def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"): OWWidget.__init__(self, parent, signalManager, name) self.selectionChanged = False self.filterString = "" self.datasetName = "" ## GUI box = gui.widgetBox(self.controlArea, "Info", addSpace=True) self.infoBox = gui.widgetLabel(box, "Initializing\n\n") box = gui.widgetBox(self.controlArea, "Output", addSpace=True) gui.radioButtonsInBox(box, self, "outputRows", ["Genes in rows", "Samples in rows"], "Rows", callback=self.commitIf) gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene", callback=self.commitIf) gui.separator(box) self.nameEdit = gui.lineEdit( box, self, "datasetName", "Data set name", tooltip="Override the default output data set name", callback=self.onNameEdited) self.nameEdit.setPlaceholderText("") if sys.version_info < (3, ): box = gui.widgetBox(self.controlArea, "Commit", addSpace=True) self.commitButton = gui.button(box, self, "Commit", callback=self.commit) cb = gui.checkBox(box, self, "autoCommit", "Commit on any change") gui.setStopper(self, self.commitButton, cb, "selectionChanged", self.commit) else: gui.auto_commit(self.controlArea, self, "autoCommit", "Commit", box="Commit") self.commitIf = self.commit gui.rubber(self.controlArea) gui.widgetLabel(self.mainArea, "Filter") self.filterLineEdit = QLineEdit(textChanged=self.filter) self.completer = TokenListCompleter(self, caseSensitivity=Qt.CaseInsensitive) self.filterLineEdit.setCompleter(self.completer) self.mainArea.layout().addWidget(self.filterLineEdit) splitter = QSplitter(Qt.Vertical, self.mainArea) self.mainArea.layout().addWidget(splitter) self.treeWidget = QTreeView(splitter) self.treeWidget.setSelectionMode(QTreeView.SingleSelection) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSortingEnabled(True) self.treeWidget.setAlternatingRowColors(True) self.treeWidget.setUniformRowHeights(True) self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers) linkdelegate = LinkStyledItemDelegate(self.treeWidget) self.treeWidget.setItemDelegateForColumn(1, linkdelegate) self.treeWidget.setItemDelegateForColumn(8, linkdelegate) self.treeWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole)) proxyModel = MySortFilterProxyModel(self.treeWidget) self.treeWidget.setModel(proxyModel) self.treeWidget.selectionModel().selectionChanged.connect( self.updateSelection) self.treeWidget.viewport().setMouseTracking(True) splitterH = QSplitter(Qt.Horizontal, splitter) box = gui.widgetBox(splitterH, "Description") self.infoGDS = gui.widgetLabel(box, "") self.infoGDS.setWordWrap(True) gui.rubber(box) box = gui.widgetBox(splitterH, "Sample Annotations") self.annotationsTree = QTreeWidget(box) self.annotationsTree.setHeaderLabels( ["Type (Sample annotations)", "Sample count"]) self.annotationsTree.setRootIsDecorated(True) box.layout().addWidget(self.annotationsTree) self.annotationsTree.itemChanged.connect( self.annotationSelectionChanged) self._annotationsUpdating = False self.splitters = splitter, splitterH for sp, setting in zip(self.splitters, self.splitterSettings): sp.splitterMoved.connect(self.splitterMoved) sp.restoreState(setting) self.searchKeys = [ "dataset_id", "title", "platform_organism", "description" ] self.gds = [] self.gds_info = None self.resize(1000, 600) self.setBlocking(True) self.setEnabled(False) self.progressBarInit() self._executor = ThreadExecutor() func = partial(get_gds_model, methodinvoke(self, "_setProgress", (float, ))) self._inittask = Task(function=func) self._inittask.finished.connect(self._initializemodel) self._executor.submit(self._inittask) self._datatask = None
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"): OWWidget.__init__(self, parent, signalManager, name) self.selectionChanged = False self.filterString = "" self.datasetName = "" ## GUI box = gui.widgetBox(self.controlArea, "Info", addSpace=True) self.infoBox = gui.widgetLabel(box, "Initializing\n\n") box = gui.widgetBox(self.controlArea, "Output", addSpace=True) gui.radioButtonsInBox(box, self, "outputRows", ["Genes in rows", "Samples in rows"], "Rows", callback=self.commitIf) gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene", callback=self.commitIf) gui.separator(box) self.nameEdit = gui.lineEdit( box, self, "datasetName", "Data set name", tooltip="Override the default output data set name", callback=self.onNameEdited ) self.nameEdit.setPlaceholderText("") if sys.version_info < (3, ): box = gui.widgetBox(self.controlArea, "Commit", addSpace=True) self.commitButton = gui.button( box, self, "Commit", callback=self.commit) cb = gui.checkBox(box, self, "autoCommit", "Commit on any change") gui.setStopper(self, self.commitButton, cb, "selectionChanged", self.commit) else: gui.auto_commit(self.controlArea, self, "autoCommit", "Commit", box="Commit") self.commitIf = self.commit gui.rubber(self.controlArea) gui.widgetLabel(self.mainArea, "Filter") self.filterLineEdit = QLineEdit( textChanged=self.filter ) self.completer = TokenListCompleter( self, caseSensitivity=Qt.CaseInsensitive ) self.filterLineEdit.setCompleter(self.completer) self.mainArea.layout().addWidget(self.filterLineEdit) splitter = QSplitter(Qt.Vertical, self.mainArea) self.mainArea.layout().addWidget(splitter) self.treeWidget = QTreeView(splitter) self.treeWidget.setSelectionMode(QTreeView.SingleSelection) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSortingEnabled(True) self.treeWidget.setAlternatingRowColors(True) self.treeWidget.setUniformRowHeights(True) self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers) linkdelegate = LinkStyledItemDelegate(self.treeWidget) self.treeWidget.setItemDelegateForColumn(1, linkdelegate) self.treeWidget.setItemDelegateForColumn(8, linkdelegate) self.treeWidget.setItemDelegateForColumn( 0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole)) proxyModel = MySortFilterProxyModel(self.treeWidget) self.treeWidget.setModel(proxyModel) self.treeWidget.selectionModel().selectionChanged.connect( self.updateSelection ) self.treeWidget.viewport().setMouseTracking(True) splitterH = QSplitter(Qt.Horizontal, splitter) box = gui.widgetBox(splitterH, "Description") self.infoGDS = gui.widgetLabel(box, "") self.infoGDS.setWordWrap(True) gui.rubber(box) box = gui.widgetBox(splitterH, "Sample Annotations") self.annotationsTree = QTreeWidget(box) self.annotationsTree.setHeaderLabels( ["Type (Sample annotations)", "Sample count"] ) self.annotationsTree.setRootIsDecorated(True) box.layout().addWidget(self.annotationsTree) self.annotationsTree.itemChanged.connect( self.annotationSelectionChanged ) self._annotationsUpdating = False self.splitters = splitter, splitterH for sp, setting in zip(self.splitters, self.splitterSettings): sp.splitterMoved.connect(self.splitterMoved) sp.restoreState(setting) self.searchKeys = ["dataset_id", "title", "platform_organism", "description"] self.gds = [] self.gds_info = None self.resize(1000, 600) self.setBlocking(True) self.setEnabled(False) self.progressBarInit() self._executor = ThreadExecutor() func = partial(get_gds_model, methodinvoke(self, "_setProgress", (float,))) self._inittask = Task(function=func) self._inittask.finished.connect(self._initializemodel) self._executor.submit(self._inittask) self._datatask = None
