def __init__(self, parent=None, signalManager = None, name='GSEA'): OWWidget.__init__(self, parent, signalManager, name) self.inputs = [("Examples", ExampleTable, self.setData)] self.outputs = [("Examples with selected genes only", ExampleTable), ("Results", ExampleTable), ("Distance Matrix", orange.SymMatrix) ] self.res = None self.dm = None self.name = 'GSEA' self.minSubsetSize = 3 self.minSubsetSizeC = True self.maxSubsetSize = 1000 self.maxSubsetSizeC = True self.minSubsetPart = 10 self.minSubsetPartC = True self.perms = 100 self.csgm = False self.gsgo = False self.gskegg = False self.buildDistances = False self.selectedPhenVar = 0 self.organismIndex = 0 self.atLeast = 3 self.permutationTypes = [("Phenotype", "p"),("Gene", "g") ] self.ptype = 0 self.correlationTypes = [ ("Signal2Noise", "s2n") ] self.ctype = 0 self.data = None self.geneSets = {} self.tabs = OWGUI.tabWidget(self.controlArea) ca = OWGUI.createTabPage(self.tabs, "Basic") box = OWGUI.widgetBox(ca, 'Organism') #FROM KEGG WIDGET - organism selection self.organismTaxids = [] self.organismComboBox = cb = OWGUI.comboBox(box, self, "organismIndex", items=[], debuggingEnabled=0) #changed cb.setMaximumWidth(200) #OWGUI.checkBox(box, self, "csgm", "Case sensitive gene matching") box2 = OWGUI.widgetBox(ca, "Descriptors") self.phenCombo = OWGUI.comboBox(box2, self, "selectedPhenVar", items=[], callback=self.phenComboChange, label="Phenotype:") self.geneCombo = OWGUI.comboBox(box2, self, "selectedGeneVar", items=[], label = "Gene:") self.allowComboChangeCallback = False ma = self.mainArea self.listView = QTreeWidget(ma) ma.layout().addWidget(self.listView) self.listView.setAllColumnsShowFocus(1) self.listView.setColumnCount(9) self.listView.setHeaderLabels(["Collection", "Geneset", "NES", "ES", "P-value", "FDR", "Size", "Matched Size", "Genes"]) self.listView.header().setStretchLastSection(True) self.listView.header().setClickable(True) self.listView.header().setSortIndicatorShown(True) self.listView.setSortingEnabled(True) #self.listView.header().setResizeMode(0, QHeaderView.Stretch) self.listView.setSelectionMode(QAbstractItemView.NoSelection) self.connect(self.listView, SIGNAL("itemSelectionChanged()"), self.newPathwaySelected) OWGUI.separator(ca) OWGUI.widgetLabel(ca, "Phenotype selection:") self.psel = PhenotypesSelection(ca) self.resize(600,50) OWGUI.separator(ca) OWGUI.checkBox(ca, self, "buildDistances", "Compute geneset distances") self.btnApply = OWGUI.button(ca, self, "&Compute", callback = self.compute, disabled=0) fileBox = OWGUI.widgetBox(ca, orientation='horizontal') OWGUI.button(fileBox, self, "Load", callback = self.loadData, disabled=0, debuggingEnabled=0) OWGUI.button(fileBox, self, "Save", callback = self.saveData, disabled=0, debuggingEnabled=0) #ca.layout().addStretch(1) ca = OWGUI.createTabPage(self.tabs, "Gene sets") box = OWGUI.widgetBox(ca) self.gridSel = [] self.geneSel = [] #FIXME temporary disabled - use the same as in new "David" widget self.lbgs = OWGUI.listBox(box, self, "gridSel", "geneSel", selectionMode = QListWidget.MultiSelection) OWGUI.button(box, self, "From &File", callback = self.addCollection, disabled=0, debuggingEnabled=0) box = OWGUI.widgetBox(box, "Additional sources:") OWGUI.checkBox(box, self, "gskegg", "KEGG pathways") OWGUI.checkBox(box, self, "gsgo", "GO terms") #ca.layout().addStretch(1) ca = OWGUI.createTabPage(self.tabs, "Settings") box = OWGUI.widgetBox(ca, 'Properties') self.permTypeF = OWGUI.comboBoxWithCaption(box, self, "ptype", items=nth(self.permutationTypes, 0), \ tooltip="Permutation type.", label="Permute") _ = OWGUI.spin(box, self, "perms", 50, 1000, orientation="horizontal", label="Times") self.corTypeF = OWGUI.comboBoxWithCaption(box, self, "ctype", items=nth(self.correlationTypes, 0), \ tooltip="Correlation type.", label="Correlation") box = OWGUI.widgetBox(ca, 'Subset Filtering') _,_ = OWGUI.checkWithSpin(box, self, "Min. Subset Size", 1, 10000, "minSubsetSizeC", "minSubsetSize", "") #TODO check sizes _,_ = OWGUI.checkWithSpin(box, self, "Max. Subset Size", 1, 10000, "maxSubsetSizeC", "maxSubsetSize", "") _,_ = OWGUI.checkWithSpin(box, self, "Min. Subset Part (%)", 1, 100, "minSubsetPartC", "minSubsetPart", "") box = OWGUI.widgetBox(ca, 'Gene Filtering') _ = OWGUI.spin(box, self, "atLeast", 2, 10, label="Min. Values in Group") ca.layout().addStretch(1) self.addComment("Computation was not started.") if sys.platform == "darwin": self.loadFileName = os.path.expanduser("~/") else: self.loadFileName = "." self.gridSels = [] self.loadSettings() self.setBlocking(True) QTimer.singleShot(0, self.UpdateOrganismComboBox) def cleanInvalid(maxn): """ Removes invalid gene set selection """ notAllOk = True while notAllOk: self.gridSels = getattr(self, "gridSels") notAllOk = False for i,a in enumerate(self.gridSels): if a >= maxn: self.gridSels.pop(i) notAllOk = True break cleanInvalid(len(self.geneSel)) self.gridSel = self.gridSels self.gridSels = self.gridSel
