def __init__(self): super().__init__() dbox = gui.widgetBox(self.controlArea, "Image values") rbox = gui.radioButtons( dbox, self, "value_type", callback=self._change_integration) gui.appendRadioButton(rbox, "From spectra") self.box_values_spectra = gui.indentedBox(rbox) gui.comboBox( self.box_values_spectra, self, "integration_method", valueType=int, items=(a.name for a in self.integration_methods), callback=self._change_integral_type) gui.rubber(self.controlArea) gui.appendRadioButton(rbox, "Use feature") self.box_values_feature = gui.indentedBox(rbox) self.feature_value_model = DomainModel(DomainModel.METAS | DomainModel.CLASSES, valid_types=DomainModel.PRIMITIVE) self.feature_value = gui.comboBox( self.box_values_feature, self, "attr_value", callback=self.update_feature_value, model=self.feature_value_model, sendSelectedValue=True, valueType=str) splitter = QSplitter(self) splitter.setOrientation(Qt.Vertical) self.imageplot = ImagePlot(self) self.imageplot.selection_changed.connect(self.output_image_selection) self.curveplot = CurvePlotHyper(self, select=SELECTONE) self.curveplot.selection_changed.connect(self.redraw_data) self.curveplot.plot.vb.x_padding = 0.005 # pad view so that lines are not hidden splitter.addWidget(self.imageplot) splitter.addWidget(self.curveplot) self.mainArea.layout().addWidget(splitter) self.line1 = MovableVline(position=self.lowlim, label="", report=self.curveplot) self.line1.sigMoved.connect(lambda v: setattr(self, "lowlim", v)) self.line2 = MovableVline(position=self.highlim, label="", report=self.curveplot) self.line2.sigMoved.connect(lambda v: setattr(self, "highlim", v)) self.line3 = MovableVline(position=self.choose, label="", report=self.curveplot) self.line3.sigMoved.connect(lambda v: setattr(self, "choose", v)) for line in [self.line1, self.line2, self.line3]: line.sigMoveFinished.connect(self.changed_integral_range) self.curveplot.add_marking(line) line.hide() self.data = None self.disable_integral_range = False self.resize(900, 700) self._update_integration_type() # prepare interface according to the new context self.contextAboutToBeOpened.connect(lambda x: self.init_interface_data(x[0]))
def test_dock(self): reg = registry_tests.small_testing_registry() reg = QtWidgetRegistry(reg, parent=self.app) toolbox = WidgetToolBox() toolbox.setObjectName("widgets-toolbox") toolbox.setModel(reg.model()) text = QTextEdit() splitter = QSplitter() splitter.setOrientation(Qt.Vertical) splitter.addWidget(toolbox) splitter.addWidget(text) dock = CollapsibleDockWidget() dock.setExpandedWidget(splitter) toolbar = QToolBar() toolbar.addAction("1") toolbar.setOrientation(Qt.Vertical) toolbar.setMovable(False) toolbar.setFloatable(False) dock.setCollapsedWidget(toolbar) dock.show() self.qWait()
def test_dock(self): reg = global_registry() reg = QtWidgetRegistry(reg, parent=self.app) toolbox = WidgetToolBox() toolbox.setObjectName("widgets-toolbox") toolbox.setModel(reg.model()) text = QTextEdit() splitter = QSplitter() splitter.setOrientation(Qt.Vertical) splitter.addWidget(toolbox) splitter.addWidget(text) dock = CollapsibleDockWidget() dock.setExpandedWidget(splitter) toolbar = QToolBar() toolbar.addAction("1") toolbar.setOrientation(Qt.Vertical) toolbar.setMovable(False) toolbar.setFloatable(False) dock.setCollapsedWidget(toolbar) dock.show() self.app.exec_()
def __init__(self): super().