def __init__(self):
super().__init__()
self.data = None
self.test_data = None
self.preprocessor = None
self.train_data_missing_vals = False
self.test_data_missing_vals = False
self.scorers = []
#: An Ordered dictionary with current inputs and their testing results.
self.learners = OrderedDict() # type: Dict[Any, Input]
self.__state = State.Waiting
# Do we need to [re]test any learners, set by _invalidate and
# cleared by __update
self.__needupdate = False
self.__task = None # type: Optional[Task]
self.__executor = ThreadExecutor()
sbox = gui.vBox(self.controlArea, "Sampling")
rbox = gui.radioButtons(sbox,
self,
"resampling",
callback=self._param_changed)
gui.appendRadioButton(rbox, "Cross validation")
ibox = gui.indentedBox(rbox)
gui.comboBox(ibox,
self,
"n_folds",
label="Number of folds: ",
items=[str(x) for x in self.NFolds],
maximumContentsLength=3,
orientation=Qt.Horizontal,
callback=self.kfold_changed)
gui.checkBox(ibox,
self,
"cv_stratified",
"Stratified",
callback=self.kfold_changed)
gui.appendRadioButton(rbox, "Cross validation by feature")
ibox = gui.indentedBox(rbox)
self.feature_model = DomainModel(order=DomainModel.METAS,
valid_types=DiscreteVariable)
self.features_combo = gui.comboBox(ibox,
self,
"fold_feature",
model=self.feature_model,
orientation=Qt.Horizontal,
callback=self.fold_feature_changed)
gui.appendRadioButton(rbox, "Random sampling")
ibox = gui.indentedBox(rbox)
gui.comboBox(ibox,
self,
"n_repeats",
label="Repeat train/test: ",
items=[str(x) for x in self.NRepeats],
maximumContentsLength=3,
orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.comboBox(ibox,
self,
"sample_size",
label="Training set size: ",
items=["{} %".format(x) for x in self.SampleSizes],
maximumContentsLength=5,
orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.checkBox(ibox,
self,
"shuffle_stratified",
"Stratified",
callback=self.shuffle_split_changed)
gui.appendRadioButton(rbox, "Leave one out")
gui.appendRadioButton(rbox, "Test on train data")
gui.appendRadioButton(rbox, "Test on test data")
self.cbox = gui.vBox(self.controlArea, "Target Class")
self.class_selection_combo = gui.comboBox(
self.cbox,
self,
"class_selection",
items=[],
sendSelectedValue=True,
valueType=str,
callback=self._on_target_class_changed,
contentsLength=8)
gui.rubber(self.controlArea)
self.score_table = ScoreTable(self)
self.score_table.shownScoresChanged.connect(self.update_stats_model)
box = gui.vBox(self.mainArea, "Evaluation Results")
box.layout().addWidget(self.score_table.view)
def __init__(self):
self.model = None
self._task = None # type: Optional[self.Task]
self._executor = ThreadExecutor(self)
self.is_downloading = False
box = gui.vBox(self.controlArea, 'Database Connection')
gui.lineEdit(box,
self,
'con_hostname',
label='Hostname:',
orientation=Qt.Horizontal,
validator=Validator.Hostname())
gui.lineEdit(box,
self,
'con_port',
label='Port:',
orientation=Qt.Horizontal,
validator=Validator.Port())
gui.lineEdit(box,
self,
'con_username',
label='Username:'******'con_password',
label='Password:'******'con_database',
label='Database:',
orientation=Qt.Horizontal)
gui.spin(box, self, 'con_timeout', 5, 300, 5, label='Timeout [s]:')
self.btn_connect = gui.button(box,
self,
self.LABEL_CONNECT,
callback=self.load_data)
box = gui.vBox(self.controlArea, 'Download')
def _dateTimeChanged(editted):
def handler():
minTime = self.date_from.dateTime().toMSecsSinceEpoch() / 1000
maxTime = self.date_to.dateTime().toMSecsSinceEpoch() / 1000
if minTime > maxTime:
minTime = maxTime = minTime if editted == self.date_from else maxTime
other = self.date_to if editted == self.date_from else self.date_from
with blockSignals(other):
other.setDateTime(editted.dateTime())
self.btn_download.setEnabled(minTime != maxTime)
# Update saved settings
self.sample_ts_from = minTime
self.sample_ts_to = maxTime
return handler
kwargs = dict(calendarPopup=True,
displayFormat=' '.join(self.DATE_FORMATS),
timeSpec=Qt.UTC)
date_from = self.date_from = QDateTimeEdit(self, **kwargs)
date_to = self.date_to = QDateTimeEdit(self, **kwargs)
date_from.setDateTime(
QDateTime.fromMSecsSinceEpoch(self.sample_ts_from * 1000, Qt.UTC))
date_to.setDateTime(
QDateTime.fromMSecsSinceEpoch(self.sample_ts_to * 1000, Qt.UTC))
date_from.dateTimeChanged.connect(_dateTimeChanged(date_from))
date_to.dateTimeChanged.connect(_dateTimeChanged(date_to))
hbox = gui.hBox(box)
hbox.layout().addWidget(QLabel('From:'))
hbox.layout().addWidget(date_from)
hbox = gui.hBox(box)
hbox.layout().addWidget(QLabel('To:'))
hbox.layout().addWidget(date_to)
self.box_include_data = gui.vBox(box, 'Include')
gui.spin(box,
self,
'sample_size',
100,
20000,
100,
label='Sample size:')
gui.comboBox(box,
self,
'sample_resolution',
label='Resolution:',
orientation=Qt.Horizontal,
items=tuple(self.RESOLUTION.keys()),
sendSelectedValue=True)
gui.comboBox(box,
self,
'sample_interpolation',
label='Interpolation:',
orientation=Qt.Horizontal,
items=tuple(self.INTERPOLATION.keys()),
sendSelectedValue=True)
self.btn_download = gui.button(box,
self,
self.LABEL_DOWNLOAD,
callback=self.download)
gui.rubber(self.controlArea)
## Main area
class Model(PyTableModel):
def update_row(self, i, row):
self[i] = row
model = self.model = Model(parent=self)
model.setHorizontalHeaderLabels([
'Node Id', 'Interfaces', 'Start Time', 'Stop Time',
'Available Data'
])
view = self.view = gui.TableView(self)
view.horizontalHeader().setStretchLastSection(False)
view.setModel(self.model)
self.mainArea.layout().addWidget(view)
# Restore node info table from cache, if any
try:
lst = CachedNodeInfoTable.load_list()
except Exception:
pass # Cache not exists
else:
model.wrap(lst)
# Restore tables checkboxes from cache
try:
tables = CachedNodeInfoTable.load_tables()
except Exception:
pass
else:
for table in tables:
self.box_include_data.layout().addWidget(
QCheckBox(table, self, checked=table
in self.included_data))
# Establish default database connection from settings
set_connection_params(self.con_hostname,
self.con_port,
self.con_username,
self.con_password,
self.con_database,
timeout=self.con_timeout)
def __init__(self):
super().__init__()
#: widget's runtime state
self.__state = State.NoState
self.corpus = None
self.n_text_categories = 0
self.n_text_data = 0
self.n_skipped = 0
self.__invalidated = False
self.__pendingTask = None
vbox = gui.vBox(self.controlArea)
hbox = gui.hBox(vbox)
self.recent_cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=16,
acceptDrops=True)
self.recent_cb.installEventFilter(self)
self.recent_cb.activated[int].connect(self.__onRecentActivated)
browseaction = QAction(
"Open/Load Documents",
self,
iconText="\N{HORIZONTAL ELLIPSIS}",
icon=self.style().standardIcon(QStyle.SP_DirOpenIcon),
toolTip="Select a folder from which to load the documents")
browseaction.triggered.connect(self.__runOpenDialog)
reloadaction = QAction("Reload",
self,
icon=self.style().standardIcon(
QStyle.SP_BrowserReload),
toolTip="Reload current document set")
reloadaction.triggered.connect(self.reload)
self.__actions = namespace(
browse=browseaction,
reload=reloadaction,
)
browsebutton = QPushButton(browseaction.iconText(),
icon=browseaction.icon(),
toolTip=browseaction.toolTip(),
clicked=browseaction.trigger)
reloadbutton = QPushButton(
reloadaction.iconText(),
icon=reloadaction.icon(),
clicked=reloadaction.trigger,
default=True,
)
hbox.layout().addWidget(self.recent_cb)
hbox.layout().addWidget(browsebutton)
hbox.layout().addWidget(reloadbutton)
self.addActions([browseaction, reloadaction])
reloadaction.changed.connect(
lambda: reloadbutton.setEnabled(reloadaction.isEnabled()))
box = gui.vBox(vbox, "Info")
self.infostack = QStackedWidget()
self.info_area = QLabel(text="No document set selected", wordWrap=True)
self.progress_widget = QProgressBar(minimum=0, maximum=100)
self.cancel_button = QPushButton(
"Cancel",
icon=self.style().standardIcon(QStyle.SP_DialogCancelButton),
)
self.cancel_button.clicked.connect(self.cancel)
w = QWidget()
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.addWidget(self.progress_widget)
hlayout.addWidget(self.cancel_button)
vlayout.addLayout(hlayout)
self.pathlabel = TextLabel()
self.pathlabel.setTextElideMode(Qt.ElideMiddle)
self.pathlabel.setAttribute(Qt.WA_MacSmallSize)
vlayout.addWidget(self.pathlabel)
w.setLayout(vlayout)
self.infostack.addWidget(self.info_area)
self.infostack.addWidget(w)
box.layout().addWidget(self.infostack)
self.__initRecentItemsModel()
self.__invalidated = True
self.__executor = ThreadExecutor(self)
QApplication.postEvent(self, QEvent(RuntimeEvent.Init))
def __init__(self):
super().__init__()
self.data = None
self.test_data = None
self.preprocessor = None
self.train_data_missing_vals = False
self.test_data_missing_vals = False
self.scorers = []
self.__pending_comparison_criterion = self.comparison_criterion
#: An Ordered dictionary with current inputs and their testing results.
