def __init__(self, parent=None):
widget.OWWidget.__init__(self, parent)
self.data = None
self.target_group = None, []
self.targets = []
self.current_selection = []
self.validindices = numpy.empty((0, ), dtype=int)
self.graph = VolcanoGraph(symbolSize=self.symbol_size, background="w")
self.graph.setSelectionMode(
VolcanoGraph.SymetricSelection if self.
symetric_selections else VolcanoGraph.RectSelection)
self.graph.selectionChanged.connect(self.on_selection_changed)
self.graph.scene().installEventFilter(self)
self.graph.getViewBox().setMouseEnabled(False, False)
self.graph.getViewBox().enableAutoRange(enable=True)
self.graph.plotItem.showGrid(True, True, 0.3)
self.mainArea.layout().addWidget(self.graph)
## GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.label(box, self, "")
self.infoLabel.setText("No data on input")
self.infoLabel2 = gui.label(box, self, "")
self.infoLabel2.setText("0 selected genes")
box = gui.widgetBox(self.controlArea, "Target Labels")
self.target_widget = guiutils.LabelSelectionWidget(
self,
groupChanged=self.on_label_activated,
groupSelectionChanged=self.on_target_changed)
box.layout().addWidget(self.target_widget)
box = gui.widgetBox(self.controlArea, "Settings")
gui.hSlider(
box,
self,
"symbol_size",
label="Symbol size: ",
minValue=2,
maxValue=20,
step=1,
callback=lambda: self.graph.setSymbolSize(self.symbol_size))
gui.checkBox(box,
self,
"symetric_selections",
"Symmetric selection",
callback=self.__on_selectionModeChanged)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
gui.rubber(self.controlArea)
def __init__(self, parent=None):
widget.OWWidget.__init__(self, parent)
self.min_value, self.max_value = \
self.thresholds.get(self.Scores[self.score_index][0], (1, 0))
#: Input data set
self.data = None
#: Current target group selection
self.targets = []
#: The computed scores
self.scores = None
#: The computed scores from label permutations
self.nulldist = None
self.__scores_future = self.__scores_state = None
self.__in_progress = False
self.test_f = {
OWFeatureSelection.LowTail: test_low,
OWFeatureSelection.HighTail: test_high,
OWFeatureSelection.TwoTail: test_two_tail,
}
self.histogram = Histogram(enableMouse=False,
enableMenu=False,
background="w")
self.histogram.enableAutoRange(enable=False)
self.histogram.getPlotItem().hideButtons() # hide auto range button
self.histogram.getViewBox().setMouseEnabled(False, False)
self.histogram.selectionChanged.connect(
self.__on_histogram_plot_selection_changed)
self.histogram.selectionEdited.connect(self._invalidate_selection)
self.mainArea.layout().addWidget(self.histogram)
box = gui.widgetBox(self.controlArea, "Info")
self.dataInfoLabel = gui.widgetLabel(box, "No data on input.\n")
self.dataInfoLabel.setWordWrap(True)
self.selectedInfoLabel = gui.widgetLabel(box, "\n")
box1 = gui.widgetBox(self.controlArea, "Scoring Method")
gui.comboBox(
box1,
self,
"score_index",
items=[sm[0] for sm in self.Scores],
callback=[self.on_scoring_method_changed, self.update_scores])
box = gui.widgetBox(self.controlArea, "Target Labels")
self.label_selection_widget = guiutils.LabelSelectionWidget(self)
self.label_selection_widget.setMaximumHeight(150)
box.layout().addWidget(self.label_selection_widget)
self.label_selection_widget.groupChanged.connect(
self.on_label_activated)
self.label_selection_widget.groupSelectionChanged.connect(
self.on_target_changed)
box = gui.widgetBox(self.controlArea, "Selection")
box.layout().setSpacing(0)
self.max_value_spin = gui.doubleSpin(box,
self,
"max_value",
minv=-1e6,
maxv=1e6,
step=1e-6,
label="Upper threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
self.low_value_spin = gui.doubleSpin(box,
self,
"min_value",
minv=-1e6,
maxv=1e6,
step=1e-6,
