enable=True) self.histogram.getViewBox().setMouseEnabled(False, False) self.histogram.selectionChanged.connect( self.__on_histogram_plot_selection_changed) self.histogram.selectionEdited.connect(self._invalidate_selection) self.mainArea.layout().addWidget(self.histogram) box = gui.widgetBox(self.controlArea, "Info") self.dataInfoLabel = gui.widgetLabel(box, "No data on input.\n") self.dataInfoLabel.setWordWrap(True) self.selectedInfoLabel = gui.widgetLabel(box, "\n") box1 = gui.widgetBox(self.controlArea, "Scoring Method") gui.comboBox( box1, self, "score_index", items=[sm[0] for sm in self.Scores], callback=[self.on_scoring_method_changed, self.update_scores]) box = gui.widgetBox(self.controlArea, "Target Labels") self.label_selection_widget = guiutils.LabelSelectionWidget(self) self.label_selection_widget.setMaximumHeight(150) box.layout().addWidget(self.label_selection_widget) self.label_selection_widget.groupChanged.connect( self.on_label_activated) self.label_selection_widget.groupSelectionChanged.connect( self.on_target_changed) box = gui.widgetBox(self.controlArea, "Selection") box.layout().setSpacing(0) self.max_value_spin = gui.doubleSpin(box, self, "max_value", minv=-1e6, maxv=1e6, step=1e-6, label="Upper threshold:", callback=self.update_boundary, callbackOnReturn=True) self.low_value_spin = gui.doubleSpin(box, self, "min_value", minv=-1e6, maxv=1e6, step=1e-6, label="Lower threshold:", callback=self.update_boundary, callbackOnReturn=True) check = gui.checkBox(box, self, "compute_null", "Compute null distribution", callback=self.update_scores) perm_spin = gui.spin(box, self, "permutations_count", minv=1, maxv=50, label="Permutations:", callback=self.update_scores, callbackOnReturn=True) check.disables.append(perm_spin) box1 = gui.widgetBox(box, orientation='horizontal') pval_spin = gui.doubleSpin(box1, self, "alpha_value", minv=2e-7, maxv=1.0, step=1e-7, label="α-value:") pval_select = gui.button(box1, self, "Select", callback=self.select_p_best, autoDefault=False) check.disables.append(pval_spin) check.disables.append(pval_select) check.makeConsistent() box1 = gui.widgetBox(box, orientation='horizontal') gui.spin(box1, self, "n_best", 0, 10000, step=1, label="Best Ranked:") gui.button(box1, self, "Select", callback=self.select_n_best, autoDefault=False) box = gui.widgetBox(self.controlArea, "Output") acbox = gui.auto_commit(box, self, "auto_commit", "Commit", box=None) acbox.button.setDefault(True) gui.checkBox(box, self, "add_scores_to_output", "Add gene scores to output", callback=self._invalidate_selection) gui.rubber(self.controlArea) self.on_scoring_method_changed() self._executor = concurrent.ThreadExecutor()
def __init__(self): super().__init__() self.data = None # type: Optional[Orange.data.Table] self.learner = None # type: Optional[Learner] self.default_learner = SimpleTreeLearner() self.modified = False self.executor = qconcurrent.ThreadExecutor(self) self.__task = None main_layout = QVBoxLayout() main_layout.setContentsMargins(10, 10, 10, 10) self.controlArea.layout().addLayout(main_layout) box = QGroupBox(title=self.tr("Default Method"), flat=False) box_layout = QVBoxLayout(box) main_layout.addWidget(box) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for method, _ in list(METHODS.items())[1:-1]: imputer = self.create_imputer(method) button = QRadioButton(imputer.name) button.setChecked(method == self.default_method_index) button_group.addButton(button, method) box_layout.addWidget(button) self.default_button_group = button_group box = QGroupBox(title=self.tr("Individual Attribute Settings"), flat=False) main_layout.addWidget(box) horizontal_layout = QHBoxLayout(box) main_layout.addWidget(box) self.varview = QListView(selectionMode=QListView.ExtendedSelection, uniformItemSizes=True) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed) self.selection = self.varview.selectionModel() horizontal_layout.addWidget(self.varview) method_layout = QVBoxLayout() horizontal_layout.addLayout(method_layout) button_group = QButtonGroup() for method in Method: imputer = self.create_imputer(method) button = QRadioButton(text=imputer.name) button_group.addButton(button, method) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength, activated=self._on_value_selected) self.value_double = QDoubleSpinBox( editingFinished=self._on_value_selected, minimum=-1000., maximum=1000., singleStep=.1, decimals=3, ) self.value_stack = value_stack = QStackedWidget() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addWidget(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection) method_layout.addStretch(2) reset_button = QPushButton("Restore All to Default", checked=False, checkable=False, clicked=self.reset_variable_state, default=False, autoDefault=False) method_layout.addWidget(reset_button) self.variable_button_group = button_group box = gui.auto_commit(self.controlArea, self, "autocommit", "Apply", orientation=Qt.Horizontal, checkbox_label="Apply automatically") box.button.setFixedWidth(180) box.layout().insertStretch(0)
def __init__(self, parent=None): super().__init__(parent) self._changedFlag = False self.__invalidated = False self.__runstate = OWKEGGPathwayBrowser.Initializing self.__in_setProgress = False self.controlArea.setMaximumWidth(250) box = gui.widgetBox(self.controlArea, "Info") self.infoLabel = gui.widgetLabel(box, "No data on input\n") gui.separator(self.controlArea) gui.checkBox(self.controlArea, self, "useReference", "From signal", box="Reference", callback=self.Update) gui.separator(self.controlArea) gui.checkBox( self.controlArea, self, "showOrthology", "Show pathways in full orthology", box="Orthology", callback=self.UpdateListView, ) gui.checkBox( self.controlArea, self, "autoResize", "Resize to fit", box="Image", callback=self.UpdatePathwayViewTransform, ) box = gui.widgetBox(self.controlArea, "Cache Control") gui.button( box, self, "Clear cache", callback=self.ClearCache, tooltip="Clear all locally cached KEGG data.", default=False, autoDefault=False, ) gui.separator(self.controlArea) gui.auto_commit(self.controlArea, self, "autoCommit", "Commit") gui.rubber(self.controlArea) spliter = QSplitter(Qt.Vertical, self.mainArea) self.pathwayView = PathwayView(self, spliter) self.pathwayView.scene().selectionChanged.connect( self._onSelectionChanged) self.mainArea.layout().addWidget(spliter) self.listView = QTreeWidget(allColumnsShowFocus=True, selectionMode=QTreeWidget.SingleSelection, sortingEnabled=True, maximumHeight=200) spliter.addWidget(self.listView) self.listView.setColumnCount(4) self.listView.setHeaderLabels( ["Pathway", "P value", "Genes", "Reference"]) self.listView.itemSelectionChanged.connect(self.UpdatePathwayView) select = QAction("Select All", self, shortcut=QKeySequence.SelectAll) select.triggered.connect(self.selectAll) self.addAction(select) self.data = None self.input_genes = [] self.tax_id = None self.use_attr_names = None self.gene_id_attribute = None self.gene_id_column = None self.ref_data = None self.ref_genes = [] self.ref_tax_id = None self.ref_use_attr_names = None self.ref_gene_id_attribute = None self.ref_gene_id_column = None self.pathways = {} self.org = None self._executor = concurrent.ThreadExecutor() self.setEnabled(False) self.setBlocking(True) progress = concurrent.methodinvoke(self, "setProgress", (float, )) def get_genome(): """Return a KEGGGenome with the common org entries precached.""" genome = kegg.KEGGGenome() essential = genome.essential_organisms() common = genome.common_organisms() # Remove duplicates of essential from common. # (essential + common list as defined here will be used in the # GUI.) common = [c for c in common if c not in essential] # TODO: Add option to specify additional organisms not # in the common list. keys = list(map(genome.org_code_to_entry_key, essential + common)) genome.pre_cache(keys, progress_callback=progress) return (keys, genome) self._genomeTask = task = concurrent.Task(function=get_genome) task.finished.connect(self.__initialize_finish) self.progressBarInit() self.infoLabel.setText("Fetching organism definitions\n") self._executor.submit(task)