self.learners = OrderedDict() # type: Dict[Any, Input]
self.__state = State.Waiting
# Do we need to [re]test any learners, set by _invalidate and
# cleared by __update
self.__needupdate = False
self.__task = None # type: Optional[TaskState]
self.__executor = ThreadExecutor()
self.info.set_input_summary(self.info.NoInput)
self.info.set_output_summary(self.info.NoOutput)
sbox = gui.vBox(self.controlArea, "Sampling")
rbox = gui.radioButtons(sbox,
self,
"resampling",
callback=self._param_changed)
gui.appendRadioButton(rbox, "Cross validation")
ibox = gui.indentedBox(rbox)
gui.comboBox(ibox,
self,
"n_folds",
label="Number of folds: ",
items=[str(x) for x in self.NFolds],
orientation=Qt.Horizontal,
callback=self.kfold_changed)
gui.checkBox(ibox,
self,
"cv_stratified",
"Stratified",
callback=self.kfold_changed)
gui.appendRadioButton(rbox, "Cross validation by feature")
ibox = gui.indentedBox(rbox)
self.feature_model = DomainModel(order=DomainModel.METAS,
valid_types=DiscreteVariable)
self.features_combo = gui.comboBox(ibox,
self,
"fold_feature",
model=self.feature_model,
orientation=Qt.Horizontal,
searchable=True,
callback=self.fold_feature_changed)
gui.appendRadioButton(rbox, "Random sampling")
ibox = gui.indentedBox(rbox)
gui.comboBox(ibox,
self,
"n_repeats",
label="Repeat train/test: ",
items=[str(x) for x in self.NRepeats],
orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.comboBox(ibox,
self,
"sample_size",
label="Training set size: ",
items=["{} %".format(x) for x in self.SampleSizes],
orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.checkBox(ibox,
self,
"shuffle_stratified",
"Stratified",
callback=self.shuffle_split_changed)
gui.appendRadioButton(rbox, "Leave one out")
gui.appendRadioButton(rbox, "Test on train data")
gui.appendRadioButton(rbox, "Test on test data")
self.cbox = gui.vBox(self.controlArea, "Target Class")
self.class_selection_combo = gui.comboBox(
self.cbox,
self,
"class_selection",
items=[],
sendSelectedValue=True,
contentsLength=8,
searchable=True,
callback=self._on_target_class_changed)
self.modcompbox = box = gui.vBox(self.controlArea, "Model Comparison")
gui.comboBox(box,
self,
"comparison_criterion",
callback=self.update_comparison_table)
hbox = gui.hBox(box)
gui.checkBox(hbox,
self,
"use_rope",
"Negligible difference: ",
callback=self._on_use_rope_changed)
gui.lineEdit(hbox,
self,
"rope",
validator=QDoubleValidator(),
controlWidth=70,
callback=self.update_comparison_table,
alignment=Qt.AlignRight)
self.controls.rope.setEnabled(self.use_rope)
gui.rubber(self.controlArea)
self.score_table = ScoreTable(self)
self.score_table.shownScoresChanged.connect(self.update_stats_model)
view = self.score_table.view
view.setSizeAdjustPolicy(view.AdjustToContents)
box = gui.vBox(self.mainArea, "Evaluation Results")
box.layout().addWidget(self.score_table.view)
self.compbox = box = gui.vBox(self.mainArea, box="Model comparison")
table = self.comparison_table = QTableWidget(
wordWrap=False,
editTriggers=QTableWidget.NoEditTriggers,
selectionMode=QTableWidget.NoSelection)
table.setSizeAdjustPolicy(table.AdjustToContents)
header = table.verticalHeader()
header.setSectionResizeMode(QHeaderView.Fixed)
header.setSectionsClickable(False)
header = table.horizontalHeader()
header.setTextElideMode(Qt.ElideRight)
header.setDefaultAlignment(Qt.AlignCenter)
header.setSectionsClickable(False)
header.setStretchLastSection(False)
header.setSectionResizeMode(QHeaderView.ResizeToContents)
avg_width = self.fontMetrics().averageCharWidth()
header.setMinimumSectionSize(8 * avg_width)
header.setMaximumSectionSize(15 * avg_width)
header.setDefaultSectionSize(15 * avg_width)
box.layout().addWidget(table)
box.layout().addWidget(
QLabel(
"<small>Table shows probabilities that the score for the model in "
"the row is higher than that of the model in the column. "
"Small numbers show the probability that the difference is "
"negligible.</small>",
wordWrap=True))
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)
def __init__(self):
super().__init__()
#: Effective data used for plot styling/annotations.
self.data = None # type: Optional[Orange.data.Table]
#: Input subset data table
self.subset_data = None # type: Optional[Orange.data.Table]
#: Input data table
self.signal_data = None
# resolwe variables
self.data_table_object = None # type: Optional[resolwe.Data]
self._tsne_slug = 't-sne'
self._tsne_selection_slug = 't-sne-selection'
self._embedding_data_object = None
self._embedding = None
self._embedding_clas_var = None
self.variable_x = ContinuousVariable("tsne-x")
self.variable_y = ContinuousVariable("tsne-y")
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
self.res = ResolweHelper()
self._subset_mask = None # type: Optional[np.ndarray]
self._invalidated = False
self.pca_data = None
self._curve = None
self._data_metas = None
self.variable_x = ContinuousVariable("tsne-x")
self.variable_y = ContinuousVariable("tsne-y")
self.__update_loop = None
self.__in_next_step = False
self.__draw_similar_pairs = False
box = gui.vBox(self.controlArea, "t-SNE")
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 250, 2000, step=50))
form.addRow("Perplexity:",
gui.spin(box, self, "perplexity", 1, 100, step=1))
box.layout().addLayout(form)
gui.separator(box, 10)
self.runbutton = gui.button(box,
self,
"Run",
callback=self._run_embeding)
box = gui.vBox(self.controlArea, "PCA Preprocessing")
gui.hSlider(box,
self,
'pca_components',
label="Components: ",
minValue=2,
maxValue=50,
step=1) #, callback=self._initialize)
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWMDSGraph(self,
box,
"MDSGraph",
view_box=MDSInteractiveViewBox)
box.layout().addWidget(self.graph.plot_widget)
self.plot = self.graph.plot_widget
g = self.graph.gui
box = g.point_properties_box(self.controlArea)
self.models = g.points_models
# Because sc data frequently has many genes,
# showing all attributes in combo boxes can cause problems
# QUICKFIX: Remove a separator and attributes from order
# (leaving just the class and metas)
for model in self.models:
model.order = model.order[:-2]
g.add_widgets(ids=[g.JitterSizeSlider], widget=box)
box = gui.vBox(self.controlArea, "Plot Properties")
g.add_widgets([
g.ShowLegend, g.ToolTipShowsAll, g.ClassDensity,
g.LabelOnlySelected
], box)
self.controlArea.layout().addStretch(100)
self.icons = gui.attributeIconDict
palette = self.graph.plot_widget.palette()
self.graph.set_palette(palette)
gui.rubber(self.controlArea)
self.graph.box_zoom_select(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit",
"Send Selection", "Send Automatically")
self.plot.getPlotItem().hideButtons()
self.plot.setRenderHint(QPainter.Antialiasing)
self.graph.jitter_continuous = True
def __init__(self, parent=None):
super().__init__(self, parent)
self.clusterDataset = None
self.referenceDataset = None
self.ontology = None
self.annotations = None
self.loadedAnnotationCode = None
self.treeStructRootKey = None
self.probFunctions = [stats.Binomial(), stats.Hypergeometric()]
self.selectedTerms = []
self.selectionChanging = 0
self.__state = State.Ready
self.__scheduletimer = QTimer(self, singleShot=True)
self.__scheduletimer.timeout.connect(self.__update)
#############
## GUI
#############
self.tabs = gui.tabWidget(self.controlArea)
## Input tab
self.inputTab = gui.createTabPage(self.tabs, "Input")
box = gui.widgetBox(self.inputTab, "Info")
self.infoLabel = gui.widgetLabel(box, "No data on input\n")
gui.button(
box,
self,
"Ontology/Annotation Info",
callback=self.ShowInfo,
tooltip="Show information on loaded ontology and annotations")
box = gui.widgetBox(self.inputTab, "Organism")
self.annotationComboBox = gui.comboBox(
box,
self,
"annotationIndex",
items=[],
callback=self.__invalidateAnnotations,
tooltip="Select organism")
genebox = gui.widgetBox(self.inputTab, "Gene Names")
