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)