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"): OWWidget.__init__(self, parent, signalManager, name) self.outputs = [("Expression Data", ExampleTable)] ## Settings self.selectedAnnotation = 0 self.includeIf = False self.minSamples = 3 self.autoCommit = False self.outputRows = 0 self.mergeSpots = True self.filterString = "" self.currentGds = None self.selectionChanged = False self.autoCommit = False self.gdsSelectionStates = {} self.splitterSettings = [ '\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02', '\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01' ] self.datasetNames = {} self.loadSettings() self.datasetName = "" ## GUI self.infoBox = OWGUI.widgetLabel( OWGUI.widgetBox(self.controlArea, "Info", addSpace=True), "Initializing\n\n" ) box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True) OWGUI.radioButtonsInBox(box, self, "outputRows", ["Genes or spots", "Samples"], "Rows", callback=self.commitIf) OWGUI.checkBox(box, self, "mergeSpots", "Merge spots of same gene", callback=self.commitIf) OWGUI.separator(box) self.nameEdit = OWGUI.lineEdit( box, self, "datasetName", "Data set name", tooltip="Override the default output data set name", callback=self.onNameEdited ) self.nameEdit.setPlaceholderText("") box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True) self.commitButton = OWGUI.button(box, self, "Commit", callback=self.commit) cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on any change") OWGUI.setStopper(self, self.commitButton, cb, "selectionChanged", self.commit) OWGUI.rubber(self.controlArea) self.filterLineEdit = OWGUIEx.lineEditHint( self.mainArea, self, "filterString", "Filter", caseSensitive=False, matchAnywhere=True, callback=self.filter, delimiters=" ") splitter = QSplitter(Qt.Vertical, self.mainArea) self.mainArea.layout().addWidget(splitter) self.treeWidget = QTreeView(splitter) self.treeWidget.setSelectionMode(QAbstractItemView.SingleSelection) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSortingEnabled(True) self.treeWidget.setAlternatingRowColors(True) self.treeWidget.setUniformRowHeights(True) self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers) linkdelegate = LinkStyledItemDelegate(self.treeWidget) self.treeWidget.setItemDelegateForColumn(1, linkdelegate) self.treeWidget.setItemDelegateForColumn(8, linkdelegate) self.treeWidget.setItemDelegateForColumn( 0, OWGUI.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole)) proxyModel = MySortFilterProxyModel(self.treeWidget) self.treeWidget.setModel(proxyModel) self.treeWidget.selectionModel().selectionChanged.connect( self.updateSelection ) self.treeWidget.viewport().setMouseTracking(True) splitterH = QSplitter(Qt.Horizontal, splitter) box = OWGUI.widgetBox(splitterH, "Description") self.infoGDS = OWGUI.widgetLabel(box, "") self.infoGDS.setWordWrap(True) OWGUI.rubber(box) box = OWGUI.widgetBox(splitterH, "Sample Annotations") self.annotationsTree = QTreeWidget(box) self.annotationsTree.setHeaderLabels( ["Type (Sample annotations)", "Sample count"] ) self.annotationsTree.setRootIsDecorated(True) box.layout().addWidget(self.annotationsTree) self.annotationsTree.itemChanged.connect( self.annotationSelectionChanged ) self._annotationsUpdating = False self.splitters = splitter, splitterH for sp, setting in zip(self.splitters, self.splitterSettings): sp.splitterMoved.connect(self.splitterMoved) sp.restoreState(setting) self.searchKeys = ["dataset_id", "title", "platform_organism", "description"] self.gds = [] self.gds_info = None self.resize(1000, 600) self.setBlocking(True) self.setEnabled(False) self.progressBarInit() self._executor = ThreadExecutor() func = partial(get_gds_model, methodinvoke(self, "_setProgress", (float,))) self._inittask = Task(function=func) self._inittask.finished.connect(self._initializemodel) self._executor.submit(self._inittask) self._datatask = None
def __init__(self, parent=None, signalManager=None, title="Expression Profile Distances"): OWWidget.__init__(self, parent, signalManager, title) self.inputs = [("Example Table", ExampleTable, self.set_data)] self.outputs = [("Distances", Orange.core.SymMatrix), ("Sorted Example Table", ExampleTable)] self.distance_measure = 0 self.auto_commit = False self.changed_flag = False self.loadSettings() ######## # GUI ######## self.info_box = OWGUI.widgetLabel( OWGUI.widgetBox(self.controlArea, "Input", addSpace=True), "No data on input\n" ) box = OWGUI.widgetBox(self.controlArea, "Separate By", addSpace=True) self.separate_view = QListView() self.separate_view.setSelectionMode(QListView.MultiSelection) box.layout().addWidget(self.separate_view) box = OWGUI.widgetBox(self.controlArea, "Sort By", addSpace=True) self.relevant_view = QListView() self.relevant_view.setSelectionMode(QListView.MultiSelection) box.layout().addWidget(self.relevant_view) self.distance_view = OWGUI.comboBox( self.controlArea, self, "distance_measure", box="Distance Measure", items=[d[0] for d in self.DISTANCE_FUNCTIONS], ) OWGUI.rubber(self.controlArea) box = OWGUI.widgetBox(self.controlArea, "Commit") cb = OWGUI.checkBox( box, self, "auto_commit", "Commit on any change", tooltip="Compute and send the distances on any change.", callback=self.commit_if, ) b = OWGUI.button( box, self, "Commit", tooltip="Compute the distances and send the output signals.", callback=self.commit, default=True, ) OWGUI.setStopper(self, b, cb, "changed_flag", callback=self.commit) self.groups_box = OWGUI.widgetBox(self.mainArea, "Groups") self.groups_scroll_area = QScrollArea() self.groups_box.layout().addWidget(self.groups_scroll_area) self.data = None self.partitions = [] self.matrix = None self.split_groups = [] self._disable_updates = False self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"): OWWidget.__init__(self, parent, signalManager, name) self.outputs = [("Expression Data", ExampleTable)] ## Settings self.selectedAnnotation = 0 self.includeIf = False self.minSamples = 3 self.autoCommit = False self.outputRows = 1 self.mergeSpots = True self.filterString = "" self.currentGds = None self.selectionChanged = False self.autoCommit = False self.gdsSelectionStates = {} self.splitterSettings = [ '\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02', '\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01' ] self.datasetNames = {} self.loadSettings() self.datasetName = "" ## GUI self.infoBox = OWGUI.widgetLabel( OWGUI.widgetBox(self.controlArea, "Info", addSpace=True), "Initializing\n\n" ) box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True) OWGUI.radioButtonsInBox(box, self, "outputRows", ["Genes in rows", "Samples in rows"], "Rows", callback=self.commitIf) OWGUI.checkBox(box, self, "mergeSpots", "Merge spots of same gene", callback=self.commitIf) OWGUI.separator(box) self.nameEdit = OWGUI.lineEdit( box, self, "datasetName", "Data set name", tooltip="Override the default output data set name", callback=self.onNameEdited ) self.nameEdit.setPlaceholderText("") box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True) self.commitButton = OWGUI.button(box, self, "Commit", callback=self.commit) cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on any change") OWGUI.setStopper(self, self.commitButton, cb, "selectionChanged", self.commit) OWGUI.rubber(self.controlArea) self.filterLineEdit = OWGUIEx.lineEditHint( self.mainArea, self, "filterString", "Filter", caseSensitive=False, matchAnywhere=True, callback=self.filter, delimiters=" ") splitter = QSplitter(Qt.Vertical, self.mainArea) self.mainArea.layout().addWidget(splitter) self.treeWidget = QTreeView(splitter) self.treeWidget.setSelectionMode(QAbstractItemView.SingleSelection) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSortingEnabled(True) self.treeWidget.setAlternatingRowColors(True) self.treeWidget.setUniformRowHeights(True) self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers) linkdelegate = LinkStyledItemDelegate(self.treeWidget) self.treeWidget.setItemDelegateForColumn(1, linkdelegate) self.treeWidget.setItemDelegateForColumn(8, linkdelegate) self.treeWidget.setItemDelegateForColumn( 0, OWGUI.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole)) proxyModel = MySortFilterProxyModel(self.treeWidget) self.treeWidget.setModel(proxyModel) self.treeWidget.selectionModel().selectionChanged.connect( self.updateSelection ) self.treeWidget.viewport().setMouseTracking(True) splitterH = QSplitter(Qt.Horizontal, splitter) box = OWGUI.widgetBox(splitterH, "Description") self.infoGDS = OWGUI.widgetLabel(box, "") self.infoGDS.setWordWrap(True) OWGUI.rubber(box) box = OWGUI.widgetBox(splitterH, "Sample Annotations") self.annotationsTree = QTreeWidget(box) self.annotationsTree.setHeaderLabels( ["Type (Sample annotations)", "Sample count"] ) self.annotationsTree.setRootIsDecorated(True) box.layout().addWidget(self.annotationsTree) self.annotationsTree.itemChanged.connect( self.annotationSelectionChanged ) self._annotationsUpdating = False self.splitters = splitter, splitterH for sp, setting in zip(self.splitters, self.splitterSettings): sp.splitterMoved.connect(self.splitterMoved) sp.restoreState(setting) self.searchKeys = ["dataset_id", "title", "platform_organism", "description"] self.gds = [] self.gds_info = None self.resize(1000, 600) self.setBlocking(True) self.setEnabled(False) self.progressBarInit() self._executor = ThreadExecutor() func = partial(get_gds_model, methodinvoke(self, "_setProgress", (float,))) self._inittask = Task(function=func) self._inittask.finished.connect(self._initializemodel) self._executor.submit(self._inittask) self._datatask = None
def __init__(self, parent=None, signalManager = None): # self.callbackDeposit = [] # deposit for OWGUI callback functions OWWidget.__init__(self, parent, signalManager, 'Expression Profiles', 1) #set default settings self.ShowAverageProfile = 1 self.ShowSingleProfiles = 0 self.PointWidth = 2 self.CurveWidth = 1 self.AverageCurveWidth = 4 self.BoxPlotWidth = 2 self.SelectedClasses = [] self.Classes = [] self.autoSendSelected = 0 self.selectionChangedFlag = False self.CutLow = 0; self.CutHigh = 0; self.CutEnabled = 0 self.profileLabel = None #load settings self.loadSettings() # GUI self.graph = profilesGraph(self, self.mainArea, "") self.mainArea.layout().addWidget(self.graph) self.graph.hide() self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile) # GUI definition self.tabs = OWGUI.tabWidget(self.space) # GRAPH TAB GraphTab = OWGUI.createTabPage(self.tabs, "Graph") ## display options self.infoLabel = OWGUI.widgetLabel(OWGUI.widgetBox(GraphTab, "Info"), "No data on input.") displayOptBox = OWGUI.widgetBox(GraphTab, "Display") #QVButtonGroup("Display", GraphTab) displayOptButtons = ['Majority Class', 'Majority Class Probability', 'Target Class Probability', 'Number of Instances'] OWGUI.checkBox(displayOptBox, self, 'ShowSingleProfiles', 'Expression Profiles', tooltip='', callback=self.updateShowSingleProfiles) OWGUI.checkBox(displayOptBox, self, 'ShowAverageProfile', 'Box Plot', tooltip='', callback=self.updateShowAverageProfile) ## class selection (classQLB) self.classQVGB = OWGUI.widgetBox(GraphTab, "Classes") #QVGroupBox(GraphTab) ## self.classQVGB.setTitle("Classes") self.classQLB = OWGUI.listBox(self.classQVGB, self, "SelectedClasses", "Classes", selectionMode=QListWidget.MultiSelection, callback=self.classSelectionChange) #QListBox(self.classQVGB) ## self.classQLB.setSelectionMode(QListBox.Multi) self.unselectAllClassedQLB = OWGUI.button(self.classQVGB, self, "Unselect all", callback=self.SUAclassQLB) #QPushButton("(Un)Select All", self.classQVGB) ## self.connect(self.unselectAllClassedQLB, SIGNAL("clicked()"), self.SUAclassQLB) ## self.connect(self.classQLB, SIGNAL("selectionChanged()"), self.classSelectionChange) ## show single/average profile ## self.showAverageQLB = QPushButton("Box Plot", self.classQVGB) ## self.showAverageQLB.setToggleButton(1) ## self.showAverageQLB.setOn(self.ShowAverageProfile) ## self.showSingleQLB = QPushButton("Single Profiles", self.classQVGB) ## self.showSingleQLB.setToggleButton(1) ## self.showSingleQLB.setOn(self.ShowSingleProfiles) ## self.connect(self.showAverageQLB, SIGNAL("toggled(bool)"), self.updateShowAverageProfile) ## self.connect(self.showSingleQLB, SIGNAL("toggled(bool)"), self.updateShowSingleProfiles) ## self.tabs.insertTab(GraphTab, "Graph") # SETTINGS TAB SettingsTab = OWGUI.createTabPage(self.tabs, "Settings") #QVGroupBox(self) self.profileLabelComboBox = OWGUI.comboBox(SettingsTab, self, 'profileLabel', 'Profile Labels', sendSelectedValue=True, valueType=str) OWGUI.hSlider(SettingsTab, self, 'PointWidth', box='Point Width', minValue=0, maxValue=9, step=1, callback=self.updatePointWidth, ticks=1) OWGUI.hSlider(SettingsTab, self, 'CurveWidth', box='Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateCurveWidth, ticks=1) OWGUI.hSlider(SettingsTab, self, 'AverageCurveWidth', box='Average Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateAverageCurveWidth, ticks=1) OWGUI.hSlider(SettingsTab, self, 'BoxPlotWidth', box='Box Plot Width', minValue=0, maxValue=9, step=1, callback=self.updateBoxPlotWidth, ticks=1) OWGUI.checkBox(SettingsTab, self, 'graph.renderAntialiased', "Render antialiased", callback=self.graph.setCurveRenderHints) ## graph y scale box = OWGUI.widgetBox(SettingsTab, "Threshold/ Values") #QVButtonGroup("Threshol/ Values", SettingsTab) OWGUI.checkBox(box, self, 'CutEnabled', "Enabled", callback=self.setCutEnabled) self.sliderCutLow = OWGUI.qwtHSlider(box, self, 'CutLow', label='Low:', labelWidth=33, minValue=-20, maxValue=0, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis) self.sliderCutHigh = OWGUI.qwtHSlider(box, self, 'CutHigh', label='High:', labelWidth=33, minValue=0, maxValue=20, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis) if not self.CutEnabled: self.sliderCutLow.box.setDisabled(1) self.sliderCutHigh.box.setDisabled(1) ## self.tabs.insertTab(SettingsTab, "Settings") self.toolbarSelection = ZoomSelectToolbar(self, self.controlArea, self.graph, self.autoSendSelected, buttons=(ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan, ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconSpace, ZoomSelectToolbar.IconRemoveLast, ZoomSelectToolbar.IconRemoveAll, ZoomSelectToolbar.IconSendSelection)) cb = OWGUI.checkBox(self.controlArea, self, "autoSendSelected", "Auto send on selection change") OWGUI.setStopper(self, self.toolbarSelection.buttonSendSelections, cb, "selectionChangedFlag", self.commit) # inputs # data and graph temp variables self.inputs = [("Examples", ExampleTable, self.data, Default + Multiple)] self.outputs = [("Examples", ExampleTable, Default)] # temp variables self.MAdata = [] self.classColor = None self.classBrighterColor = None self.numberOfClasses = 0 self.classValues = [] self.ctrlPressed = False self.attrIcons = self.createAttributeIconDict() self.graph.canvas().setMouseTracking(1) # self.zoomStack = [] ## self.connect(self.graph, ## SIGNAL('plotMousePressed(const QMouseEvent&)'), ## self.onMousePressed) ## self.connect(self.graph, ## SIGNAL('plotMouseReleased(const QMouseEvent&)'), ## self.onMouseReleased) self.resize(800,600)
def __init__(self, parent=None, signalManager=None, name="Vulcano Plot"): OWWidget.__init__(self, parent, signalManager, name, wantGraph=True) self.inputs = [("Examples", ExampleTable, self.setData)] self.outputs = [("Examples with selected attributes", ExampleTable)] self.genes_in_columns = False self.showXTitle = True self.showYTitle = True self.auto_commit = False self.selection_changed_flag = False self.target_group = None, [] self.label_selections = [] self.graph = VulcanoGraph(self) self.connect(self.graph, SIGNAL("selectionChanged()"), self.on_selection_changed) self.mainArea.layout().addWidget(self.graph) self.loadSettings() ## GUI box = OWGUI.widgetBox(self.controlArea, "Info") self.infoLabel = OWGUI.label(box, self, "") self.infoLabel.setText("No data on input") self.infoLabel2 = OWGUI.label(box, self, "") self.infoLabel2.setText("0 selected genes") box = OWGUI.widgetBox(self.controlArea, "Target Labels") self.target_widget = LabelSelectionWidget(self) self.connect(self.target_widget, SIGNAL("selection_changed(PyQt_PyObject, PyQt_PyObject)"), self.on_target_changed) self.connect(self.target_widget, SIGNAL("label_activated(int)"), self.on_label_activated) box.layout().addWidget(self.target_widget) self.genesInColumnsCheck = OWGUI.checkBox(box, self, "genes_in_columns", "Genes in columns", callback=[self.init_from_data, self.plot]) box = OWGUI.widgetBox(self.controlArea, "Settings") OWGUI.hSlider(box, self, "graph.symbolSize", label="Symbol size: ", minValue=2, maxValue=20, step=1, callback = self.graph.updateSymbolSize) OWGUI.checkBox(box, self, "showXTitle", "X axis title", callback=self.setAxesTitles) OWGUI.checkBox(box, self, "showYTitle", "Y axis title", callback=self.setAxesTitles) toolbar = ZoomSelectToolbar(self, self.controlArea, self.graph, buttons=[ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan]) top_layout = toolbar.layout() top_layout.setDirection(QBoxLayout.TopToBottom) button_layotu = QHBoxLayout() top_layout.insertLayout(0, button_layotu) for i in range(1, top_layout.count()): item = top_layout.itemAt(1) top_layout.removeItem(item) button_layotu.addItem(item) OWGUI.checkBox(toolbar, self, "graph.symetricSelections", "Symetric selection", callback=self.graph.reselect) box = OWGUI.widgetBox(self.controlArea, "Commit") b = OWGUI.button(box, self, "Commit", callback=self.commit, default=True) cb = OWGUI.checkBox(box, self, "auto_commit", "Commit automatically") OWGUI.setStopper(self, b, cb, "selection_changed_flag", self.commit_if) self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile) OWGUI.rubber(self.controlArea) self.data = None self.target_group = None, [] self.current_selection = [] self.graph.reselect(True) self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Gene selection"): OWWidget.__init__(self, parent, signalManager, name, wantGraph=True, showSaveGraph=True) self.inputs = [("Examples", ExampleTable, self.set_data)] self.outputs = [("Example table with selected genes", ExampleTable), ("Example table with remaining genes", ExampleTable), ("Selected genes", ExampleTable)] self.method_index = 0 self.genes_in_columns = False self.compute_null = False self.permutations_count = 10 self.auto_commit = False self.selectNBest = 20 self.selectPValue = 0.01 self.data_changed_flag = False self.add_scores_to_output = True self.thresholds = { "fold change": (0.5, 2.), "log2 fold change": (-1, 1), "t-test": (-2, 2), "t-test p-value": (0.01, 0.01), } self.oneTailTestHi = oneTailTestHi = lambda array, low, hi: array >= hi self.oneTailTestLow = oneTailTestLow = lambda array, low, hi: array <= low self.twoTailTest = twoTailTest = lambda array, low, hi: ( array >= hi) | (array <= low) self.middleTest = middleTest = lambda array, low, hi: (array <= hi) | ( array >= low) self.histType = { oneTailTestHi: "hiTail", oneTailTestLow: "lowTail", twoTailTest: "twoTail", middleTest: "middle" } # [(name, func, tail test, two sample test), ...] self.score_methods = [ ("fold change", ExpressionSignificance_FoldChange, twoTailTest, True), ("log2 fold change", ExpressionSignificance_Log2FoldChange, twoTailTest, True), ("t-test", ExpressionSignificance_TTest_T, twoTailTest, True), ("t-test p-value", ExpressionSignificance_TTest_PValue, oneTailTestLow, True), ("anova", ExpressionSignificance_ANOVA_F, oneTailTestHi, False), ("anova p-value", ExpressionSignificance_ANOVA_PValue, oneTailTestLow, False), ("signal to noise ratio", ExpressionSignificance_SignalToNoise, twoTailTest, True), ("info gain", ExpressionSignificance_Info, oneTailTestHi, True), ("chi-square", ExpressionSignificance_ChiSquare, oneTailTestHi, True), ("mann-whitney", ExpressionSignigicance_MannWhitneyu_U, oneTailTestLow, True) ] boxHistogram = OWGUI.widgetBox(self.mainArea) self.histogram = ScoreHist(self, boxHistogram) boxHistogram.layout().addWidget(self.histogram) self.histogram.show() box = OWGUI.widgetBox(self.controlArea, "Info") self.dataInfoLabel = OWGUI.widgetLabel(box, "\n\n") self.dataInfoLabel.setWordWrap(True) self.selectedInfoLabel = OWGUI.widgetLabel(box, "") box1 = OWGUI.widgetBox(self.controlArea, "Scoring Method") self.testRadioBox = OWGUI.comboBox( box1, self, "method_index", items=[sm[0] for sm in self.score_methods], callback=[self.on_scoring_method_changed, self.update_scores]) box = OWGUI.widgetBox(self.controlArea, "Target Labels") self.label_selection_widget = LabelSelectionWidget(self) self.label_selection_widget.setMaximumHeight(150) box.layout().addWidget(self.label_selection_widget) self.connect(self.label_selection_widget, SIGNAL("selection_changed()"), self.on_target_changed) self.connect(self.label_selection_widget, SIGNAL("label_activated(int)"), self.on_label_activated) self.genes_in_columns_check = OWGUI.checkBox( box, self, "genes_in_columns", "Genes in columns", callback=self.on_genes_in_columns_change) box = OWGUI.widgetBox(self.controlArea, "Selection") box.layout().setSpacing(0) self.upperBoundarySpin = OWGUI.doubleSpin( box, self, "histogram.upperBoundary", min=-1e6, max=1e6, step=1e-6, label="Upper