self.geneAttrIndexCombo = gui.comboBox(
genebox,
self,
"geneAttrIndex",
callback=self.__invalidate,
tooltip="Use this attribute to extract gene names from input data")
self.geneAttrIndexCombo.setDisabled(self.useAttrNames)
cb = gui.checkBox(genebox,
self,
"useAttrNames",
"Use column names",
tooltip="Use column names for gene names",
callback=self.__invalidate)
cb.toggled[bool].connect(self.geneAttrIndexCombo.setDisabled)
gui.button(genebox,
self,
"Gene matcher settings",
callback=self.UpdateGeneMatcher,
tooltip="Open gene matching settings dialog")
self.referenceRadioBox = gui.radioButtonsInBox(
self.inputTab,
self,
"useReferenceDataset", ["Entire genome", "Reference set (input)"],
tooltips=[
"Use entire genome for reference",
"Use genes from Referece Examples input signal as reference"
],
box="Reference",
callback=self.__invalidate)
self.referenceRadioBox.buttons[1].setDisabled(True)
gui.radioButtonsInBox(
self.inputTab,
self,
"aspectIndex",
["Biological process", "Cellular component", "Molecular function"],
box="Aspect",
callback=self.__invalidate)
## Filter tab
self.filterTab = gui.createTabPage(self.tabs, "Filter")
box = gui.widgetBox(self.filterTab, "Filter GO Term Nodes")
gui.checkBox(
box,
self,
"filterByNumOfInstances",
"Genes",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by number of input genes mapped to a term")
ibox = gui.indentedBox(box)
gui.spin(ibox,
self,
'minNumOfInstances',
1,
100,
step=1,
label='#:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Min. number of input genes mapped to a term")
gui.checkBox(box,
self,
"filterByPValue_nofdr",
"p-value",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by term p-value")
gui.doubleSpin(gui.indentedBox(box),
self,
'maxPValue_nofdr',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Max term p-value")
#use filterByPValue for FDR, as it was the default in prior versions
gui.checkBox(box,
self,
"filterByPValue",
"FDR",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by term FDR")
gui.doubleSpin(gui.indentedBox(box),
self,
'maxPValue',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Max term p-value")
box = gui.widgetBox(box, "Significance test")
gui.radioButtonsInBox(
box,
self,
"probFunc", ["Binomial", "Hypergeometric"],
tooltips=[
"Use binomial distribution test",
"Use hypergeometric distribution test"
],
callback=self.__invalidate) # TODO: only update the p values
box = gui.widgetBox(self.filterTab,
"Evidence codes in annotation",
addSpace=True)
self.evidenceCheckBoxDict = {}
for etype in go.evidenceTypesOrdered:
ecb = QCheckBox(etype,
toolTip=go.evidenceTypes[etype],
checked=self.useEvidenceType[etype])
ecb.toggled.connect(self.__on_evidenceChanged)
box.layout().addWidget(ecb)
self.evidenceCheckBoxDict[etype] = ecb
## Select tab
self.selectTab = gui.createTabPage(self.tabs, "Select")
box = gui.radioButtonsInBox(self.selectTab,
self,
"selectionDirectAnnotation",
["Directly or Indirectly", "Directly"],
box="Annotated genes",
callback=self.ExampleSelection)
box = gui.widgetBox(self.selectTab, "Output", addSpace=True)
gui.radioButtonsInBox(
box,
self,
"selectionDisjoint",
btnLabels=[
"All selected genes", "Term-specific genes",
"Common term genes"
],
tooltips=[
"Outputs genes annotated to all selected GO terms",
"Outputs genes that appear in only one of selected GO terms",
"Outputs genes common to all selected GO terms"
],
callback=[self.ExampleSelection, self.UpdateAddClassButton])
self.addClassCB = gui.checkBox(box,
self,
"selectionAddTermAsClass",
"Add GO Term as class",
callback=self.ExampleSelection)
# ListView for DAG, and table for significant GOIDs
self.DAGcolumns = [
'GO term', 'Cluster', 'Reference', 'p-value', 'FDR', 'Genes',
'Enrichment'
]
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.listView = GOTreeWidget(self.splitter)
self.listView.setSelectionMode(QTreeView.ExtendedSelection)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(len(self.DAGcolumns))
self.listView.setHeaderLabels(self.DAGcolumns)
self.listView.header().setSectionsClickable(True)
self.listView.header().setSortIndicatorShown(True)
self.listView.setSortingEnabled(True)
self.listView.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.listView.setRootIsDecorated(True)
self.listView.itemSelectionChanged.connect(self.ViewSelectionChanged)
# table of significant GO terms
self.sigTerms = QTreeWidget(self.splitter)
self.sigTerms.setColumnCount(len(self.DAGcolumns))
self.sigTerms.setHeaderLabels(self.DAGcolumns)
self.sigTerms.setSortingEnabled(True)
self.sigTerms.setSelectionMode(QTreeView.ExtendedSelection)
self.sigTerms.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.sigTerms.itemSelectionChanged.connect(self.TableSelectionChanged)
self.sigTableTermsSorted = []
self.graph = {}
self.originalGraph = None
self.inputTab.layout().addStretch(1)
self.filterTab.layout().addStretch(1)
self.selectTab.layout().addStretch(1)
class AnnotationSlot(SimpleNamespace):
taxid = ... # type: str
name = ... # type: str
orgcode = ... # type: str
filename = ... # type:str
available_annotations = [
AnnotationSlot(taxid=taxid,
name=taxonomy.common_taxid_to_name(taxid),
orgcode=go.from_taxid(taxid),
filename="gene_association.{}.tar.gz".format(
go.from_taxid(taxid)))
for taxid in taxonomy.common_taxids() if go.from_taxid(taxid)
]
self.availableAnnotations = sorted(available_annotations,
key=lambda a: a.name)
self.annotationComboBox.clear()
for a in self.availableAnnotations:
self.annotationComboBox.addItem(a.name)
self.annotationComboBox.setCurrentIndex(self.annotationIndex)
self.annotationIndex = self.annotationComboBox.currentIndex()
self._executor = ThreadExecutor()
def __init__(self):
super().__init__()
self.data = None # type: Optional[Table]
self.graph = None # type: Optional[nx.Graph]
self.partition = None # type: Optional[np.array]
self.__executor = ThreadExecutor(parent=self)
self.__future = None # type: Optional[Future]
self.__state = self.State.Pending
pca_box = gui.vBox(self.controlArea, 'PCA Preprocessing')
self.apply_pca_cbx = gui.checkBox(
pca_box,
self,
'apply_pca',
label='Apply PCA preprocessing',
callback=self._invalidate_graph,
) # type: QCheckBox
self.pca_components_slider = gui.hSlider(
pca_box,
self,
'pca_components',
label='Components: ',
minValue=2,
maxValue=_MAX_PCA_COMPONENTS,
callback=self._invalidate_pca_projection,
) # type: QSlider
graph_box = gui.vBox(self.controlArea, 'Graph parameters')
self.metric_combo = gui.comboBox(
graph_box,
self,
'metric_idx',
label='Distance metric',
items=[m[0] for m in METRICS],
callback=self._invalidate_graph,
orientation=Qt.Horizontal,
) # type: gui.OrangeComboBox
self.k_neighbours_spin = gui.spin(
graph_box,
self,
'k_neighbours',
minv=1,
maxv=_MAX_K_NEIGBOURS,
label='k neighbours',
controlWidth=80,
alignment=Qt.AlignRight,
callback=self._invalidate_graph,
) # type: gui.SpinBoxWFocusOut
self.cls_epsilon_spin = gui.spin(
graph_box,
self,
'resolution',
0,
5.,
1e-2,
spinType=float,
label='Resolution',
controlWidth=80,
alignment=Qt.AlignRight,
callback=self._invalidate_partition,
) # type: gui.SpinBoxWFocusOut
self.apply_button = gui.auto_commit(
self.controlArea,
self,
'auto_commit',
'Apply',
box=False,
commit=lambda: self.commit(force=True),
callback=self.commit,
) # type: QWidget
def __init__(self):
#: The current evaluating task (if any)
self._task = None # type: Optional[Task]
#: An executor we use to submit learner evaluations into a thread pool
self._executor = ThreadExecutor()
def __init__(self):
super().__init__()
self.data_table_object = None # type: Optional[resolwe.Data]
self._counts = None # type: Optional[np.ndarray]
self._counts_data_obj = None # type: Optional[resolwe.Data]
self._counts_slug = 'data-filter-counts' # type: str
self._selection_data_obj = None # type: Optional[resolwe.Data]
