def _genematcher(self): """ Return a Future[gene.SequenceMatcher] """ taxid = self.taxid_list[self.speciesIndex] current, matcher_f = self.__genematcher if taxid == current and \ not matcher_f.cancelled(): return matcher_f self._invalidateGeneMatcher() if taxid is None: self.__genematcher = (None, fulfill(gene.matcher([]))) return self.__genematcher[1] matchers = [gene.GMGO, gene.GMKEGG, gene.GMNCBI, gene.GMAffy] matchers = [ m for m, use in zip(matchers, self.geneMatcherSettings) if use ] def create(): return gene.matcher([m(taxid) for m in matchers]) matcher_f = self._executor.submit(create) self.__genematcher = (taxid, matcher_f) return self.__genematcher[1]
def _genematcher(self): """ Return a Future[gene.SequenceMatcher] """ taxid = self.taxid_list[self.speciesIndex] current, matcher_f = self.__genematcher if taxid == current and \ not matcher_f.cancelled(): return matcher_f self._invalidateGeneMatcher() if taxid is None: self.__genematcher = (None, fulfill(gene.matcher([]))) return self.__genematcher[1] matchers = [gene.GMGO, gene.GMKEGG, gene.GMNCBI, gene.GMAffy] matchers = [m for m, use in zip(matchers, self.geneMatcherSettings) if use] def create(): return gene.matcher([m(taxid) for m in matchers]) matcher_f = self._executor.submit(create) self.__genematcher = (taxid, matcher_f) return self.__genematcher[1]
import Orange from orangecontrib.bio import dicty, geneset, gsea, gene dbc = dicty.DictyExpress() data = dbc.get_data(sample='pkaC-', time="8") #select the first chip (the first attribute) data = data.translate([data.domain.attributes[0]], True) matcher = gene.matcher([[gene.GMKEGG("dicty"), gene.GMDicty()]]) genesets = geneset.collections((("KEGG",), "dicty")) res = gsea.direct(data, matcher=matcher, min_part=0.05, gene_sets=genesets) print "%-40s %6s %6s %6s %7s" % ("LABEL", "NES", "P-VAL", "SIZE", "MATCHED") for name,resu in sorted(res.items()[:10], key=lambda x: x[1]["p"]): print "%-40s %6.3f %6.3f %6d %7d" % (name.name[:35], resu["nes"], resu["p"], resu["size"], resu["matched_size"])
def create(): return gene.matcher([m(taxid) for m in matchers])
def _invalidateGeneMatcher(self): _, f = self.__genematcher f.cancel() self.__genematcher = (None, fulfill(gene.matcher([])))
def __init__(self, parent=None): super().__init__(parent) self.geneMatcherSettings = [False, False, True, False] self.data = None self.referenceData = None self.taxid_list = [] self.__genematcher = (None, fulfill(gene.matcher([]))) self.__invalidated = False self.currentAnnotatedCategories = [] self.state = None self.__state = OWSetEnrichment.Initializing box = gui.widgetBox(self.controlArea, "Info") self.infoBox = gui.widgetLabel(box, "Info") self.infoBox.setText("No data on input.\n") self.speciesComboBox = gui.comboBox( self.controlArea, self, "speciesIndex", "Species", callback=self.__on_speciesIndexChanged) box = gui.widgetBox(self.controlArea, "Entity names") self.geneAttrComboBox = gui.comboBox( box, self, "geneattr", "Entity feature", sendSelectedValue=0, callback=self.updateAnnotations) cb = gui.checkBox( box, self, "genesinrows", "Use feature names", callback=self.updateAnnotations, disables=[(-1, self.geneAttrComboBox)]) cb.makeConsistent() # gui.button(box, self, "Gene matcher settings", # callback=self.updateGeneMatcherSettings, # tooltip="Open gene matching settings dialog") self.referenceRadioBox = gui.radioButtonsInBox( self.controlArea, self, "useReferenceData", ["All entities", "Reference set (input)"], tooltips=["Use entire genome (for gene set enrichment) or all " + "available entities for reference", "Use entities from Reference Examples input signal " + "as reference"], box="Reference", callback=self.updateAnnotations) box = gui.widgetBox(self.controlArea, "Entity Sets") self.groupsWidget = QtGui.QTreeWidget(self) self.groupsWidget.setHeaderLabels(["Category"]) box.layout().addWidget(self.groupsWidget) hLayout = QtGui.QHBoxLayout() hLayout.setSpacing(10) hWidget = gui.widgetBox(self.mainArea, orientation=hLayout) gui.spin(hWidget, self, "minClusterCount", 0, 100, label="Entities", tooltip="Minimum entity count", callback=self.filterAnnotationsChartView, callbackOnReturn=True, checked="useMinCountFilter", checkCallback=self.filterAnnotationsChartView) pvalfilterbox = gui.widgetBox(hWidget, orientation="horizontal") cb = gui.checkBox( pvalfilterbox, self, "useMaxPValFilter", "p-value", callback=self.filterAnnotationsChartView) sp = gui.doubleSpin( pvalfilterbox, self, "maxPValue", 0.0, 1.0, 0.0001, tooltip="Maximum p-value", callback=self.filterAnnotationsChartView, callbackOnReturn=True, ) sp.setEnabled(self.useMaxFDRFilter) cb.toggled[bool].connect(sp.setEnabled) pvalfilterbox.layout().setAlignment(cb, Qt.AlignRight) pvalfilterbox.layout().setAlignment(sp, Qt.AlignLeft) fdrfilterbox = gui.widgetBox(hWidget, orientation="horizontal") cb = gui.checkBox( fdrfilterbox, self, "useMaxFDRFilter", "FDR", callback=self.filterAnnotationsChartView) sp = gui.doubleSpin( fdrfilterbox, self, "maxFDR", 0.0, 1.0, 0.0001, tooltip="Maximum False discovery rate", callback=self.filterAnnotationsChartView, callbackOnReturn=True, ) sp.setEnabled(self.useMaxFDRFilter) cb.toggled[bool].connect(sp.setEnabled) fdrfilterbox.layout().setAlignment(cb, Qt.AlignRight) fdrfilterbox.layout().setAlignment(sp, Qt.AlignLeft) self.filterLineEdit = QtGui.QLineEdit( self, placeholderText="Filter ...") self.filterCompleter = QtGui.QCompleter(self.filterLineEdit) self.filterCompleter.setCaseSensitivity(Qt.CaseInsensitive) self.filterLineEdit.setCompleter(self.filterCompleter) hLayout.addWidget(self.filterLineEdit) self.mainArea.layout().addWidget(hWidget) self.filterLineEdit.textChanged.connect( self.filterAnnotationsChartView) self.annotationsChartView = QtGui.QTreeView( alternatingRowColors=True, sortingEnabled=True, selectionMode=QtGui.QTreeView.ExtendedSelection, rootIsDecorated=False, editTriggers=QtGui.QTreeView.NoEditTriggers, ) self.annotationsChartView.viewport().setMouseTracking(True) self.mainArea.layout().addWidget(self.annotationsChartView) contextEventFilter = gui.VisibleHeaderSectionContextEventFilter( self.annotationsChartView) self.annotationsChartView.header().installEventFilter(contextEventFilter) self.groupsWidget.itemClicked.connect(self.subsetSelectionChanged) gui.auto_commit(self.controlArea, self, "autocommit", "Commit") self.setBlocking(True) task = EnsureDownloaded( [("Taxonomy", "ncbi_taxonomy.tar.gz"), (geneset.sfdomain, "index.pck")] ) task.finished.connect(self.__initialize_finish) self.setStatusMessage("Initializing") self._executor = ThreadExecutor( parent=self, threadPool=QtCore.QThreadPool(self)) self._executor.submit(task)
def __init__(self, parent=None): super().__init__(parent) self.geneMatcherSettings = [False, False, True, False] self.data = None self.referenceData = None self.taxid_list = [] self.__genematcher = (None, fulfill(gene.matcher([]))) self.__invalidated = False self.currentAnnotatedCategories = [] self.state = None self.__state = OWSetEnrichment.Initializing box = gui.widgetBox(self.controlArea, "Info") self.infoBox = gui.widgetLabel(box, "Info") self.infoBox.setText("No data on input.\n") self.speciesComboBox = gui.comboBox( self.controlArea, self, "speciesIndex", "Species", callback=self.__on_speciesIndexChanged) box = gui.widgetBox(self.controlArea, "Entity names") self.geneAttrComboBox = gui.comboBox(box, self, "geneattr", "Entity feature", sendSelectedValue=0, callback=self.updateAnnotations) cb = gui.checkBox(box, self, "genesinrows", "Use feature names", callback=self.updateAnnotations, disables=[(-1, self.geneAttrComboBox)]) cb.makeConsistent() # gui.button(box, self, "Gene matcher settings", # callback=self.updateGeneMatcherSettings, # tooltip="Open gene matching settings dialog") self.referenceRadioBox = gui.radioButtonsInBox( self.controlArea, self, "useReferenceData", ["All entities", "Reference set (input)"], tooltips=[ "Use entire genome (for gene set enrichment) or all " + "available entities for reference", "Use entities from Reference Examples input signal " + "as reference" ], box="Reference", callback=self.updateAnnotations) box = gui.widgetBox(self.controlArea, "Entity Sets") self.groupsWidget = QTreeWidget(self) self.groupsWidget.setHeaderLabels(["Category"]) box.layout().addWidget(self.groupsWidget) hLayout = QHBoxLayout() hLayout.setSpacing(10) hWidget = gui.widgetBox(self.mainArea, orientation=hLayout) gui.spin(hWidget, self, "minClusterCount", 0, 100, label="Entities", tooltip="Minimum entity count", callback=self.filterAnnotationsChartView, callbackOnReturn=True, checked="useMinCountFilter", checkCallback=self.filterAnnotationsChartView) pvalfilterbox = gui.widgetBox(hWidget, orientation="horizontal") cb = gui.checkBox(pvalfilterbox, self, "useMaxPValFilter", "p-value", callback=self.filterAnnotationsChartView) sp = gui.doubleSpin( pvalfilterbox, self, "maxPValue", 0.0, 1.0, 0.0001, tooltip="Maximum p-value", callback=self.filterAnnotationsChartView, callbackOnReturn=True, ) sp.setEnabled(self.useMaxFDRFilter) cb.toggled[bool].connect(sp.setEnabled) pvalfilterbox.layout().setAlignment(cb, Qt.AlignRight) pvalfilterbox.layout().setAlignment(sp, Qt.AlignLeft) fdrfilterbox = gui.widgetBox(hWidget, orientation="horizontal") cb = gui.checkBox(fdrfilterbox, self, "useMaxFDRFilter", "FDR", callback=self.filterAnnotationsChartView) sp = gui.doubleSpin( fdrfilterbox, self, "maxFDR", 0.0, 1.0, 0.0001, tooltip="Maximum False discovery rate", callback=self.filterAnnotationsChartView, callbackOnReturn=True, ) sp.setEnabled(self.useMaxFDRFilter) cb.toggled[bool].connect(sp.setEnabled) fdrfilterbox.layout().setAlignment(cb, Qt.AlignRight) fdrfilterbox.layout().setAlignment(sp, Qt.AlignLeft) self.filterLineEdit = QLineEdit(self, placeholderText="Filter ...") self.filterCompleter = QCompleter(self.filterLineEdit) self.filterCompleter.setCaseSensitivity(Qt.CaseInsensitive) self.filterLineEdit.setCompleter(self.filterCompleter) hLayout.addWidget(self.filterLineEdit) self.mainArea.layout().addWidget(hWidget) self.filterLineEdit.textChanged.connect( self.filterAnnotationsChartView) self.annotationsChartView = QTreeView( alternatingRowColors=True, sortingEnabled=True, selectionMode=QTreeView.ExtendedSelection, rootIsDecorated=False, editTriggers=QTreeView.NoEditTriggers, ) self.annotationsChartView.viewport().setMouseTracking(True) self.mainArea.layout().addWidget(self.annotationsChartView) contextEventFilter = gui.VisibleHeaderSectionContextEventFilter( self.annotationsChartView) self.annotationsChartView.header().installEventFilter( contextEventFilter) self.groupsWidget.itemClicked.connect(self.subsetSelectionChanged) gui.auto_commit(self.controlArea, self, "autocommit", "Commit") self.setBlocking(True) task = EnsureDownloaded([(taxonomy.Taxonomy.DOMAIN, taxonomy.Taxonomy.FILENAME), (geneset.sfdomain, "index.pck")]) task.finished.connect(self.__initialize_finish) self.setStatusMessage("Initializing") self._executor = ThreadExecutor(parent=self, threadPool=QThreadPool(self)) self._executor.submit(task)
import Orange from orangecontrib.bio import dicty, geneset, gsea, gene, geo gds = geo.GDS("GDS10") data = gds.getdata(transpose=True) matcher = gene.matcher([gene.GMKEGG("H**o sapiens")]) genesets = geneset.collections((("KEGG", ), "H**o sapiens")) #the number of permutations (n) should be much higher res = gsea.run(data, gene_sets=genesets, matcher=matcher, min_part=0.05, permutation="phenotype", n=10, phen_desc=data.domain["tissue"], gene_desc=True) print print "GSEA results (descriptor: tissue)" print "%-40s %6s %6s %6s %7s" % ("LABEL", "NES", "FDR", "SIZE", "MATCHED") for gs, resu in sorted(res.items(), key=lambda x: x[1]["fdr"])[:10]: print "%-40s %6.3f %6.3f %6d %7d" % (gs.name[:30], resu["nes"], resu["fdr"], resu["size"], resu["matched_size"])
import Orange from orangecontrib.bio import dicty, geneset, gsea, gene, geo gds = geo.GDS("GDS10") data = gds.getdata() matcher = gene.matcher([gene.GMKEGG("H**o sapiens")]) genesets = geneset.collections((("KEGG",), "H**o sapiens")) #the number of permutations (n) should be much higher res = gsea.run(data, gene_sets=genesets, matcher=matcher, min_part=0.05, permutation="phenotype", n=10, phen_desc="tissue", gene_desc="gene") print print "GSEA results (descriptor: tissue)" print "%-40s %6s %6s %6s %7s" % ("LABEL", "NES", "FDR", "SIZE", "MATCHED") for gs, resu in sorted(res.items(), key=lambda x: x[1]["fdr"])[:10]: print "%-40s %6.3f %6.3f %6d %7d" % (gs.name[:30], resu["nes"], resu["fdr"], resu["size"], resu["matched_size"])