__init__() dbox = gui.widgetBox(self.controlArea, "Image values") rbox = gui.radioButtons( dbox, self, "value_type", callback=self._change_integration) gui.appendRadioButton(rbox, "From spectra") self.box_values_spectra = gui.indentedBox(rbox) gui.comboBox( self.box_values_spectra, self, "integration_method", valueType=int, items=(a.name for a in self.integration_methods), callback=self._change_integral_type) gui.rubber(self.controlArea) gui.appendRadioButton(rbox, "Use feature") self.box_values_feature = gui.indentedBox(rbox) self.feature_value_model = DomainModel(DomainModel.METAS | DomainModel.CLASSES, valid_types=DomainModel.PRIMITIVE) self.feature_value = gui.comboBox( self.box_values_feature, self, "attr_value", callback=self.update_feature_value, model=self.feature_value_model, sendSelectedValue=True, valueType=str) splitter = QSplitter(self) splitter.setOrientation(Qt.Vertical) self.imageplot = ImagePlot(self, self.image_selection_changed) self.curveplot = CurvePlotHyper(self, select=SELECTONE) self.curveplot.plot.vb.x_padding = 0.005 # pad view so that lines are not hidden splitter.addWidget(self.imageplot) splitter.addWidget(self.curveplot) self.mainArea.layout().addWidget(splitter) self.line1 = MovableVlineWD(position=self.lowlim, label="", setvalfn=self.set_lowlim, confirmfn=self.edited, report=self.curveplot) self.line2 = MovableVlineWD(position=self.highlim, label="", setvalfn=self.set_highlim, confirmfn=self.edited, report=self.curveplot) self.line3 = MovableVlineWD(position=self.choose, label="", setvalfn=self.set_choose, confirmfn=self.edited, report=self.curveplot) self.curveplot.add_marking(self.line1) self.curveplot.add_marking(self.line2) self.curveplot.add_marking(self.line3) self.line1.hide() self.line2.hide() self.line3.hide() self.data = None self.resize(900, 700) self.graph_name = "imageplot.plotview" self._update_integration_type()
class CanvasToolDock(QWidget): """Canvas dock widget with widget toolbox, quick help and canvas actions. """ def __init__(self, parent=None, **kwargs): super().__init__(parent, **kwargs) self.__setupUi() def __setupUi(self): layout = QVBoxLayout() layout.setContentsMargins(0, 0, 0, 0) layout.setSpacing(0) self.toolbox = WidgetToolBox() self.help = QuickHelpWidget(objectName="quick-help") self.__splitter = QSplitter() self.__splitter.setOrientation(Qt.Vertical) self.__splitter.addWidget(self.toolbox) self.__splitter.addWidget(self.help) self.toolbar = DynamicResizeToolBar() self.toolbar.setMovable(False) self.toolbar.setFloatable(False) self.toolbar.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Preferred) layout.addWidget(self.__splitter, 10) layout.addWidget(self.toolbar) self.setLayout(layout) self.__splitterResizer = SplitterResizer(self) self.__splitterResizer.setSplitterAndWidget(self.__splitter, self.help) def setQuickHelpVisible(self, state): """Set the quick help box visibility status. """ self.__splitterResizer.setExpanded(state) def quickHelpVisible(self): return self.__splitterResizer.expanded() def setQuickHelpAnimationEnabled(self, enabled): """Enable/disable the quick help animation. """ self.__splitterResizer.setAnimationEnabled(enabled) def toogleQuickHelpAction(self): """Return a checkable QAction for help show/hide. """ return self.__splitterResizer.toogleExpandedAction()
class CanvasToolDock(QWidget): """Canvas dock widget with widget toolbox, quick help and canvas actions. """ def __init__(self, parent=None, **kwargs): QWidget.__init__(self, parent, **kwargs) self.__setupUi() def __setupUi(self): layout = QVBoxLayout() layout.setContentsMargins(0, 0, 0, 0) layout.setSpacing(0) self.toolbox = WidgetToolBox() self.help = QuickHelpWidget(objectName="quick-help") self.__splitter = QSplitter() self.__splitter.setOrientation(Qt.Vertical) self.__splitter.addWidget(self.toolbox) self.__splitter.addWidget(self.help) self.toolbar = DynamicResizeToolBar() self.toolbar.setMovable(False) self.toolbar.setFloatable(False) self.toolbar.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Preferred) layout.addWidget(self.__splitter, 10) layout.addWidget(self.toolbar) self.setLayout(layout) self.__splitterResizer = SplitterResizer(self) self.__splitterResizer.setSplitterAndWidget(self.__splitter, self.help) def setQuickHelpVisible(self, state): """Set the quick help box visibility status. """ self.__splitterResizer.setExpanded(state) def quickHelpVisible(self): return self.__splitterResizer.expanded() def setQuickHelpAnimationEnabled(self, enabled): """Enable/disable the quick help animation. """ self.__splitterResizer.setAnimationEnabled(enabled) def toogleQuickHelpAction(self): """Return a checkable QAction for help show/hide. """ return self.__splitterResizer.toogleExpandedAction()