self._selection_slug = 'data-table-filter' # type: str
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
self.res = ResolweHelper()
box = gui.widgetBox(self.controlArea, "Info")
self._info = QLabel(box)
self._info.setWordWrap(True)
self._info.setText("No data in input\n")
box.layout().addWidget(self._info)
box = gui.widgetBox(self.controlArea, "Filter Type", spacing=-1)
rbg = QButtonGroup(box, exclusive=True)
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
for id_ in [Cells, Genes]:
name, _, tip = FilterInfo[id_]
b = QRadioButton(name,
toolTip=tip,
checked=id_ == self.selected_filter_type)
rbg.addButton(b, id_)
layout.addWidget(b, stretch=10, alignment=Qt.AlignCenter)
box.layout().addLayout(layout)
rbg.buttonClicked[int].connect(self.set_filter_type)
self.filter_metric_cb = gui.comboBox(box,
self,
"selected_filter_metric",
callback=self._update_metric)
for id_ in [DetectionCount, TotalCounts]:
text, ttip = MeasureInfo[id_]
self.filter_metric_cb.addItem(text)
idx = self.filter_metric_cb.count() - 1
self.filter_metric_cb.setItemData(idx, ttip, Qt.ToolTipRole)
self.filter_metric_cb.setCurrentIndex(self.selected_filter_metric)
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow)
self._filter_box = box = gui.widgetBox(
self.controlArea, "Filter", orientation=form) # type: QGroupBox
self.threshold_stacks = (
QStackedWidget(enabled=self.limit_lower_enabled),
QStackedWidget(enabled=self.limit_upper_enabled),
)
finfo = np.finfo(np.float64)
for filter_ in [Cells, Genes]:
if filter_ in {Cells, Genes}:
minimum = 0.0
ndecimals = 1
metric = self.selected_filter_metric
else:
minimum = finfo.min
ndecimals = 3
metric = -1
spinlower = QDoubleSpinBox(
self,
minimum=minimum,
maximum=finfo.max,
decimals=ndecimals,
keyboardTracking=False,
)
spinupper = QDoubleSpinBox(
self,
minimum=minimum,
maximum=finfo.max,
decimals=ndecimals,
keyboardTracking=False,
)
lower, upper = self.thresholds.get((filter_, metric), (0, 0))
spinlower.setValue(lower)
spinupper.setValue(upper)
self.threshold_stacks[0].addWidget(spinlower)
self.threshold_stacks[1].addWidget(spinupper)
spinlower.valueChanged.connect(self._limitchanged)
spinupper.valueChanged.connect(self._limitchanged)
self.threshold_stacks[0].setCurrentIndex(self.selected_filter_type)
self.threshold_stacks[1].setCurrentIndex(self.selected_filter_type)
self.limit_lower_enabled_cb = cb = QCheckBox(
"Min", checked=self.limit_lower_enabled)
cb.toggled.connect(self.set_lower_limit_enabled)
cb.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
form.addRow(cb, self.threshold_stacks[0])
self.limit_upper_enabled_cb = cb = QCheckBox(
"Max", checked=self.limit_upper_enabled)
cb.toggled.connect(self.set_upper_limit_enabled)
cb.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
form.addRow(cb, self.threshold_stacks[1])
box = gui.widgetBox(self.controlArea, "View")
self._showpoints = gui.checkBox(box,
self,
"display_dotplot",
"Show data points",
callback=self._update_dotplot)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
self._view = pg.GraphicsView()
self._view.enableMouse(False)
self._view.setAntialiasing(True)
self._plot = plot = ViolinPlot()
self._plot.setDataPointsVisible(self.display_dotplot)
self._plot.setSelectionMode(
(ViolinPlot.Low if self.limit_lower_enabled else 0)
| (ViolinPlot.High if self.limit_upper_enabled else 0))
self._plot.selectionEdited.connect(self._limitchanged_plot)
self._view.setCentralWidget(self._plot)
self._plot.setTitle(FilterInfo[self.selected_filter_metric][1])
bottom = self._plot.getAxis("bottom") # type: pg.AxisItem
bottom.hide()
plot.setMouseEnabled(False, False)
plot.hideButtons()
self.mainArea.layout().addWidget(self._view)
self.addAction(
QAction("Select All",
self,
shortcut=QKeySequence.SelectAll,
triggered=self._select_all))
def test_executor_map(self):
executor = ThreadExecutor()
r = executor.map(pow, list(range(1000)), list(range(1000)))
results = list(r)
self.assertTrue(len(results) == 1000)
def __init__(self):
super().__init__()
#: widget's runtime state
self.__state = State.NoState
self.corpus = None
self.n_text_categories = 0
self.n_text_data = 0
self.skipped_documents = []
self.__invalidated = False
self.__pendingTask = None
layout = QGridLayout()
layout.setSpacing(4)
gui.widgetBox(self.controlArea, orientation=layout, box='Source')
source_box = gui.radioButtons(None, self, "source", box=True,
callback=self.start, addToLayout=False)
rb_button = gui.appendRadioButton(source_box, "Folder:",
addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Fixed)
self.recent_cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=16,
acceptDrops=True
)
self.recent_cb.installEventFilter(self)
self.recent_cb.activated[int].connect(self.__onRecentActivated)
browseaction = QAction(
"Open/Load Documents", self,
iconText="\N{HORIZONTAL ELLIPSIS}",
icon=self.style().standardIcon(QStyle.SP_DirOpenIcon),
toolTip="Select a folder from which to load the documents"
)
browseaction.triggered.connect(self.__runOpenDialog)
reloadaction = QAction(
"Reload", self,
icon=self.style().standardIcon(QStyle.SP_BrowserReload),
toolTip="Reload current document set"
)
reloadaction.triggered.connect(self.reload)
self.__actions = namespace(
browse=browseaction,
reload=reloadaction,
)
browsebutton = QPushButton(
browseaction.iconText(),
icon=browseaction.icon(),
toolTip=browseaction.toolTip(),
clicked=browseaction.trigger,
default=False,
autoDefault=False,
)
reloadbutton = QPushButton(
reloadaction.iconText(),
icon=reloadaction.icon(),
clicked=reloadaction.trigger,
default=False,
autoDefault=False,
)
box.layout().addWidget(self.recent_cb)
layout.addWidget(box, 0, 1)
layout.addWidget(browsebutton, 0, 2)
layout.addWidget(reloadbutton, 0, 3)
rb_button = gui.appendRadioButton(source_box, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = PyListModel()
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Fixed)
url_combo.setEditable(True)
url_combo.setInsertPolicy(url_combo.InsertAtTop)
url_edit = url_combo.lineEdit()
l, t, r, b = url_edit.getTextMargins()
url_edit.setTextMargins(l + 5, t, r, b)
layout.addWidget(url_combo, 3, 1, 1, 3)
url_combo.activated.connect(self._url_set)
# whit completer we set that combo box is case sensitive when
# matching the history
completer = QCompleter()
completer.setCaseSensitivity(Qt.CaseSensitive)
url_combo.setCompleter(completer)
self.addActions([browseaction, reloadaction])
reloadaction.changed.connect(
lambda: reloadbutton.setEnabled(reloadaction.isEnabled())
)
box = gui.vBox(self.controlArea, "Info")
self.infostack = QStackedWidget()
self.info_area = QLabel(
text="No document set selected",
wordWrap=True
)
self.progress_widget = QProgressBar(
minimum=0, maximum=100
)
self.cancel_button = QPushButton(
"Cancel",
icon=self.style().standardIcon(QStyle.SP_DialogCancelButton),
default=False,
autoDefault=False,
)
self.cancel_button.clicked.connect(self.cancel)
w = QWidget()
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.addWidget(self.progress_widget)
hlayout.addWidget(self.cancel_button)
vlayout.addLayout(hlayout)
self.pathlabel = TextLabel()
self.pathlabel.setTextElideMode(Qt.ElideMiddle)
self.pathlabel.setAttribute(Qt.WA_MacSmallSize)
vlayout.addWidget(self.pathlabel)
w.setLayout(vlayout)
self.infostack.addWidget(self.info_area)
self.infostack.addWidget(w)
box.layout().addWidget(self.infostack)
self.__initRecentItemsModel()
self.__invalidated = True
self.__executor = ThreadExecutor(self)
QApplication.postEvent(self, QEvent(RuntimeEvent.Init))
def __init__(self):
super().__init__()
self.data = None
self.test_data = None
self.preprocessor = None
self.train_data_missing_vals = False
self.test_data_missing_vals = False
self.scorers = []
self.__pending_comparison_criterion = self.comparison_criterion
#: An Ordered dictionary with current inputs and their testing results.