threshold:", callback=self.update_boundary, callbackOnReturn=True) self.lowerBoundarySpin = OWGUI.doubleSpin( box, self, "histogram.lowerBoundary", min=-1e6, max=1e6, step=1e-6, label="Lower threshold:", callback=self.update_boundary, callbackOnReturn=True) check = OWGUI.checkBox(box, self, "compute_null", "Compute null distribution", callback=self.update_scores) check.disables.append( OWGUI.spin(box, self, "permutations_count", min=1, max=10, label="Permutations:", callback=self.update_scores, callbackOnReturn=True)) box1 = OWGUI.widgetBox(box, orientation='horizontal') check.disables.append( OWGUI.doubleSpin(box1, self, "selectPValue", min=2e-7, max=1.0, step=1e-7, label="P-value:")) check.disables.append( OWGUI.button(box1, self, "Select", callback=self.select_p_best)) check.makeConsistent() box1 = OWGUI.widgetBox(box, orientation='horizontal') OWGUI.spin(box1, self, "selectNBest", 0, 10000, step=1, label="Best Ranked:") OWGUI.button(box1, self, "Select", callback=self.select_n_best) box = OWGUI.widgetBox(self.controlArea, "Output") b = OWGUI.button(box, self, "&Commit", callback=self.commit) cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change") OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit) OWGUI.checkBox(box, self, "add_scores_to_output", "Add gene scores to output", callback=self.commit_if) OWGUI.rubber(self.controlArea) self.connect(self.graphButton, SIGNAL("clicked()"), self.histogram.saveToFile) self.loadSettings() self.data = None self.discData = None self.scoreCache = {} self.nullDistCache = {} self.cuts = {} self.null_dist = [] self.targets = [] self.scores = {} self.genes_in_columns = True self.target_selections = None self.on_scoring_method_changed() self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Gene selection"): OWWidget.__init__(self, parent, signalManager, name, wantGraph=True, showSaveGraph=True) self.inputs = [("Examples", ExampleTable, self.set_data)] self.outputs = [("Example table with selected genes", ExampleTable), ("Example table with remaining genes", ExampleTable), ("Selected genes", ExampleTable)] self.method_index = 0 self.genes_in_columns = False self.compute_null = False self.permutations_count = 10 self.auto_commit = False self.selectNBest = 20 self.selectPValue = 0.01 self.data_changed_flag = False self.add_scores_to_output = True self.thresholds = { "fold change": (0.5, 2.), "log2 fold change": (-1, 1), "t-test": (-2, 2), "t-test p-value": (0.01, 0.01), } self.oneTailTestHi = oneTailTestHi = lambda array, low, hi: array >= hi self.oneTailTestLow = oneTailTestLow = lambda array, low, hi: array <= low self.twoTailTest = twoTailTest = lambda array, low, hi: (array >= hi) | (array <= low) self.middleTest = middleTest = lambda array, low, hi: (array <= hi) | (array >= low) self.histType = {oneTailTestHi:"hiTail", oneTailTestLow:"lowTail", twoTailTest:"twoTail", middleTest:"middle"} # [(name, func, tail test, two sample test), ...] self.score_methods = [("fold change", ExpressionSignificance_FoldChange, twoTailTest, True), ("log2 fold change", ExpressionSignificance_Log2FoldChange, twoTailTest, True), ("t-test", ExpressionSignificance_TTest_T, twoTailTest, True), ("t-test p-value", ExpressionSignificance_TTest_PValue, oneTailTestLow, True), ("anova", ExpressionSignificance_ANOVA_F, oneTailTestHi, False), ("anova p-value", ExpressionSignificance_ANOVA_PValue, oneTailTestLow, False), ("signal to noise ratio", ExpressionSignificance_SignalToNoise, twoTailTest, True), ("info gain", ExpressionSignificance_Info, oneTailTestHi, True), ("chi-square", ExpressionSignificance_ChiSquare, oneTailTestHi, True), ("mann-whitney", ExpressionSignigicance_MannWhitneyu_U, oneTailTestLow, True)] boxHistogram = OWGUI.widgetBox(self.mainArea) self.histogram = ScoreHist(self, boxHistogram) boxHistogram.layout().addWidget(self.histogram) self.histogram.show() box = OWGUI.widgetBox(self.controlArea, "Info") self.dataInfoLabel = OWGUI.widgetLabel(box, "\n\n") self.dataInfoLabel.setWordWrap(True) self.selectedInfoLabel = OWGUI.widgetLabel(box, "") box1 = OWGUI.widgetBox(self.controlArea, "Scoring Method") self.testRadioBox = OWGUI.comboBox(box1, self, "method_index", items=[sm[0] for sm in self.score_methods], callback=[self.on_scoring_method_changed, self.update_scores]) box = OWGUI.widgetBox(self.controlArea, "Target Labels") self.label_selection_widget = LabelSelectionWidget(self) self.label_selection_widget.setMaximumHeight(150) box.layout().addWidget(self.label_selection_widget) self.connect(self.label_selection_widget, SIGNAL("selection_changed()"), self.on_target_changed) self.connect(self.label_selection_widget, SIGNAL("label_activated(int)"), self.on_label_activated) self.genes_in_columns_check = OWGUI.checkBox(box, self, "genes_in_columns", "Genes in columns", callback=self.on_genes_in_columns_change) box = OWGUI.widgetBox(self.controlArea, "Selection") box.layout().setSpacing(0) self.upperBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.upperBoundary", min=-1e6, max=1e6, step= 1e-6, label="Upper threshold:", callback=self.update_boundary, callbackOnReturn=True) self.lowerBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.lowerBoundary", min=-1e6, max=1e6, step= 1e-6, label="Lower threshold:", callback=self.update_boundary, callbackOnReturn=True) check = OWGUI.checkBox(box, self, "compute_null", "Compute null distribution", callback=self.update_scores) check.disables.append(OWGUI.spin(box, self, "permutations_count", min=1, max=10, label="Permutations:", callback=self.update_scores, callbackOnReturn=True)) box1 = OWGUI.widgetBox(box, orientation='horizontal') check.disables.append(OWGUI.doubleSpin(box1, self, "selectPValue", min=2e-7, max=1.0, step=1e-7, label="P-value:")) check.disables.append(OWGUI.button(box1, self, "Select", callback=self.select_p_best)) check.makeConsistent() box1 = OWGUI.widgetBox(box, orientation='horizontal') OWGUI.spin(box1, self, "selectNBest", 0, 10000, step=1, label="Best Ranked:") OWGUI.button(box1, self, "Select", callback=self.select_n_best) box = OWGUI.widgetBox(self.controlArea, "Output") b = OWGUI.button(box, self, "&Commit", callback=self.commit) cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change") OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit) OWGUI.checkBox(box, self, "add_scores_to_output", "Add gene scores to output", callback=self.commit_if) OWGUI.rubber(self.controlArea) self.connect(self.graphButton, SIGNAL("clicked()"), self.histogram.saveToFile) self.loadSettings() self.data = None self.discData = None self.scoreCache = {} self.nullDistCache = {} self.cuts = {} self.null_dist = [] self.targets = [] self.scores = {} self.genes_in_columns = True self.target_selections = None self.on_scoring_method_changed() self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Normalize Expression Array"): OWWidget.