label="Lower threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
check = gui.checkBox(box,
self,
"compute_null",
"Compute null distribution",
callback=self.update_scores)
perm_spin = gui.spin(box,
self,
"permutations_count",
minv=1,
maxv=50,
label="Permutations:",
callback=self.update_scores,
callbackOnReturn=True)
check.disables.append(perm_spin)
box1 = gui.widgetBox(box, orientation='horizontal')
pval_spin = gui.doubleSpin(box1,
self,
"alpha_value",
minv=2e-7,
maxv=1.0,
step=1e-7,
label="α-value:")
pval_select = gui.button(box1,
self,
"Select",
callback=self.select_p_best,
autoDefault=False)
check.disables.append(pval_spin)
check.disables.append(pval_select)
check.makeConsistent()
box1 = gui.widgetBox(box, orientation='horizontal')
gui.spin(box1, self, "n_best", 0, 10000, step=1, label="Best Ranked:")
gui.button(box1,
self,
"Select",
callback=self.select_n_best,
autoDefault=False)
box = gui.widgetBox(self.controlArea, "Output")
acbox = gui.auto_commit(box, self, "auto_commit", "Commit", box=None)
acbox.button.setDefault(True)
gui.checkBox(box,
self,
"add_scores_to_output",
"Add gene scores to output",
callback=self._invalidate_selection)
gui.rubber(self.controlArea)
self.on_scoring_method_changed()
self._executor = concurrent.ThreadExecutor()
def __init__(self, parent=None):
widget.OWWidget.__init__(self, parent)
self.data = None
self.target_group = None, []
self.targets = []
self.current_selection = []
self.validindices = numpy.empty((0, ), dtype=int)
self.graph = VolcanoGraph(symbolSize=self.symbol_size, background="w")
self.graph.setSelectionCut(self.cut_log_r, self.cut_log_p)
self.graph.setSelectionMode(
VolcanoGraph.SymetricSelection if self.
symetric_selections else VolcanoGraph.RectSelection)
self.graph.selectionChanged.connect(self.on_selection_changed)
self.graph.scene().installEventFilter(self)
self.graph.getViewBox().setMouseEnabled(False, False)
self.graph.getViewBox().enableAutoRange(enable=True)
self.graph.getViewBox().setMenuEnabled(False)
self.graph.getPlotItem().hideButtons()
self.graph.plotItem.showGrid(True, True, 0.3)
self.mainArea.layout().addWidget(self.graph)
## GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.label(box, self, "")
self.infoLabel.setText("No data on input")
self.infoLabel2 = gui.label(box, self, "")
self.infoLabel2.setText("0 selected genes")
box = gui.widgetBox(self.controlArea, "Target Labels")
self.target_widget = guiutils.LabelSelectionWidget(
self,
groupChanged=self.on_label_activated,
groupSelectionChanged=self.on_target_changed)
box.layout().addWidget(self.target_widget)
box = gui.widgetBox(self.controlArea, "Selection")
cb = gui.checkBox(
box,
self,
"symetric_selections",
"Symmetric selection",
callback=self.__on_selectionModeChanged) # type: QCheckBox
form = QFormLayout(
labelAlignment=Qt.AlignRight,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow(
"|log(ratio)|:",
gui.spin(box,
self,
"cut_log_r",
0.0,
20.0,
step=0.01,
decimals=4,
spinType=float,
callback=self.on_cut_changed))
form.addRow(
"-log<sub>10</sub>(P_value):",
gui.spin(box,
self,
"cut_log_p",
0.0,
20.0,
step=0.01,
decimals=4,
spinType=float,
callback=self.on_cut_changed))
box.layout().addLayout(form)
def set_enable_all(layout, enabled):
for i in range(layout.count()):
item = layout.itemAt(i)
if item is not None and item.widget() is not None:
item.widget().setEnabled(enabled)
set_enable_all(form, self.symetric_selections)
cb.toggled.connect(partial(set_enable_all, form))
box = gui.widgetBox(self.controlArea, "Settings")
gui.hSlider(
box,
self,
"symbol_size",
label="Symbol size: ",
minValue=2,
maxValue=20,
step=1,
callback=lambda: self.graph.setSymbolSize(self.symbol_size))
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")