def __init__(self): super().__init__() dbox = gui.widgetBox(self.controlArea, "Integration") rbox = gui.radioButtons(dbox, self, "integration_method", callback=self._change_integration) gui.appendRadioButton(rbox, "Integrate from 0") gui.appendRadioButton(rbox, "Integrate from baseline") gui.appendRadioButton(rbox, "Peak from 0") gui.appendRadioButton(rbox, "Peak from baseline") gui.rubber(self.controlArea) splitter = QSplitter(self) splitter.setOrientation(Qt.Vertical) self.imageplot = ImagePlot(self) self.curveplot = CurvePlot(self, select=SELECTONE) splitter.addWidget(self.imageplot) splitter.addWidget(self.curveplot) self.mainArea.layout().addWidget(splitter) self.line1 = MovableVlineWD(position=self.lowlim, label="", setvalfn=self.set_lowlim, confirmfn=self.edited, report=self.curveplot) self.line2 = MovableVlineWD(position=self.highlim, label="", setvalfn=self.set_highlim, confirmfn=self.edited, report=self.curveplot) self.curveplot.add_marking(self.line1) self.curveplot.add_marking(self.line2) self.resize(900, 700) self.graph_name = "imageplot.plotview"
class OWGenes(OWWidget, ConcurrentWidgetMixin): name = "Genes" description = "Tool for working with genes" icon = "../widgets/icons/OWGeneInfo.svg" priority = 40 want_main_area = True selected_organism: int = Setting(11) search_pattern: str = Setting('') exclude_unmatched = Setting(True) replace_id_with_symbol = Setting(True) auto_commit = Setting(True) settingsHandler = DomainContextHandler() selected_gene_col = ContextSetting(None) use_attr_names = ContextSetting(True) replaces = [ 'orangecontrib.bioinformatics.widgets.OWGeneNameMatcher.OWGeneNameMatcher' ] class Inputs: data_table = Input("Data", Table) class Outputs: data_table = Output("Data", Table) gene_matcher_results = Output("Genes", Table) class Information(OWWidget.Information): pass def sizeHint(self): return QSize(1280, 960) def __init__(self): OWWidget.__init__(self) ConcurrentWidgetMixin.__init__(self) # ATTRIBUTES # self.target_database = ENTREZ_ID # input data self.input_data = None self.input_genes = None self.tax_id = None self.column_candidates = [] # input options self.organisms = [] # gene matcher self.gene_matcher = None # progress bar self.progress_bar = None self._timer = QTimer() self._timer.timeout.connect(self._apply_filter) self._timer.setSingleShot(True) # GUI SECTION # # Control area self.info_box = widgetLabel( widgetBox(self.controlArea, "Info", addSpace=True), 'No data on input.\n') organism_box = vBox(self.controlArea, 'Organism') self.organism_select_combobox = comboBox( organism_box, self, 'selected_organism', callback=self.on_input_option_change) self.get_available_organisms() self.organism_select_combobox.setCurrentIndex(self.selected_organism) box = widgetBox(self.controlArea, 'Gene IDs in the input data') self.gene_columns_model = itemmodels.DomainModel( valid_types=(StringVariable, DiscreteVariable)) self.gene_column_combobox = comboBox( box, self, 'selected_gene_col', label='Stored in data column', model=self.gene_columns_model, sendSelectedValue=True, callback=self.on_input_option_change, ) self.attr_names_checkbox = checkBox( box, self, 'use_attr_names', 'Stored as feature (column) names', disables=[(-1, self.gene_column_combobox)], callback=self.on_input_option_change, ) self.gene_column_combobox.setDisabled(bool(self.use_attr_names)) output_box = vBox(self.controlArea, 'Output') # separator(output_box) # output_box.layout().addWidget(horizontal_line()) # separator(output_box) self.exclude_radio = checkBox(output_box, self, 'exclude_unmatched', 'Exclude unmatched genes', callback=self.commit) self.replace_radio = checkBox(output_box, self, 'replace_id_with_symbol', 'Replace feature IDs with gene