def __init__(self): super().__init__() self.data = None # type: Optional[Orange.data.Table] self.learner = None # type: Optional[Learner] self.default_learner = SimpleTreeLearner(min_instances=10, max_depth=10) self.modified = False self.executor = qconcurrent.ThreadExecutor(self) self.__task = None main_layout = self.controlArea.layout() box = gui.vBox(self.controlArea, "默认方法") box_layout = QGridLayout() box_layout.setSpacing(8) box.layout().addLayout(box_layout) button_group = QButtonGroup() button_group.buttonClicked[int].connect(self.set_default_method) for i, (method, _) in enumerate(list(METHODS.items())[1:-1]): imputer = self.create_imputer(method) button = QRadioButton(imputer.name) button.setChecked(method == self.default_method_index) button_group.addButton(button, method) box_layout.addWidget(button, i % 3, i // 3) def set_default_time(datetime): datetime = datetime.toSecsSinceEpoch() if datetime != self.default_time: self.default_time = datetime if self.default_method_index == Method.Default: self._invalidate() hlayout = QHBoxLayout() box.layout().addLayout(hlayout) button = QRadioButton("固定值; 数值变量:") button_group.addButton(button, Method.Default) button.setChecked(Method.Default == self.default_method_index) hlayout.addWidget(button) self.numeric_value_widget = DoubleSpinBox( minimum=DBL_MIN, maximum=DBL_MAX, singleStep=.1, value=self.default_numeric_value, alignment=Qt.AlignRight, enabled=self.default_method_index == Method.Default, ) self.numeric_value_widget.editingFinished.connect( self.__on_default_numeric_value_edited) self.connect_control("default_numeric_value", self.numeric_value_widget.setValue) hlayout.addWidget(self.numeric_value_widget) hlayout.addWidget(QLabel(", 时间:")) self.time_widget = gui.DateTimeEditWCalendarTime(self) self.time_widget.setEnabled( self.default_method_index == Method.Default) self.time_widget.setKeyboardTracking(False) self.time_widget.setContentsMargins(0, 0, 0, 0) self.time_widget.set_datetime( QDateTime.fromSecsSinceEpoch(self.default_time)) self.connect_control( "default_time", lambda value: self.time_widget.set_datetime( QDateTime.fromSecsSinceEpoch(value))) self.time_widget.dateTimeChanged.connect(set_default_time) hlayout.addWidget(self.time_widget) self.default_button_group = button_group box = gui.hBox(self.controlArea, self.tr("设置单个属性"), flat=False) self.varview = ListViewSearch( selectionMode=QListView.ExtendedSelection, uniformItemSizes=True) self.varview.setItemDelegate(DisplayFormatDelegate()) self.varmodel = itemmodels.VariableListModel() self.varview.setModel(self.varmodel) self.varview.selectionModel().selectionChanged.connect( self._on_var_selection_changed) self.selection = self.varview.selectionModel() box.layout().addWidget(self.varview) vertical_layout = QVBoxLayout(margin=0) self.methods_container = QWidget(enabled=False) method_layout = QVBoxLayout(margin=0) self.methods_container.setLayout(method_layout) button_group = QButtonGroup() for method in Method: imputer = self.create_imputer(method) button = QRadioButton(text=imputer.name) button_group.addButton(button, method) method_layout.addWidget(button) self.value_combo = QComboBox( minimumContentsLength=8, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon, activated=self._on_value_selected) self.value_double = DoubleSpinBox( editingFinished=self._on_value_selected, minimum=DBL_MIN, maximum=DBL_MAX, singleStep=.1, ) self.value_stack = value_stack = QStackedWidget() value_stack.addWidget(self.value_combo) value_stack.addWidget(self.value_double) method_layout.addWidget(value_stack) button_group.buttonClicked[int].connect( self.set_method_for_current_selection) self.reset_button = QPushButton( "Restore All to Default", enabled=False, default=False, autoDefault=False, clicked=self.reset_variable_state, ) vertical_layout.addWidget(self.methods_container) vertical_layout.addStretch(2) vertical_layout.addWidget(self.reset_button) box.layout().addLayout(vertical_layout) self.variable_button_group = button_group gui.auto_apply(self.buttonsArea, self, "autocommit")