def __init__(self,parent=None, signalManager = None): OWWidget.__init__(self, parent, signalManager, "Nomogram", 1) #self.setWFlags(Qt.WResizeNoErase | Qt.WRepaintNoErase) #this works like magic.. no flicker during repaint! self.parent = parent # self.setWFlags(self.getWFlags()+Qt.WStyle_Maximize) self.callbackDeposit = [] # deposit for OWGUI callback functions self.alignType = 0 self.contType = 0 self.yAxis = 0 self.probability = 0 self.verticalSpacing = 60 self.verticalSpacingContinuous = 100 self.diff_between_ordinal = 30 self.fontSize = 9 self.lineWidth = 1 self.histogram = 0 self.histogram_size = 10 self.data = None self.cl = None self.confidence_check = 0 self.confidence_percent = 95 self.sort_type = 0 self.loadSettings() self.pointsName = ["Total", "Total"] self.totalPointsName = ["Probability", "Probability"] self.bnomogram = None self.inputs=[("Classifier", orange.Classifier, self.classifier), ("Data", Orange.data.Table, self.data)] self.TargetClassIndex = 0 self.targetCombo = OWGUI.comboBox(self.controlArea, self, "TargetClassIndex", " Target Class ", addSpace=True, tooltip='Select target (prediction) class in the model.', callback = self.setTarget) self.alignRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'alignType', ['Align left', 'Align by zero influence'], box='Attribute placement', tooltips=['Attributes in nomogram are left aligned', 'Attributes are not aligned, top scale represents true (normalized) regression coefficient value'], addSpace=True, callback=self.showNomogram) self.verticalSpacingLabel = OWGUI.spin(self.alignRadio, self, 'verticalSpacing', 15, 200, label = 'Vertical spacing:', orientation = 0, tooltip='Define space (pixels) between adjacent attributes.', callback = self.showNomogram) self.ContRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'contType', ['1D projection', '2D curve'], 'Continuous attributes', tooltips=['Continuous attribute are presented on a single scale', 'Two dimensional space is used to present continuous attributes in nomogram.'], addSpace=True, callback=[lambda:self.verticalSpacingContLabel.setDisabled(not self.contType), self.showNomogram]) self.verticalSpacingContLabel = OWGUI.spin(OWGUI.indentedBox(self.ContRadio, sep=OWGUI.checkButtonOffsetHint(self.ContRadio.buttons[-1])), self, 'verticalSpacingContinuous', 15, 200, label = "Height", orientation=0, tooltip='Define space (pixels) between adjacent 2d presentation of attributes.', callback = self.showNomogram) self.verticalSpacingContLabel.setDisabled(not self.contType) self.yAxisRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'yAxis', ['Point scale', 'Log odds ratios'], 'Scale', tooltips=['values are normalized on a 0-100 point scale','values on top axis show log-linear contribution of attribute to full model'], addSpace=True, callback=self.showNomogram) layoutBox = OWGUI.widgetBox(self.controlArea, "Display", orientation=1, addSpace=True) self.probabilityCheck = OWGUI.checkBox(layoutBox, self, 'probability', 'Show prediction', tooltip='', callback = self.setProbability) self.CICheck, self.CILabel = OWGUI.checkWithSpin(layoutBox, self, 'Confidence intervals (%):', min=1, max=99, step = 1, checked='confidence_check', value='confidence_percent', checkCallback=self.showNomogram, spinCallback = self.showNomogram) self.histogramCheck, self.histogramLabel = OWGUI.checkWithSpin(layoutBox, self, 'Show histogram, size', min=1, max=30, checked='histogram', value='histogram_size', step = 1, tooltip='-(TODO)-', checkCallback=self.showNomogram, spinCallback = self.showNomogram) OWGUI.separator(layoutBox) self.sortOptions = ["No sorting", "Absolute importance", "Positive influence", "Negative influence"] self.sortBox = OWGUI.comboBox(layoutBox, self, "sort_type", label="Sort by ", items=self.sortOptions, callback = self.sortNomogram, orientation="horizontal") OWGUI.rubber(self.controlArea) self.connect(self.graphButton, SIGNAL("clicked()"), self.menuItemPrinter) #add a graph widget self.header = OWNomogramHeader(None, self.mainArea) self.header.setFixedHeight(60) self.header.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff) self.header.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff) self.graph = OWNomogramGraph(self.bnomogram, self.mainArea) self.graph.setMinimumWidth(200) self.graph.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff) self.footer = OWNomogramHeader(None, self.mainArea) self.footer.setFixedHeight(60*2+10) self.footer.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff) self.footer.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff) self.mainArea.layout().addWidget(self.header) self.mainArea.layout().addWidget(self.graph) self.mainArea.layout().addWidget(self.footer) self.resize(700,500) #self.repaint() #self.update() # mouse pressed flag self.mousepr = False