self.learners = OrderedDict() # type: Dict[Any, Input]
self.__state = State.Waiting
# Do we need to [re]test any learners, set by _invalidate and
# cleared by __update
self.__needupdate = False
self.__task = None # type: Optional[TaskState]
self.__executor = ThreadExecutor()
sbox = gui.vBox(self.controlArea, "抽样")
rbox = gui.radioButtons(
sbox, self, "resampling", callback=self._param_changed)
gui.appendRadioButton(rbox, "交叉验证(Cross validation)")
ibox = gui.indentedBox(rbox)
gui.comboBox(
ibox, self, "n_folds", label="折叠次数(Number of folds): ",
items=[str(x) for x in self.NFolds], maximumContentsLength=3,
orientation=Qt.Horizontal, callback=self.kfold_changed)
gui.checkBox(
ibox, self, "cv_stratified", "分层(Stratified)",
callback=self.kfold_changed)
gui.appendRadioButton(rbox, "按特征交叉验证(Cross validation by feature)")
ibox = gui.indentedBox(rbox)
self.feature_model = DomainModel(
order=DomainModel.METAS, valid_types=DiscreteVariable)
self.features_combo = gui.comboBox(
ibox, self, "fold_feature", model=self.feature_model,
orientation=Qt.Horizontal, callback=self.fold_feature_changed)
gui.appendRadioButton(rbox, "随机抽样(Random sampling)")
ibox = gui.indentedBox(rbox)
gui.comboBox(
ibox, self, "n_repeats", label="重复训练/测试: ",
items=[str(x) for x in self.NRepeats], maximumContentsLength=3,
orientation=Qt.Horizontal, callback=self.shuffle_split_changed)
gui.comboBox(
ibox, self, "sample_size", label="训练集大小: ",
items=["{} %".format(x) for x in self.SampleSizes],
maximumContentsLength=5, orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.checkBox(
ibox, self, "shuffle_stratified", "分层(Stratified)",
callback=self.shuffle_split_changed)
gui.appendRadioButton(rbox, "留一法(Leave one out)")
gui.appendRadioButton(rbox, "测试训练数据")
gui.appendRadioButton(rbox, "测试测试数据")
self.cbox = gui.vBox(self.controlArea, "目标类别")
self.class_selection_combo = gui.comboBox(
self.cbox, self, "class_selection", items=[],
sendSelectedValue=True, valueType=str,
callback=self._on_target_class_changed,
contentsLength=8)
self.modcompbox = box = gui.vBox(self.controlArea, "模型比较")
gui.comboBox(
box, self, "comparison_criterion", model=PyListModel(),
callback=self.update_comparison_table)
hbox = gui.hBox(box)
gui.checkBox(hbox, self, "use_rope",
"可忽略区别: ",
callback=self._on_use_rope_changed)
gui.lineEdit(hbox, self, "rope", validator=QDoubleValidator(),
controlWidth=70, callback=self.update_comparison_table,
alignment=Qt.AlignRight)
self.controls.rope.setEnabled(self.use_rope)
gui.rubber(self.controlArea)
self.score_table = ScoreTable(self)
self.score_table.shownScoresChanged.connect(self.update_stats_model)
view = self.score_table.view
view.setSizeAdjustPolicy(view.AdjustToContents)
box = gui.vBox(self.mainArea, "评价结果")
box.layout().addWidget(self.score_table.view)
self.compbox = box = gui.vBox(self.mainArea, box='模型比较')
table = self.comparison_table = QTableWidget(
wordWrap=False, editTriggers=QTableWidget.NoEditTriggers,
selectionMode=QTableWidget.NoSelection)
table.setSizeAdjustPolicy(table.AdjustToContents)
header = table.verticalHeader()
header.setSectionResizeMode(QHeaderView.Fixed)
header.setSectionsClickable(False)
header = table.horizontalHeader()
header.setTextElideMode(Qt.ElideRight)
header.setDefaultAlignment(Qt.AlignCenter)
header.setSectionsClickable(False)
header.setStretchLastSection(False)
header.setSectionResizeMode(QHeaderView.ResizeToContents)
avg_width = self.fontMetrics().averageCharWidth()
header.setMinimumSectionSize(8 * avg_width)
header.setMaximumSectionSize(15 * avg_width)
header.setDefaultSectionSize(15 * avg_width)
box.layout().addWidget(table)
box.layout().addWidget(QLabel(
"<small>此表显示数值为一概率. 此概率表示\"行模型\"的评价指标大于"
"\"列模型\"的评价指标. "
"值小说明概率很小, 区别可以忽略不计.</small>", wordWrap=True))
def __init__(self):
super().__init__()
self.data = None # type: Optional[Table]
self.preprocessed_data = None # type: Optional[Table]
self.graph = None # type: Optional[nx.Graph]
self.partition = None # type: Optional[np.array]
self.__executor = ThreadExecutor(parent=self)
self.__future = None # type: Optional[Future]
self.__queue = None # type: Optional[TaskQueue]
pca_box = gui.vBox(self.controlArea, 'PCA Preprocessing')
self.apply_pca_cbx = gui.checkBox(
pca_box,
self,
'apply_pca',
label='Apply PCA preprocessing',
callback=self._update_graph,
) # type: QCheckBox
self.pca_components_slider = gui.hSlider(
pca_box,
self,
'pca_components',
label='Components: ',
minValue=2,
maxValue=_MAX_PCA_COMPONENTS,
callback=self._update_pca_components,
tracking=False) # type: QSlider
graph_box = gui.vBox(self.controlArea, 'Graph parameters')
self.metric_combo = gui.comboBox(
graph_box,
self,
'metric_idx',
label='Distance metric',
items=[m[0] for m in METRICS],
callback=self._update_graph,
orientation=Qt.Horizontal,
) # type: gui.OrangeComboBox
self.k_neighbors_spin = gui.spin(
graph_box,
self,
'k_neighbors',
minv=1,
maxv=_MAX_K_NEIGBOURS,
label='k neighbors',
controlWidth=80,
alignment=Qt.AlignRight,
callback=self._update_graph,
) # type: gui.SpinBoxWFocusOut
self.resolution_spin = gui.hSlider(
graph_box,
self,
'resolution',
minValue=0,
maxValue=5.,
step=1e-1,
label='Resolution',
intOnly=False,
labelFormat='%.1f',
callback=self._update_resolution,
tracking=False,
) # type: QSlider
self.resolution_spin.parent().setToolTip(
'The resolution parameter affects the number of clusters to find. '
'Smaller values tend to produce more clusters and larger values '
'retrieve less clusters.')