__init__(self, parent, signalManager, name, wantGraph=True) self.inputs = [("Expression array", ExampleTable, self.setData)] self.outputs = [("Normalized expression array", ExampleTable, Default), ("Filtered expression array", ExampleTable)] self.selectedGroup = 0 self.selectedCenterMethod = 0 self.selectedMergeMethod = 0 self.zCutoff = 1.96 self.appendZScore = False self.appendRIValues = False self.autoCommit = False self.loadSettings() ## GUI self.infoBox = OWGUI.widgetLabel( OWGUI.widgetBox(self.controlArea, "Info", addSpace=True), "No data on input.") box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True) self.groupCombo = OWGUI.comboBox(box, self, "selectedGroup", callback=self.onGroupSelection) self.centerCombo = OWGUI.comboBox( self.controlArea, self, "selectedCenterMethod", box="Center Fold-change Using", items=[name for name, _ in self.CENTER_METHODS], callback=self.onCenterMethodChange, addSpace=True) self.mergeCombo = OWGUI.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 = OWGUI.doubleSpin(self.controlArea, self, "zCutoff", 0.0, 3.0, 0.01, box="Z-Score Cutoff", callback=[self.replotMA, self.commitIf]) OWGUI.separator(self.controlArea) box = OWGUI.widgetBox(self.controlArea, "Ouput") OWGUI.checkBox(box, self, "appendZScore", "Append Z-Scores", tooltip="Append calculated Z-Scores to output", callback=self.commitIf) OWGUI.checkBox( box, self, "appendRIValues", "Append Log Ratio and Intensity values", tooltip= "Append calculated Log Ratio and Intensity values to output data", callback=self.commitIf) cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on change", tooltip="Commit data on any change", callback=self.commitIf) b = OWGUI.button(box, self, "Commit", callback=self.commit) OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit) self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph) OWGUI.rubber(self.controlArea) self.graph = OWGraph(self.mainArea) self.graph.setAxisTitle(QwtPlot.xBottom, "Intensity: log<sub>10</sub>(R*G)") self.graph.setAxisTitle(QwtPlot.yLeft, "Log ratio: log<sub>2</sub>(R/G)") self.graph.showFilledSymbols = True 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.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Gene Info"): OWWidget.__init__(self, parent, signalManager, name) self.inputs = [("Examples", Orange.data.Table, self.setData)] self.outputs = [("Selected Examples", Orange.data.Table)] self.organismIndex = 0 self.taxid = None self.geneAttr = 0 self.useAttr = False self.autoCommit = False self.searchString = "" self.selectionChangedFlag = False self.useAltSource = 0 self.loadSettings() self.__initialized = False self.initfuture = None self.itemsfuture = None self.infoLabel = OWGUI.widgetLabel( OWGUI.widgetBox(self.controlArea, "Info", addSpace=True), "Initializing\n" ) self.organisms = None self.organismBox = OWGUI.widgetBox( self.controlArea, "Organism", addSpace=True) self.organismComboBox = OWGUI.comboBox( self.organismBox, self, "organismIndex", callback=self._onSelectedOrganismChanged, debuggingEnabled=0) # For now only support one alt source, with a checkbox # In the future this can be extended to multiple selections self.altSourceCheck = OWGUI.checkBox(self.organismBox, self, "useAltSource", "Show information from dictyBase", callback=self.onAltSourceChange, # debuggingEnabled=0, ) self.altSourceCheck.hide() box = OWGUI.widgetBox(self.controlArea, "Gene names", addSpace=True) self.geneAttrComboBox = OWGUI.comboBox( box, self, "geneAttr", "Gene atttibute", callback=self.updateInfoItems ) OWGUI.checkBox(box, self, "useAttr", "Use attribute names", callback=self.updateInfoItems, disables=[(-1, self.geneAttrComboBox)]) self.geneAttrComboBox.setDisabled(bool(self.useAttr)) box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True) b = OWGUI.button(box, self, "Commit", callback=self.commit) c = OWGUI.checkBox(box, self, "autoCommit", "Commit on change") OWGUI.setStopper(self, b, c, "selectionChangedFlag", callback=self.commit) # A label for dictyExpress link self.dictyExpressBox = OWGUI.widgetBox( self.controlArea, "Dicty Express") self.linkLabel = OWGUI.widgetLabel(self.dictyExpressBox, "") self.linkLabel.setOpenExternalLinks(False) self.connect(self.linkLabel, SIGNAL("linkActivated(QString)"), self.onDictyExpressLink) self.dictyExpressBox.hide() OWGUI.rubber(self.controlArea) OWGUI.lineEdit(self.mainArea, self, "searchString", "Filter", callbackOnType=True, callback=self.searchUpdate) self.treeWidget = QTreeView(self.mainArea) self.treeWidget.setRootIsDecorated(False) self.treeWidget.setSelectionMode( QAbstractItemView.ExtendedSelection) self.treeWidget.setItemDelegate( LinkStyledItemDelegate(self.treeWidget)) self.treeWidget.setUniformRowHeights(True) self.treeWidget.viewport().setMouseTracking(True) self.treeWidget.setSortingEnabled(True) self.mainArea.layout().addWidget(self.treeWidget) box = OWGUI.widgetBox(self.mainArea, "", orientation="horizontal") OWGUI.button(box, self, "Select Filtered", callback=self.selectFiltered) OWGUI.button(box, self, "Clear Selection", callback=self.treeWidget.clearSelection) self.resize(1000, 700) self.geneinfo = [] self.cells = [] self.row2geneinfo = {} self.data = None # : (# input genes, # matches genes) self.matchedInfo = 0, 0 self.selectionUpdateInProgress = False self.setBlocking(True) self.executor = ThreadExecutor(self) self.progressBarInit() task = Task( function=partial( taxonomy.ensure_downloaded, callback=methodinvoke(self, "advance", ()) ) ) task.resultReady.connect(self.initialize) task.exceptionReady.connect(self._onInitializeError) self.initfuture = self.executor.submit(task)
def __init__(self, parent=None, signalManager=None, name="KEGG Pathways"): OWWidget.__init__(self, parent, signalManager, name, wantGraph=True) self.inputs = [("Examples", Orange.data.Table, self.SetData), ("Reference", Orange.data.Table, self.SetRefData)] self.outputs = [("Selected Examples", Orange.data.Table), ("Unselected Examples", Orange.data.Table)] self.organismIndex = 0 self.geneAttrIndex = 0 self.autoCommit = False self.autoResize = True self.useReference = False self.useAttrNames = 0 self.showOrthology = True self.loadSettings() self.organismCodes = [] self._changedFlag = False self.controlArea.setMaximumWidth(250) box = OWGUI.widgetBox(self.controlArea, "Info") self.infoLabel = OWGUI.widgetLabel(box, "No data on input\n") # Organism selection. box = OWGUI.widgetBox(self.controlArea, "Organism") self.organismComboBox = OWGUI.comboBox( box, self, "organismIndex", items=[], callback=self.Update, addSpace=True, debuggingEnabled=0, tooltip="Select the organism of the input genes") # Selection of genes attribute box = OWGUI.widgetBox(self.controlArea, "Gene attribute") self.geneAttrCandidates = VariableListModel(parent=self) self.geneAttrCombo = OWGUI.comboBox( box, self, "geneAttrIndex", callback=self.Update) self.geneAttrCombo.setModel(self.geneAttrCandidates) OWGUI.checkBox(box, self, "useAttrNames", "Use variable names", disables=[(-1, self.geneAttrCombo)], callback=self.Update) self.geneAttrCombo.setDisabled(bool(self.useAttrNames)) OWGUI.separator(self.controlArea) OWGUI.checkBox(self.controlArea, self, "useReference", "From signal", box="Reference", callback=self.Update) OWGUI.separator(self.controlArea) OWGUI.checkBox(self.controlArea, self, "showOrthology", "Show pathways in full orthology", box="Orthology", callback=self.UpdateListView) OWGUI.checkBox(self.controlArea, self, "autoResize", "Resize to fit", box="Image", callback=self.UpdatePathwayViewTransform) box = OWGUI.widgetBox(self.controlArea, "Cache Control") OWGUI.button(box, self, "Clear cache", callback=self.ClearCache, tooltip="Clear all locally cached KEGG data.") OWGUI.separator(self.controlArea) box = OWGUI.widgetBox(self.controlArea, "Selection") cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on update") button = OWGUI.button(box, self, "Commit", callback=self.Commit, default=True) OWGUI.setStopper(self, button, cb, "_changedFlag", self.Commit) OWGUI.