def __init__(self, parent=None, signalManager=None, title="Gene Network"): super(OWGeneNetwork, self).__init__(parent, signalManager, title, wantMainArea=False, resizingEnabled=False) self.taxid = "9606" self.gene_var_index = -1 self.use_attr_names = False self.network_source = 1 self.include_neighborhood = True self.autocommit = False self.min_score = 0.9 self.loadSettings() self.taxids = taxonomy.common_taxids() self.current_taxid_index = self.taxids.index(self.taxid) self.data = None self.geneinfo = None self.nettask = None self._invalidated = False box = OWGUI.widgetBox(self.controlArea, "Info") self.info = OWGUI.widgetLabel(box, "No data on input\n") box = OWGUI.widgetBox(self.controlArea, "Organism") self.organism_cb = OWGUI.comboBox(box, self, "current_taxid_index", items=map(taxonomy.name, self.taxids), callback=self._update_organism) box = OWGUI.widgetBox(self.controlArea, "Genes") self.genes_cb = OWGUI.comboBox(box, self, "gene_var_index", callback=self._update_query_genes) self.varmodel = OWItemModels.VariableListModel() self.genes_cb.setModel(self.varmodel) OWGUI.checkBox(box, self, "use_attr_names", "Use attribute names", callback=self._update_query_genes) box = OWGUI.widgetBox(self.controlArea, "Network") OWGUI.comboBox(box, self, "network_source", items=[s.name for s in SOURCES], callback=self._on_source_db_changed) OWGUI.checkBox(box, self, "include_neighborhood", "Include immediate gene neighbors", callback=self.invalidate) self.score_spin = OWGUI.doubleSpin(box, self, "min_score", 0.0, 1.0, step=0.001, label="Minimal edge score", callback=self.invalidate) self.score_spin.setEnabled(SOURCES[self.network_source].score_filter) box = OWGUI.widgetBox(self.controlArea, "Commit") OWGUI.button(box, self, "Commit", callback=self.commit, default=True) self.executor = ThreadExecutor()
def __init__(self, parent=None, signalManager=None, title="Gene Network"): super(OWGeneNetwork, self).__init__( parent, signalManager, title, wantMainArea=False, resizingEnabled=False ) self.taxid = "9606" self.gene_var_index = -1 self.use_attr_names = False self.network_source = 1 self.include_neighborhood = True self.autocommit = False self.min_score = 0.9 self.loadSettings() self.taxids = taxonomy.common_taxids() self.current_taxid_index = self.taxids.index(self.taxid) self.data = None self.geneinfo = None self.nettask = None self._invalidated = False box = OWGUI.widgetBox(self.controlArea, "Info") self.info = OWGUI.widgetLabel(box, "No data on input\n") box = OWGUI.widgetBox(self.controlArea, "Organism") self.organism_cb = OWGUI.comboBox( box, self, "current_taxid_index", items=map(taxonomy.name, self.taxids), callback=self._update_organism ) box = OWGUI.widgetBox(self.controlArea, "Genes") self.genes_cb = OWGUI.comboBox( box, self, "gene_var_index", callback=self._update_query_genes ) self.varmodel = OWItemModels.VariableListModel() self.genes_cb.setModel(self.varmodel) OWGUI.checkBox( box, self, "use_attr_names", "Use attribute names", callback=self._update_query_genes ) box = OWGUI.widgetBox(self.controlArea, "Network") OWGUI.comboBox( box, self, "network_source", items=[s.name for s in SOURCES], callback=self._on_source_db_changed ) OWGUI.checkBox( box, self, "include_neighborhood", "Include immediate gene neighbors", callback=self.invalidate ) self.score_spin = OWGUI.doubleSpin( box, self, "min_score", 0.0, 1.0, step=0.001, label="Minimal edge score", callback=self.invalidate ) self.score_spin.setEnabled(SOURCES[self.network_source].score_filter) box = OWGUI.widgetBox(self.controlArea, "Commit") OWGUI.button(box, self, "Commit", callback=self.commit, default=True) self.executor = ThreadExecutor()
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="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)