self.apply_button = gui.auto_commit(
self.controlArea,
self,
'auto_commit',
'Apply',
box=None,
commit=self.commit,
) # type: QWidget
def __init__(self):
super().__init__()
# commit
self.commit_button = None
# progress bar
self.progress_bar = None
self.progress_bar_iterations = None
# data
self.input_data = None
self.input_genes = []
self.tax_id = None
self.use_attr_names = None
self.gene_id_attribute = None
self.gene_id_column = None
# custom gene sets
self.custom_data = None
self.feature_model = DomainModel(valid_types=(DiscreteVariable, StringVariable))
self.custom_gs_col_box = None
self.gs_label_combobox = None
self.custom_tax_id = None
self.custom_use_attr_names = None
self.custom_gene_id_attribute = None
self.custom_gene_id_column = None
self.num_of_custom_sets = None
# Gene Sets widget
self.gs_widget = None
# info box
self.input_info = None
self.num_of_sel_genes = 0
# filter
self.line_edit_filter = None
self.search_pattern = ''
self.organism_select_combobox = None
# data model view
self.data_view = None
self.data_model = None
# gene matcher NCBI
self.gene_matcher = None
# filter proxy model
self.filter_proxy_model = None
# hierarchy widget
self.hierarchy_widget = None
self.hierarchy_state = None
# spinbox
self.spin_widget = None
# threads
self.threadpool = QThreadPool(self)
self.workers = None
self._task = None # type: Optional[Task]
self._executor = ThreadExecutor()
# gui
self.setup_gui()
def __init__(self, parent=None):
super().__init__(self, parent)
self.input_data = None
self.gene_info = None
self.ref_data = None
self.ontology = None
self.annotations = None
self.loaded_annotation_code = None
self.treeStructRootKey = None
self.probFunctions = [
statistics.Binomial(),
statistics.Hypergeometric()
]
self.selectedTerms = []
self.selectionChanging = 0
self.__state = State.Ready
self.__scheduletimer = QTimer(self, singleShot=True)
self.__scheduletimer.timeout.connect(self.__update)
#############
# GUI
#############
self.tabs = gui.tabWidget(self.controlArea)
# Input tab
self.inputTab = gui.createTabPage(self.tabs, "Input")
box = gui.widgetBox(self.inputTab, "Info")
self.infoLabel = gui.widgetLabel(box, "No data on input\n")
gui.button(
box,
self,
"Ontology/Annotation Info",
callback=self.show_info,
tooltip="Show information on loaded ontology and annotations",
)
self.referenceRadioBox = gui.radioButtonsInBox(
self.inputTab,
self,
"use_reference_dataset",
["Entire genome", "Reference set (input)"],
tooltips=[
"Use entire genome for reference",
"Use genes from Referece Examples input signal as reference"
],
box="Reference",
callback=self.__invalidate,
)
self.referenceRadioBox.buttons[1].setDisabled(True)
gui.radioButtonsInBox(
self.inputTab,
self,
"aspect_index",
["Biological process", "Cellular component", "Molecular function"],
box="Aspect",
callback=self.__invalidate,
)
# Filter tab
self.filterTab = gui.createTabPage(self.tabs, "Filter")
box = gui.widgetBox(self.filterTab, "Filter GO Term Nodes")
gui.checkBox(
box,
self,
"filter_by_num_of_instances",
"Genes",
callback=self.filter_and_display_graph,
tooltip="Filter by number of input genes mapped to a term",
)
ibox = gui.indentedBox(box)
gui.spin(
ibox,
self,
'min_num_of_instances',
1,
100,
step=1,
label='#:',
labelWidth=15,
callback=self.filter_and_display_graph,
callbackOnReturn=True,
tooltip="Min. number of input genes mapped to a term",
)
gui.checkBox(
box,
self,
"filter_by_p_value_nofdr",
"p-value",
callback=self.filter_and_display_graph,
tooltip="Filter by term p-value",
)
gui.doubleSpin(
gui.indentedBox(box),
self,
'max_p_value_no_fdr',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.filter_and_display_graph,
callbackOnReturn=True,
tooltip="Max term p-value",
)
# use filter_by_p_value for FDR, as it was the default in prior versions
gui.checkBox(box,
self,
"filter_by_p_value",
"FDR",
callback=self.filter_and_display_graph,
tooltip="Filter by term FDR")
gui.doubleSpin(
gui.indentedBox(box),
self,
'max_p_value',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.filter_and_display_graph,
callbackOnReturn=True,
tooltip="Max term p-value",
)
box = gui.widgetBox(box, "Significance test")
gui.radioButtonsInBox(
box,
self,
"prob_func",
["Binomial", "Hypergeometric"],
tooltips=[
"Use binomial distribution test",
"Use hypergeometric distribution test"
],
callback=self.__invalidate,
) # TODO: only update the p values
box = gui.widgetBox(self.filterTab,
"Evidence codes in annotation",
addSpace=True)
self.evidenceCheckBoxDict = {}
for etype in go.evidence_types_ordered:
ecb = QCheckBox(etype,
toolTip=go.evidence_types[etype],
checked=self.use_evidence_type[etype])
ecb.toggled.connect(self.__on_evidence_changed)
box.layout().addWidget(ecb)
self.evidenceCheckBoxDict[etype] = ecb
# Select tab
self.selectTab = gui.createTabPage(self.tabs, "Select")
box = gui.radioButtonsInBox(
self.selectTab,
self,
"selection_direct_annotation",
["Directly or Indirectly", "Directly"],
box="Annotated genes",
callback=self.example_selection,
)
box = gui.widgetBox(self.selectTab, "Output", addSpace=True)
gui.radioButtonsInBox(
box,
self,
"selection_disjoint",
btnLabels=[
"All selected genes", "Term-specific genes",
"Common term genes"
],
tooltips=[
"Outputs genes annotated to all selected GO terms",
"Outputs genes that appear in only one of selected GO terms",
"Outputs genes common to all selected GO terms",
],
callback=self.example_selection,
)
# ListView for DAG, and table for significant GOIDs
self.DAGcolumns = [
'GO term', 'Cluster', 'Reference', 'p-value', 'FDR', 'Genes',
'Enrichment'
]
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.listView = GOTreeWidget(self.splitter)
self.listView.setSelectionMode(QTreeView.ExtendedSelection)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(len(self.DAGcolumns))
self.listView.setHeaderLabels(self.DAGcolumns)
self.listView.header().setSectionsClickable(True)
self.listView.header().setSortIndicatorShown(True)
self.listView.header().setSortIndicator(
self.DAGcolumns.index('p-value'), Qt.AscendingOrder)
self.listView.setSortingEnabled(True)
self.listView.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.listView.setRootIsDecorated(True)
self.listView.itemSelectionChanged.connect(self.view_selection_changed)
# table of significant GO terms
self.sigTerms = QTreeWidget(self.splitter)
self.sigTerms.setColumnCount(len(self.DAGcolumns))
self.sigTerms.setHeaderLabels(self.DAGcolumns)
self.sigTerms.setSortingEnabled(True)
self.sigTerms.setSelectionMode(QTreeView.ExtendedSelection)
self.sigTerms.header().setSortIndicator(
self.DAGcolumns.index('p-value'), Qt.AscendingOrder)
self.sigTerms.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.sigTerms.itemSelectionChanged.connect(
self.table_selection_changed)
self.sigTableTermsSorted = []
self.graph = {}
self.originalGraph = None
self.inputTab.layout().addStretch(1)
self.filterTab.layout().addStretch(1)
self.selectTab.layout().addStretch(1)
class AnnotationSlot(SimpleNamespace):
taxid = ... # type: str
name = ... # type: str
filename = ... # type:str
@staticmethod
def parse_tax_id(f_name):
return f_name.split('.')[0]
try:
remote_files = serverfiles.ServerFiles().listfiles(DOMAIN)
except (ConnectTimeout, RequestException, ConnectionError):
# TODO: Warn user about failed connection to the remote server
remote_files = []
self.available_annotations = [
AnnotationSlot(
taxid=AnnotationSlot.parse_tax_id(annotation_file),
name=taxonomy.common_taxid_to_name(
AnnotationSlot.parse_tax_id(annotation_file)),
filename=FILENAME_ANNOTATION.format(
AnnotationSlot.parse_tax_id(annotation_file)),
) for _, annotation_file in set(remote_files +
serverfiles.listfiles(DOMAIN))
if annotation_file != FILENAME_ONTOLOGY
]
self._executor = ThreadExecutor()
def __init__(self):
self._task = None # type: Optional[self.Task]
self._executor = ThreadExecutor(self)
self.data = None
self.test_type = ''
self.discrete_model = DomainModel(separators=False,
valid_types=(DiscreteVariable, ),
parent=self)
self.domain_model = DomainModel(valid_types=DomainModel.PRIMITIVE,
parent=self)
box = gui.vBox(self.controlArea, 'Hypotheses Testing')
gui.listView(
box,
self,
'chosen_X',
model=self.discrete_model,
box='Grouping Variables',
selectionMode=QListView.ExtendedSelection,
callback=self.Error.no_vars_selected.clear,
toolTip='Select multiple variables with Ctrl+ or Shift+Click.')