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(spliter) spliter.addWidget(self.listView) self.listView.setAllColumnsShowFocus(1) self.listView.setColumnCount(4) self.listView.setHeaderLabels(["Pathway", "P value", "Genes", "Reference"]) self.listView.setSelectionMode(QTreeWidget.SingleSelection) self.listView.setSortingEnabled(True) self.listView.setMaximumHeight(200) self.connect(self.listView, SIGNAL("itemSelectionChanged()"), self.UpdatePathwayView) self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph) select = QAction( "Select All", self, shortcut=QKeySequence.SelectAll ) select.triggered.connect(self.selectAll) self.addAction(select) self.data = None self.refData = None self.resize(800, 600) self.connect(self, SIGNAL("widgetStateChanged(QString, int, QString)"), self.onStateChange) self.has_new_data = False self.has_new_reference_set = False self._executor = ThreadExecutor() self.setEnabled(False) self.setBlocking(True) QTimer.singleShot(0, self._initialize) self.infoLabel.setText("Fetching organism definitions\n")
def __init__(self, parent=None, signalManager=None): # self.callbackDeposit = [] # deposit for OWGUI callback functions OWWidget.__init__(self, parent, signalManager, 'Expression Profiles', 1) #set default settings self.ShowAverageProfile = 1 self.ShowSingleProfiles = 0 self.PointWidth = 2 self.CurveWidth = 1 self.AverageCurveWidth = 4 self.BoxPlotWidth = 2 self.SelectedClasses = [] self.Classes = [] self.autoSendSelected = 0 self.selectionChangedFlag = False self.CutLow = 0 self.CutHigh = 0 self.CutEnabled = 0 self.profileLabel = None #load settings self.loadSettings() # GUI self.graph = profilesGraph(self, self.mainArea, "") self.mainArea.layout().addWidget(self.graph) self.graph.hide() self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile) # GUI definition self.tabs = OWGUI.tabWidget(self.space) # GRAPH TAB GraphTab = OWGUI.createTabPage(self.tabs, "Graph") ## display options self.infoLabel = OWGUI.widgetLabel(OWGUI.widgetBox(GraphTab, "Info"), "No data on input.") displayOptBox = OWGUI.widgetBox( GraphTab, "Display") #QVButtonGroup("Display", GraphTab) displayOptButtons = [ 'Majority Class', 'Majority Class Probability', 'Target Class Probability', 'Number of Instances' ] OWGUI.checkBox(displayOptBox, self, 'ShowSingleProfiles', 'Expression Profiles', tooltip='', callback=self.updateShowSingleProfiles) OWGUI.checkBox(displayOptBox, self, 'ShowAverageProfile', 'Box Plot', tooltip='', callback=self.updateShowAverageProfile) ## class selection (classQLB) self.classQVGB = OWGUI.widgetBox(GraphTab, "Classes") #QVGroupBox(GraphTab) ## self.classQVGB.setTitle("Classes") self.classQLB = OWGUI.listBox( self.classQVGB, self, "SelectedClasses", "Classes", selectionMode=QListWidget.MultiSelection, callback=self.classSelectionChange) #QListBox(self.classQVGB) ## self.classQLB.setSelectionMode(QListBox.Multi) self.unselectAllClassedQLB = OWGUI.button( self.classQVGB, self, "Unselect all", callback=self.SUAclassQLB ) #QPushButton("(Un)Select All", self.classQVGB) ## self.connect(self.unselectAllClassedQLB, SIGNAL("clicked()"), self.SUAclassQLB) ## self.connect(self.classQLB, SIGNAL("selectionChanged()"), self.classSelectionChange) ## show single/average profile ## self.showAverageQLB = QPushButton("Box Plot", self.classQVGB) ## self.showAverageQLB.setToggleButton(1) ## self.showAverageQLB.setOn(self.ShowAverageProfile) ## self.showSingleQLB = QPushButton("Single Profiles", self.classQVGB) ## self.showSingleQLB.setToggleButton(1) ## self.showSingleQLB.setOn(self.ShowSingleProfiles) ## self.connect(self.showAverageQLB, SIGNAL("toggled(bool)"), self.updateShowAverageProfile) ## self.connect(self.showSingleQLB, SIGNAL("toggled(bool)"), self.updateShowSingleProfiles) ## self.tabs.insertTab(GraphTab, "Graph") # SETTINGS TAB SettingsTab = OWGUI.createTabPage(self.tabs, "Settings") #QVGroupBox(self) self.profileLabelComboBox = OWGUI.comboBox(SettingsTab, self, 'profileLabel', 'Profile Labels', sendSelectedValue=True, valueType=str) OWGUI.hSlider(SettingsTab, self, 'PointWidth', box='Point Width', minValue=0, maxValue=9, step=1, callback=self.updatePointWidth, ticks=1) OWGUI.hSlider(SettingsTab, self, 'CurveWidth', box='Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateCurveWidth, ticks=1) OWGUI.hSlider(SettingsTab, self, 'AverageCurveWidth', box='Average Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateAverageCurveWidth, ticks=1) OWGUI.hSlider(SettingsTab, self, 'BoxPlotWidth', box='Box Plot Width', minValue=0, maxValue=9, step=1, callback=self.updateBoxPlotWidth, ticks=1) OWGUI.checkBox(SettingsTab, self, 'graph.renderAntialiased', "Render antialiased", callback=self.graph.setCurveRenderHints) ## graph y scale box = OWGUI.widgetBox( SettingsTab, "Threshold/ Values" ) #QVButtonGroup("Threshol/ Values", SettingsTab) OWGUI.checkBox(box, self, 'CutEnabled', "Enabled", callback=self.setCutEnabled) self.sliderCutLow = OWGUI.qwtHSlider(box, self, 'CutLow', label='Low:', labelWidth=33, minValue=-20, maxValue=0, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis) self.sliderCutHigh = OWGUI.qwtHSlider(box, self, 'CutHigh', label='High:', labelWidth=33, minValue=0, maxValue=20, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis) if not self.CutEnabled: self.sliderCutLow.box.setDisabled(1) self.sliderCutHigh.box.setDisabled(1) ## self.tabs.insertTab(SettingsTab, "Settings") self.toolbarSelection = ZoomSelectToolbar( self, self.controlArea, self.graph, self.autoSendSelected, buttons=(ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan, ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconSpace, ZoomSelectToolbar.IconRemoveLast, ZoomSelectToolbar.IconRemoveAll, ZoomSelectToolbar.IconSendSelection)) cb = OWGUI.checkBox(self.controlArea, self, "autoSendSelected", "Auto send on selection change") OWGUI.setStopper(self, self.toolbarSelection.buttonSendSelections, cb, "selectionChangedFlag", self.commit) # inputs # data and graph temp variables self.inputs = [("Examples", ExampleTable, self.data, Default + Multiple)] self.outputs = [("Examples", ExampleTable, Default)] # temp variables self.MAdata = [] self.classColor = None self.classBrighterColor = None self.numberOfClasses = 0 self.classValues = [] self.ctrlPressed = False self.attrIcons = self.createAttributeIconDict() self.graph.canvas().setMouseTracking(1) # self.zoomStack = [] ## self.connect(self.graph, ## SIGNAL('plotMousePressed(const QMouseEvent&)'), ## self.onMousePressed) ## self.connect(self.graph, ## SIGNAL('plotMouseReleased(const QMouseEvent&)'), ## self.onMouseReleased) self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, title="Venn Diagram"): super(OWVennDiagram, self).