names', callback=self.commit) auto_commit(self.controlArea, self, "auto_commit", "&Commit", box=False) rubber(self.controlArea) # Main area self.filter = lineEdit(self.mainArea, self, 'search_pattern', 'Filter:', callbackOnType=True, callback=self.handle_filter_callback) # rubber(self.radio_group) self.mainArea.layout().addWidget(self.filter) # set splitter self.splitter = QSplitter() self.splitter.setOrientation(Qt.Vertical) self.table_model = GeneInfoModel() self.table_view = QTableView() self.table_view.setAlternatingRowColors(True) self.table_view.viewport().setMouseTracking(True) self.table_view.setSortingEnabled(True) self.table_view.setShowGrid(False) self.table_view.verticalHeader().hide() # self.table_view.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch) self.unknown_model = UnknownGeneInfoModel() self.unknown_view = QTableView() self.unknown_view.setModel(self.unknown_model) self.unknown_view.verticalHeader().hide() self.unknown_view.setShowGrid(False) self.unknown_view.setSelectionMode(QAbstractItemView.NoSelection) self.unknown_view.horizontalHeader().setSectionResizeMode( QHeaderView.Stretch) self.splitter.addWidget(self.table_view) self.splitter.addWidget(self.unknown_view) self.splitter.setStretchFactor(0, 90) self.splitter.setStretchFactor(1, 10) self.mainArea.layout().addWidget(self.splitter) def handle_filter_callback(self): self._timer.stop() self._timer.start(500) def _apply_filter(self): # filter only if input data is present and model is populated if self.table_model.table is not None: self.table_model.update_model( filter_pattern=str(self.search_pattern)) self.commit() def __reset_widget_state(self): self.table_view.clearSpans() self.table_view.setModel(None) self.table_model.clear() self.unknown_model.clear() self._update_info_box() def _update_info_box(self): if self.input_genes and self.gene_matcher: num_genes = len(self.gene_matcher.genes) known_genes = len(self.gene_matcher.get_known_genes()) info_text = ('{} genes in input data\n' '{} genes match Entrez database\n' '{} genes with match conflicts\n'.format( num_genes, known_genes, num_genes - known_genes)) else: info_text = 'No data on input.' self.info_box.setText(info_text) def on_done(self, _): # update info box self._update_info_box() # set output options self.toggle_radio_options() # set known genes self.table_model.initialize(self.gene_matcher.genes) self.table_view.setModel(self.table_model) self.table_view.selectionModel().selectionChanged.connect(self.commit) self.table_view.setSelectionBehavior(QAbstractItemView.SelectRows) self.table_view.setItemDelegateForColumn( self.table_model.entrez_column_index, LinkStyledItemDelegate(self.table_view)) v_header = self.table_view.verticalHeader() option = self.table_view.viewOptions() size = self.table_view.style().sizeFromContents( QStyle.CT_ItemViewItem, option, QSize(20, 20), self.table_view) v_header.setDefaultSectionSize(size.height() + 2) v_header.setMinimumSectionSize(5) self.table_view.horizontalHeader().setStretchLastSection(True) # set unknown genes self.unknown_model.initialize(self.gene_matcher.genes) self.unknown_view.verticalHeader().setStretchLastSection(True) self._apply_filter() def get_available_organisms(self): available_organism = sorted(((tax_id, taxonomy.name(tax_id)) for tax_id in taxonomy.common_taxids()), key=lambda x: x[1]) self.organisms = [tax_id[0] for tax_id in available_organism] self.organism_select_combobox.addItems( [tax_id[1] for tax_id in available_organism]) def gene_names_from_table(self): """ Extract and return gene names from `Orange.data.Table`. """ self.input_genes = [] if self.input_data: if self.use_attr_names: self.input_genes = [ str(attr.name).strip() for attr in self.input_data.domain.attributes ] else: if self.selected_gene_col is None: self.selected_gene_col = self.gene_column_identifier() self.input_genes = [ str(e[self.selected_gene_col]) for e in self.input_data if not np.isnan(e[self.selected_gene_col]) ] def _update_gene_matcher(self): self.gene_names_from_table() self.gene_matcher = GeneMatcher(self.get_selected_organism(), auto_start=False) self.gene_matcher.genes = self.input_genes # self.gene_matcher.organism = self.get_selected_organism() def get_selected_organism(self): return self.organisms[self.selected_organism] def _run(self): if self.gene_matcher is not None: self.start(run_gene_matcher, self.gene_matcher) def on_input_option_change(self): self.