target = gui.comboBox(
box,
self,
'chosen_y',
sendSelectedValue=True,
label='Test Variable',
callback=[self.set_test_type, self.Error.no_class_selected.clear])
target.setModel(self.domain_model)
gui.checkBox(box,
self,
'is_permutation',
label='Permutation test',
callback=self.set_test_type)
gui.comboBox(box,
self,
'test_statistic',
label='Statistic:',
items=tuple(self.TEST_STATISTICS),
orientation=Qt.Horizontal,
sendSelectedValue=True,
callback=self.set_test_type)
gui.label(box, self, 'Test: %(test_type)s')
box = gui.vBox(self.controlArea, 'Filter')
gui.spin(box,
self,
'min_count',
5,
1000,
5,
label='Minimum group size (count):')
self.btn_compute = gui.button(self.controlArea,
self,
'&Compute',
callback=self.compute)
gui.rubber(self.controlArea)
class Model(PyTableModel):
_n_vars = 0
_BACKGROUND = [QBrush(QColor('#eee')), QBrush(QColor('#ddd'))]
def setHorizontalHeaderLabels(self, labels, n_vars):
self._n_vars = n_vars
super().setHorizontalHeaderLabels(labels)
def data(self, index, role=Qt.DisplayRole):
if role == Qt.BackgroundRole and index.column() < self._n_vars:
return self._BACKGROUND[index.row() % 2]
if role == Qt.DisplayRole or role == Qt.ToolTipRole:
colname = self.headerData(index.column(), Qt.Horizontal)
if colname.lower() in ('count', 'count | class'):
row = self.mapToSourceRows(index.row())
return int(self[row][index.column()])
return super().data(index, role)
owwidget = self
class View(gui.TableView):
_vars = None
def set_vars(self, vars):
self._vars = vars
def selectionChanged(self, *args):
super().selectionChanged(*args)
rows = list({
index.row()
for index in self.selectionModel().selectedRows(0)
})
if not rows:
owwidget.Outputs.data.send(None)
return
model = self.model().tolist()
filters = [
Values([
FilterDiscrete(self._vars[col], {model[row][col]})
for col in range(len(self._vars))
]) for row in self.model().mapToSourceRows(rows)
]
data = Values(filters, conjunction=False)(owwidget.data)
annotated = create_annotated_table(owwidget.data, data.ids)
owwidget.Outputs.selected_data.send(data)
owwidget.Outputs.data.send(annotated)
self.view = view = View(self)
self.model = Model(parent=self)
view.setModel(self.model)
view.horizontalHeader().setStretchLastSection(False)
self.mainArea.layout().addWidget(view)
self.set_test_type()
def __init__(self):
super().__init__()
self.data = None
self.model = None
self.to_explain = None
self.explanations = None
self.stop = True
self.e = None
self._task = None
self._executor = ThreadExecutor()
info_box = gui.vBox(self.controlArea, "Info")
self.data_info = gui.widgetLabel(info_box, "Data: N/A")
self.model_info = gui.widgetLabel(info_box, "Model: N/A")
self.sample_info = gui.widgetLabel(info_box, "Sample: N/A")
criteria_box = gui.vBox(self.controlArea, "Stopping criteria")
self.error_spin = gui.spin(criteria_box,
self,
"gui_error",
0.01,
1,
step=0.01,
label="Error < ",
spinType=float,
callback=self._update_error_spin,
controlWidth=80,
keyboardTracking=False)
self.p_val_spin = gui.spin(criteria_box,
self,
"gui_p_val",
0.01,
1,
step=0.01,
label="Error p-value < ",
spinType=float,
callback=self._update_p_val_spin,
controlWidth=80,
keyboardTracking=False)
plot_properties_box = gui.vBox(self.controlArea, "Display features")
self.num_atr_spin = gui.spin(plot_properties_box,
self,
"gui_num_atr",
1,
100,
step=1,
label="Show attributes",
callback=self._update_num_atr_spin,
controlWidth=80,
keyboardTracking=False)
self.sort_combo = gui.comboBox(plot_properties_box,
self,
"sort_index",
label="Rank by",
items=SortBy.items(),
orientation=Qt.Horizontal,
callback=self._update_combo)
gui.rubber(self.controlArea)
self.cancel_button = gui.button(
self.controlArea,
self,
"Stop Computation",
callback=self.toggle_button,
autoDefault=True,
tooltip="Stops and restarts computation")
self.cancel_button.setDisabled(True)
predictions_box = gui.vBox(self.mainArea, "Model prediction")
self.predict_info = gui.widgetLabel(predictions_box, "")
self.mainArea.setMinimumWidth(700)
self.resize(700, 400)
class _GraphicsView(QGraphicsView):
def __init__(self, scene, parent, **kwargs):
for k, v in dict(
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
viewportUpdateMode=QGraphicsView.
BoundingRectViewportUpdate,
renderHints=(QPainter.Antialiasing
| QPainter.TextAntialiasing
| QPainter.SmoothPixmapTransform),
alignment=(Qt.AlignTop | Qt.AlignLeft),
sizePolicy=QSizePolicy(
QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)).items():
kwargs.setdefault(k, v)
super().__init__(scene, parent, **kwargs)
class GraphicsView(_GraphicsView):
def __init__(self, scene, parent):
super().__init__(
scene,
parent,
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn,
styleSheet='QGraphicsView {background: white}')
self.viewport().setMinimumWidth(500)
self._is_resizing = False
w = self
def resizeEvent(self, resizeEvent):
self._is_resizing = True
self.w.draw()
self._is_resizing = False
return super().resizeEvent(resizeEvent)
def is_resizing(self):
return self._is_resizing
def sizeHint(self):
return QSize(600, 300)
class FixedSizeGraphicsView(_GraphicsView):
def __init__(self, scene, parent):
super().__init__(scene,
parent,
sizePolicy=QSizePolicy(
QSizePolicy.MinimumExpanding,
QSizePolicy.Minimum))
def sizeHint(self):
return QSize(600, 30)
"""all will share the same scene, but will show different parts of it"""
self.box_scene = QGraphicsScene(self)
self.box_view = GraphicsView(self.box_scene, self)
self.header_view = FixedSizeGraphicsView(self.box_scene, self)
self.footer_view = FixedSizeGraphicsView(self.box_scene, self)
self.mainArea.layout().addWidget(self.header_view)
self.mainArea.layout().addWidget(self.box_view)
self.mainArea.layout().addWidget(self.footer_view)
self.painter = None
def __init__(
self,
parent=None,
):
super().__init__(self, parent)
self.selectionChangedFlag = False
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.infoLabel = gui.widgetLabel(
gui.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
self.organisms = None
self.organismBox = gui.widgetBox(self.controlArea,
"Organism",
addSpace=True)
self.organismComboBox = gui.comboBox(
self.organismBox,
self,
"organism_index",
callback=self._onSelectedOrganismChanged)
# For now only support one alt source, with a checkbox
# In the future this can be extended to multiple selections
self.altSourceCheck = gui.checkBox(self.organismBox,
self,
"useAltSource",
"Show information from dictyBase",
callback=self.onAltSourceChange)
self.altSourceCheck.hide()
box = gui.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = gui.comboBox(box,
self,
"gene_attr",
"Gene attribute",
callback=self.updateInfoItems)
self.geneAttrComboBox.setEnabled(not self.useAttr)
cb = gui.checkBox(box,
self,
"useAttr",
"Use attribute names",
callback=self.updateInfoItems)
cb.toggled[bool].connect(self.geneAttrComboBox.setDisabled)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
# A label for dictyExpress link (Why oh god why???)
self.dictyExpressBox = gui.widgetBox(self.controlArea, "Dicty Express")
self.linkLabel = gui.widgetLabel(self.dictyExpressBox, "")
self.linkLabel.setOpenExternalLinks(False)
self.linkLabel.linkActivated.connect(self.onDictyExpressLink)
self.dictyExpressBox.hide()
gui.rubber(self.controlArea)
gui.lineEdit(self.mainArea,
self,
"search_string",
"Filter",
callbackOnType=True,
callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.treeWidget.setItemDelegate(
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = gui.widgetBox(self.mainArea, "", orientation="horizontal")
gui.button(box, self, "Select Filtered", callback=self.selectFiltered)
gui.button(box,
self,
"Clear Selection",
callback=self.treeWidget.clearSelection)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
self.setBlocking(True)
self.executor = ThreadExecutor(self)
self.progressBarInit()
task = Task(
function=partial(taxonomy.ensure_downloaded,
callback=methodinvoke(self, "advance", ())))
task.resultReady.connect(self.initialize)
task.exceptionReady.connect(self._onInitializeError)
self.initfuture = self.executor.submit(task)
def __init__(
self,
parent=None,
):
super().__init__(self, parent)
self.selectionChangedFlag = False
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.map_input_to_ensembl = None
self.infoLabel = gui.widgetLabel(
gui.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
self.organisms = None
self.organismBox = gui.widgetBox(self.controlArea,
"Organism",
addSpace=True)
self.organismComboBox = gui.comboBox(
self.organismBox,
self,
"organism_index",
callback=self._onSelectedOrganismChanged)
box = gui.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = gui.comboBox(box,
self,
"gene_attr",
"Gene attribute",
callback=self.updateInfoItems)
self.geneAttrComboBox.setEnabled(not self.useAttr)
self.geneAttrCheckbox = gui.checkBox(box,
self,
"useAttr",
"Use column names",
callback=self.updateInfoItems)
self.geneAttrCheckbox.toggled[bool].connect(
self.geneAttrComboBox.setDisabled)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
gui.rubber(self.controlArea)
gui.lineEdit(self.mainArea,
self,
"search_string",
"Filter",
callbackOnType=True,
callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setSelectionMode(QTreeView.ExtendedSelection)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setItemDelegateForColumn(
HEADER_SCHEMA['NCBI ID'],
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.setItemDelegateForColumn(
HEADER_SCHEMA['Ensembl ID'],
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = gui.widgetBox(self.mainArea, "", orientation="horizontal")
gui.button(box, self, "Select Filtered", callback=self.selectFiltered)
gui.button(box,
self,
"Clear Selection",
callback=self.treeWidget.clearSelection)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
self.setBlocking(True)
self.executor = ThreadExecutor(self)
self.progressBarInit()
task = Task(
function=partial(taxonomy.ensure_downloaded,
callback=methodinvoke(self, "advance", ())))
task.resultReady.connect(self.initialize)
task.exceptionReady.connect(self._onInitializeError)
self.initfuture = self.executor.submit(task)
def __init__(self):
super().__init__()
self.data = None
self.test_data = None
self.preprocessor = None
self.train_data_missing_vals = False
self.test_data_missing_vals = False
self.scorers = []
#: An Ordered dictionary with current inputs and their testing results.