__init__(parent, signalManager, title, wantGraph=True) self.autocommit = False # Selected disjoint subset indices self.selection = [] # Stored input set hints # {(index, inputname, attributes): (selectedattrname, itemsettitle)} # The 'selectedattrname' can be None self.inputhints = {} # Use identifier columns for instance matching self.useidentifiers = 1 self.loadSettings() # Output changed flag self._changed = False # Diagram update is in progress self._updating = False # Input update is in progress self._inputUpdate = False # All input tables have the same domain. self.samedomain = True # Input datasets in the order they were 'connected'. self.data = OrderedDict() # Extracted input item sets in the order they were 'connected' self.itemsets = OrderedDict() # GUI box = OWGUI.widgetBox(self.controlArea, "Info") self.info = OWGUI.widgetLabel(box, "No data on input\n") self.identifiersBox = OWGUI.radioButtonsInBox( self.controlArea, self, "useidentifiers", [], box="Data Instance Identifiers", callback=self._on_useidentifiersChanged ) self.useequalityButton = OWGUI.appendRadioButton( self.identifiersBox, self, "useidentifiers", "Use instance equality" ) rb = OWGUI.appendRadioButton( self.identifiersBox, self, "useidentifiers", "Use identifiers" ) self.inputsBox = OWGUI.indentedBox( self.identifiersBox, sep=OWGUI.checkButtonOffsetHint(rb) ) self.inputsBox.setEnabled(self.useidentifiers == 1) for i in range(5): box = OWGUI.widgetBox(self.inputsBox, "Data set #%i" % (i + 1), flat=True) model = OWItemModels.VariableListModel(parent=self) cb = QComboBox() cb.setModel(model) cb.activated[int].connect(self._on_inputAttrActivated) box.setEnabled(False) # Store the combo in the box for later use. box.combo_box = cb box.layout().addWidget(cb) OWGUI.rubber(self.controlArea) box = OWGUI.widgetBox(self.controlArea, "Output") cb = OWGUI.checkBox(box, self, "autocommit", "Commit on any change") b = OWGUI.button(box, self, "Commit", callback=self.commit, default=True) OWGUI.setStopper(self, b, cb, "_changed", callback=self.commit) # Main area view self.scene = QGraphicsScene() self.view = QGraphicsView(self.scene) self.view.setRenderHint(QPainter.Antialiasing) self.view.setBackgroundRole(QPalette.Window) self.view.setFrameStyle(QGraphicsView.StyledPanel) self.mainArea.layout().addWidget(self.view) self.vennwidget = VennDiagram() self.vennwidget.resize(400, 400) self.vennwidget.itemTextEdited.connect(self._on_itemTextEdited) self.scene.selectionChanged.connect(self._on_selectionChanged) self.scene.addItem(self.vennwidget) self.resize(self.controlArea.sizeHint().width() + 550, max(self.controlArea.sizeHint().height(), 550)) self._queue = [] self.graphButton.clicked.connect(self.saveImage)
def __init__(self, parent=None, signalManager=None, name="Normalize Expression Array"): OWWidget.__init__(self, parent, signalManager, name, wantGraph=True) self.inputs = [("Expression array", ExampleTable, self.setData)] self.outputs = [("Normalized expression array", ExampleTable, Default), ("Filtered expression array", ExampleTable)] self.selectedGroup = 0 self.selectedCenterMethod = 0 self.selectedMergeMethod = 0 self.zCutoff = 1.96 self.appendZScore = False self.appendRIValues = False self.autoCommit = False self.loadSettings() ## GUI self.infoBox = OWGUI.widgetLabel(OWGUI.widgetBox(self.controlArea, "Info", addSpace=True), "No data on input.") box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True) self.groupCombo = OWGUI.comboBox(box, self, "selectedGroup", callback=self.onGroupSelection ) self.centerCombo = OWGUI.comboBox(self.controlArea, self, "selectedCenterMethod", box="Center Fold-change Using", items=[name for name, _ in self.CENTER_METHODS], callback=self.onCenterMethodChange, addSpace=True ) self.mergeCombo = OWGUI.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 = OWGUI.doubleSpin(self.controlArea, self, "zCutoff", 0.0, 3.0, 0.01, box="Z-Score Cutoff", callback=[self.replotMA, self.commitIf]) OWGUI.separator(self.controlArea) box = OWGUI.widgetBox(self.controlArea, "Ouput") OWGUI.checkBox(box, self, "appendZScore", "Append Z-Scores", tooltip="Append calculated Z-Scores to output", callback=self.commitIf ) OWGUI.checkBox(box, self, "appendRIValues", "Append Log Ratio and Intensity values", tooltip="Append calculated Log Ratio and Intensity values to output data", callback=self.commitIf ) cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on change", tooltip="Commit data on any change", callback=self.commitIf ) b = OWGUI.button(box, self, "Commit", callback=self.commit) OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit) self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph) OWGUI.rubber(self.controlArea) self.graph = OWGraph(self.mainArea) self.graph.setAxisTitle(QwtPlot.xBottom, "Intensity: log<sub>10</sub>(R*G)") self.graph.setAxisTitle(QwtPlot.yLeft, "Log ratio: log<sub>2</sub>(R/G)") self.graph.showFilledSymbols = True 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.resize(800, 600)
def __init__(self, parent=None, signalManager=None, title="Expression Profile Distances"): OWWidget.__init__(self, parent, signalManager, title) self.inputs = [("Example Table", ExampleTable, self.set_data)] self.outputs = [("Distances", Orange.core.SymMatrix), ("Sorted Example Table", ExampleTable)] self.distance_measure = 0 self.auto_commit = False self.changed_flag = False self.loadSettings() ######## # GUI ######## self.info_box = OWGUI.widgetLabel( OWGUI.widgetBox(self.controlArea, "Input", addSpace=True), "No data on input\n") box = OWGUI.widgetBox(self.controlArea, "Separate By", addSpace=True) self.separate_view = QListView() self.separate_view.setSelectionMode(QListView.MultiSelection) box.layout().addWidget(self.separate_view) box = OWGUI.widgetBox(self.controlArea, "Sort By", addSpace=True) self.relevant_view = QListView() self.relevant_view.setSelectionMode(QListView.MultiSelection) box.layout().addWidget(self.relevant_view) self.distance_view = OWGUI.comboBox( self.controlArea, self, "distance_measure", box="Distance Measure", items=[d[0] for d in self.DISTANCE_FUNCTIONS]) OWGUI.rubber(self.controlArea) box = OWGUI.widgetBox(self.controlArea, "Commit") cb = OWGUI.checkBox( box, self, "auto_commit", "Commit on any change", tooltip="Compute and send the distances on any change.", callback=self.commit_if) b = OWGUI.button( box, self, "Commit", tooltip="Compute the distances and send the output signals.", callback=self.commit, default=True) OWGUI.setStopper(self, b, cb, "changed_flag", callback=self.commit) self.groups_box = OWGUI.widgetBox(self.mainArea, "Groups") self.groups_scroll_area = QScrollArea() self.groups_box.layout().addWidget(self.groups_scroll_area) self.data = None self.partitions = [] self.matrix = None self.split_groups = [] self._disable_updates = False self.resize(800, 600)