def __init__(self, parent=None): super().__init__(parent) self.selectedDatabase = 0 self.uniqueRows = True gui.button(gui.widgetBox(self.controlArea, "Cache", addSpace=True), self, "Clear cache", tooltip="Clear saved query results", callback=self.clearCache) self.serviceindex = 0 self.serviceCombo = gui.comboBox(self.controlArea, self, "serviceindex", "Mart Service", callback=self._setServiceUrl) for name, url in MartServices: self.serviceCombo.addItem(name, userData=url) idx = self.serviceCombo.findData(self.selectedService, Qt.UserRole) self.serviceCombo.setCurrentIndex(idx) # self.selectedService = self.serviceCombo.itemData(self.serviceCombo.currentItem()) self.martsCombo = gui.comboBox(self.controlArea, self, "selectedDatabase", "Database", callback=self.setSelectedMart, addSpace=True) self.martsCombo.setMaximumWidth(250) self.datasetsCombo = gui.comboBox(self.controlArea, self, "selectedDataset", "Dataset", callback=self.setSelectedDataset, addSpace=True) self.datasetsCombo.setMaximumWidth(250) gui.rubber(self.controlArea) box = gui.widgetBox(self.controlArea, "Results") gui.checkBox( box, self, "uniqueRows", "Unique results only", tooltip="Return unique results only.", ) self.commitButton = gui.button( box, self, "Get Results", callback=self.commit, tooltip="Query the BioMart server and output the results", autoDefault=True) self.commitButton.setEnabled(False) self.mainWidget = gui.widgetBox(self.mainArea, orientation=QStackedLayout()) self.mainTab = QTabWidget() self.mainWidget.layout().addWidget(self.mainTab) self.attributesConfigurationBox = gui.createTabPage( self.mainTab, "Attributes") if self.SHOW_FILTERS: # ?? self.filtersConfigurationBox = gui.createTabPage( self.mainTab, "Filters") self.error(0) self.setEnabled(False) self._task = None self._executor = concurrent.ThreadExecutor(threadPool=QThreadPool( maxThreadCount=2)) service = self.selectedService self._task = task = concurrent.Task( function=partial(self._get_registry, url=service)) task.resultReady.connect(self.setBioMartRegistry) task.exceptionReady.connect(self._handleException) self._executor.submit(task) self._setServiceUrl() self._afterInitQueue = [] try: from Bio import SeqIO self.hasBiopython = True except ImportError: self.warning( 100, "Biopython package not found.\nTo retrieve FASTA sequence data from BioMart install Biopython." ) self.hasBiopython = False
def __init__(self, parent=None): super().__init__(parent) # GUI box = gui.widgetBox(self.controlArea, "Info", addSpace=True) self.infoBox = gui.widgetLabel(box, "No data on input.") box = gui.widgetBox(self.controlArea, "Split by", addSpace=True) self.groupCombo = gui.comboBox(box, self, "selectedGroup", callback=self.onGroupSelection) gui.comboBox(self.controlArea, self, "selectedCenterMethod", box="Center Fold-change Using", items=[name for name, _ in self.CENTER_METHODS], callback=self.onCenterMethodChange, addSpace=True) gui.comboBox(self.controlArea, self, "selectedMergeMethod", box="Merge Replicates", items=[name for name, _ in self.MERGE_METHODS], tooltip="Select the method for replicate merging", callback=self.onMergeMethodChange, addSpace=True) box = gui.doubleSpin(self.controlArea, self, "zCutoff", 0.0, 3.0, 0.01, box="Z-Score Cutoff", callback=[self.replotMA, self.commitIf]) gui.separator(self.controlArea) box = gui.widgetBox(self.controlArea, "Ouput") gui.checkBox(box, self, "appendZScore", "Append Z-Scores", tooltip="Append calculated Z-Scores to output", callback=self.commitIf) gui.checkBox(box, self, "appendRIValues", "Append Log Ratio and Intensity values", tooltip="Append calculated Log Ratio and Intensity " "values to output data", callback=self.commitIf) gui.rubber(self.controlArea) gui.auto_commit(self.controlArea, self, "autoCommit", "Commit") self.graph = pg.PlotWidget(background="w") self.graph.getAxis("bottom").setLabel( "Intensity: log<sub>10</sub>(R*G)") self.graph.getAxis("left").setLabel("Log ratio: log<sub>2</sub>(R/G)") self.mainArea.layout().addWidget(self.graph) self.groups = [] self.split_data = None, None self.merged_splits = None, None self.centered = None, None self.changedFlag = False self.data = None self._executor = concurrent.ThreadExecutor(threadPool=QThreadPool( maxThreadCount=1))