__reset_widget_state() self._update_gene_matcher() self._run() def gene_column_identifier(self): """ Get most suitable column that stores genes. If there are several suitable columns, select the one with most unique values. Take the best one. """ # candidates -> (variable, num of unique values) candidates = ((col, np.unique(self.input_data.get_column_view(col)[0]).size) for col in self.gene_columns_model if isinstance(col, DiscreteVariable) or isinstance(col, StringVariable)) best_candidate, _ = sorted(candidates, key=lambda x: x[1])[-1] return best_candidate def find_genes_location(self): """ Try locate the genes in the input data when we first load the data. Proposed rules: - when no suitable feature names are present, check the columns. - find the most suitable column, that is, the one with most unique values. """ domain = self.input_data.domain if not domain.attributes: if self.selected_gene_col is None: self.selected_gene_col = self.gene_column_identifier() self.use_attr_names = False @Inputs.data_table def handle_input(self, data): self.closeContext() self.input_data = None self.input_genes = None self.__reset_widget_state() self.gene_columns_model.set_domain(None) self.selected_gene_col = None if data: self.input_data = data self.gene_columns_model.set_domain(self.input_data.domain) # check if input table has tax_id, human is used if tax_id is not found self.tax_id = str(self.input_data.attributes.get(TAX_ID, '9606')) # check for gene location. Default is that genes are attributes in the input table. self.use_attr_names = self.input_data.attributes.get( GENE_AS_ATTRIBUTE_NAME, self.use_attr_names) if self.tax_id in self.organisms and not self.selected_organism: self.selected_organism = self.organisms.index(self.tax_id) self.openContext(self.input_data.domain) self.find_genes_location() self.on_input_option_change() def commit(self): selection = self.table_view.selectionModel().selectedRows( self.table_model.entrez_column_index) selected_genes = [row.data() for row in selection] if not len(selected_genes): selected_genes = self.table_model.get_filtered_genes() gene_ids = self.get_target_ids() known_genes = [gid for gid in gene_ids if gid != '?'] table = None gm_table = None if known_genes: # Genes are in rows (we have a column with genes). if not self.use_attr_names: if self.target_database in self.input_data.domain: gene_var = self.input_data.domain[self.target_database] metas = self.input_data.domain.metas else: gene_var = StringVariable(self.target_database) metas = self.input_data.domain.metas + (gene_var, ) domain = Domain(self.input_data.domain.attributes, self.input_data.domain.class_vars, metas) table = self.input_data.transform(domain) col, _ = table.get_column_view(gene_var) col[:] = gene_ids # filter selected rows selected_genes_set = set(selected_genes) selected_rows = [ row_index for row_index, row in enumerate(table) if str(row[gene_var]) in selected_genes_set ] # handle table attributes table.attributes[TAX_ID] = self.get_selected_organism() table.attributes[GENE_AS_ATTRIBUTE_NAME] = False table.attributes[GENE_ID_COLUMN] = self.target_database table = table[selected_rows] if selected_rows else table if self.exclude_unmatched: # create filter from selected column for genes only_known = table_filter.FilterStringList( gene_var, known_genes) # apply filter to the data table = table_filter.Values([only_known])(table) self.Outputs.data_table.send(table) # genes are are in columns (genes are features). else: domain = self.input_data.domain.copy() table = self.input_data.transform(domain) for gene in self.gene_matcher.genes: if gene.input_identifier in table.domain: table.domain[gene.input_identifier].attributes[ self.target_database] = (str(gene.gene_id) if gene.gene_id else '?') if self.replace_id_with_symbol: try: table.domain[gene.input_identifier].name = str( gene.symbol) except AttributeError: # TODO: missing gene symbol, need to handle this? pass # filter selected columns selected_genes_set = set(selected_genes) selected = [ column for column in table.domain.attributes if self.target_database in column.attributes and str(column.attributes[ self.target_database]) in selected_genes_set ] output_attrs = table.domain.attributes if selected: output_attrs = selected if self.exclude_unmatched: known_genes_set = set(known_genes) output_attrs = [ col for col in output_attrs if col.attributes[ self.target_database] in known_genes_set ] domain = Domain(output_attrs, table.domain.class_vars, table.domain.metas) table = table.from_table(domain, table) # handle table attributes table.attributes[TAX_ID] = self.get_selected_organism() table.attributes[GENE_AS_ATTRIBUTE_NAME] = True table.attributes[GENE_ID_ATTRIBUTE] = self.target_database gm_table = self.gene_matcher.to_data_table( selected_genes=selected_genes if selected_genes else None) self.Outputs.data_table.send(table) self.Outputs.gene_matcher_results.send(gm_table) def toggle_radio_options(self): self.replace_radio.setEnabled(bool(self.use_attr_names)) if self.gene_matcher.genes: # enable checkbox if unknown genes are detected self.exclude_radio.setEnabled( len(self.gene_matcher.genes) != len( self.gene_matcher.get_known_genes())) self.exclude_unmatched = len(self.gene_matcher.genes) != len( self.gene_matcher.get_known_genes()) def get_target_ids(self): return [ str(gene.gene_id) if gene.gene_id else '?' for gene in self.gene_matcher.genes ]
class ExtendedTableView(QWidget): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.ow = kwargs.get('parent', None) # set layout layout = QVBoxLayout() layout.setContentsMargins(0, 0, 0, 0) self.setLayout(layout) # set splitter self.splitter = QSplitter() self.splitter.setOrientation(Qt.Horizontal) # data models self.genes_model = None self.info_model = None # left side list view self.genes_view = QTableView() self.genes_view.horizontalHeader().hide() self.genes_view.setItemDelegate(GeneItemDelegate()) self.genes_view.horizontalHeader().setSectionResizeMode( QHeaderView.Stretch) # right side list view self.info_view = QTableView() self.info_view.setItemDelegate(HTMLDelegate()) self.info_view.horizontalHeader().hide() self.info_view.horizontalHeader().setSectionResizeMode( QHeaderView.Stretch) self.splitter.addWidget(self.genes_view) self.splitter.addWidget(self.info_view) # self.splitter.setStretchFactor(0, 60) # self.splitter.setStretchFactor(1, 40) self.layout().addWidget(self.splitter) def set_genes_model(self, rows): self.genes_model = GeneMatcherModel() self.genes_model.add_rows(rows) def get_selected_gens(self): # return a list of QModelIndex return self.genes_selection_model().selectedRows() def reset_genes_model(self): if self.genes_model: self.genes_model.deleteLater() self.genes_model = None def genes_selection_model(self): return self.genes_view.selectionModel() def reset_info_model(self): if self.info_model: self.info_model.deleteLater() self.info_model = None self.info_view.setModel(None) def set_info_model(self, rows): unique, partial, unknown = range(len(self.ow.filter_labels)) if self.ow.selected_filter == unique: # create model self.info_model = GeneMatcherModel(show_icon=False) # add rows self.info_model.add_rows(rows) # add model to the view self.info_view.setModel(self.info_model) # disable selection of gene info cards self.info_view.setSelectionMode(QAbstractItemView.NoSelection) # call sizeHint function self.info_view.resizeRowsToContents() else: self.reset_info_model()