self.learners = OrderedDict() # type: Dict[Any, Input]
self.__state = State.Waiting
# Do we need to [re]test any learners, set by _invalidate and
# cleared by __update
self.__needupdate = False
self.__task = None # type: Optional[Task]
self.__executor = ThreadExecutor()
sbox = gui.vBox(self.controlArea, "Sampling")
rbox = gui.radioButtons(sbox,
self,
"resampling",
callback=self._param_changed)
gui.appendRadioButton(rbox, "Cross validation")
ibox = gui.indentedBox(rbox)
gui.comboBox(ibox,
self,
"n_folds",
label="Number of folds: ",
items=[str(x) for x in self.NFolds],
maximumContentsLength=3,
orientation=Qt.Horizontal,
callback=self.kfold_changed)
gui.checkBox(ibox,
self,
"cv_stratified",
"Stratified",
callback=self.kfold_changed)
gui.appendRadioButton(rbox, "Cross validation by feature")
ibox = gui.indentedBox(rbox)
self.feature_model = DomainModel(order=DomainModel.METAS,
valid_types=DiscreteVariable)
self.features_combo = gui.comboBox(ibox,
self,
"fold_feature",
model=self.feature_model,
orientation=Qt.Horizontal,
callback=self.fold_feature_changed)
gui.appendRadioButton(rbox, "Random sampling")
ibox = gui.indentedBox(rbox)
gui.comboBox(ibox,
self,
"n_repeats",
label="Repeat train/test: ",
items=[str(x) for x in self.NRepeats],
maximumContentsLength=3,
orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.comboBox(ibox,
self,
"sample_size",
label="Training set size: ",
items=["{} %".format(x) for x in self.SampleSizes],
maximumContentsLength=5,
orientation=Qt.Horizontal,
callback=self.shuffle_split_changed)
gui.checkBox(ibox,
self,
"shuffle_stratified",
"Stratified",
callback=self.shuffle_split_changed)
gui.appendRadioButton(rbox, "Leave one out")
gui.appendRadioButton(rbox, "Test on train data")
gui.appendRadioButton(rbox, "Test on test data")
self.cbox = gui.vBox(self.controlArea, "Target Class")
self.class_selection_combo = gui.comboBox(
self.cbox,
self,
"class_selection",
items=[],
sendSelectedValue=True,
valueType=str,
callback=self._on_target_class_changed,
contentsLength=8)
gui.rubber(self.controlArea)
self.view = gui.TableView(wordWrap=True,
editTriggers=gui.TableView.NoEditTriggers)
header = self.view.horizontalHeader()
header.setSectionResizeMode(QHeaderView.ResizeToContents)
header.setDefaultAlignment(Qt.AlignCenter)
header.setStretchLastSection(False)
header.setContextMenuPolicy(Qt.CustomContextMenu)
header.customContextMenuRequested.connect(self.show_column_chooser)
self.result_model = QStandardItemModel(self)
self.result_model.setHorizontalHeaderLabels(["Method"])
self.view.setModel(self.result_model)
self.view.setItemDelegate(ItemDelegate())
box = gui.vBox(self.mainArea, "Evaluation Results")
box.layout().addWidget(self.view)
def __init__(self):
super().__init__()
self.data = None
self.model = None
self.to_explain = None
self.explanations = None
self.stop = True
self.e = None
self._task = None
self._executor = ThreadExecutor()
self.dataview = QTableView(verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn,
sortingEnabled=True,
selectionMode=QTableView.NoSelection,
focusPolicy=Qt.StrongFocus)
self.dataview.sortByColumn(2, Qt.DescendingOrder)
self.dataview.horizontalHeader().setResizeMode(QHeaderView.Stretch)
domain = Domain([ContinuousVariable("Score"),
ContinuousVariable("Error")],
metas=[StringVariable(name="Feature"), StringVariable(name="Value")])
self.placeholder_table_model = TableModel(
Table.from_domain(domain), parent=None)
self.dataview.setModel(self.placeholder_table_model)
info_box = gui.vBox(self.controlArea, "Info")
self.data_info = gui.widgetLabel(info_box, "Data: N/A")
self.model_info = gui.widgetLabel(info_box, "Model: N/A")
self.sample_info = gui.widgetLabel(info_box, "Sample: N/A")
criteria_box = gui.vBox(self.controlArea, "Stopping criteria")
self.error_spin = gui.spin(criteria_box,
self,
"gui_error",
0.01,
1,
step=0.01,
label="Error < ",
spinType=float,
callback=self._update_error_spin,
controlWidth=80,
keyboardTracking=False)
self.p_val_spin = gui.spin(criteria_box,
self,
"gui_p_val",
0.01,
1,
step=0.01,
label="Error p-value < ",
spinType=float,
callback=self._update_p_val_spin,
controlWidth=80, keyboardTracking=False)
gui.rubber(self.controlArea)
self.cancel_button = gui.button(self.controlArea,
self,
"Stop Computation",
callback=self.toggle_button,
autoDefault=True,
tooltip="Stops and restarts computation")
self.cancel_button.setDisabled(True)
predictions_box = gui.vBox(self.mainArea, "Model prediction")
self.predict_info = gui.widgetLabel(predictions_box, "")
self.mainArea.layout().addWidget(self.dataview)
self.resize(640, 480)
def __init__(self):
super().__init__()
self.data = None # type: Optional[Table]
self.clusterings = {}
self.__executor = ThreadExecutor(parent=self)
self.__task = None # type: Optional[Task]
layout = QGridLayout()
bg = gui.radioButtonsInBox(
self.controlArea,
self,
"optimize_k",
orientation=layout,
box="Number of Clusters",
callback=self.update_method,
)
layout.addWidget(
gui.appendRadioButton(bg, "Fixed:", addToLayout=False), 1, 1)
sb = gui.hBox(None, margin=0)
gui.spin(sb,
self,
"k",
minv=2,
maxv=30,
controlWidth=60,
alignment=Qt.AlignRight,
callback=self.update_k)
gui.rubber(sb)
layout.addWidget(sb, 1, 2)
layout.addWidget(gui.appendRadioButton(bg, "From", addToLayout=False),
2, 1)
ftobox = gui.hBox(None)
ftobox.layout().setContentsMargins(0, 0, 0, 0)
layout.addWidget(ftobox, 2, 2)
gui.spin(ftobox,
self,
"k_from",
minv=2,
maxv=29,
controlWidth=60,
alignment=Qt.AlignRight,
callback=self.update_from)
gui.widgetLabel(ftobox, "to")
gui.spin(ftobox,
self,
"k_to",
minv=3,
maxv=30,
controlWidth=60,
alignment=Qt.AlignRight,
callback=self.update_to)
gui.rubber(ftobox)
box = gui.vBox(self.controlArea, "Initialization")
gui.comboBox(box,
self,
"smart_init",
items=[m[0] for m in self.INIT_METHODS],
callback=self.invalidate)
layout = QGridLayout()
gui.widgetBox(box, orientation=layout)
layout.addWidget(gui.widgetLabel(None, "Re-runs: "), 0, 0,
Qt.AlignLeft)
sb = gui.hBox(None, margin=0)
layout.addWidget(sb, 0, 1)
gui.lineEdit(sb,
self,
"n_init",
controlWidth=60,
valueType=int,
validator=QIntValidator(),
callback=self.invalidate)
layout.addWidget(gui.widgetLabel(None, "Maximum iterations: "), 1, 0,
Qt.AlignLeft)
sb = gui.hBox(None, margin=0)
layout.addWidget(sb, 1, 1)
gui.lineEdit(sb,
self,
"max_iterations",
controlWidth=60,
valueType=int,
validator=QIntValidator(),
callback=self.invalidate)
self.apply_button = gui.auto_commit(self.buttonsArea,
self,
"auto_commit",
"Apply",
box=None,
commit=self.commit)
gui.rubber(self.controlArea)
box = gui.vBox(self.mainArea, box="Silhouette Scores")
self.mainArea.setVisible(self.optimize_k)
self.table_model = ClusterTableModel(self)
table = self.table_view = QTableView(self.mainArea)
table.setModel(self.table_model)
table.setSelectionMode(QTableView.SingleSelection)
table.setSelectionBehavior(QTableView.SelectRows)
table.setItemDelegate(gui.ColoredBarItemDelegate(self, color=Qt.cyan))
table.selectionModel().selectionChanged.connect(self.select_row)
table.setMaximumWidth(200)
table.horizontalHeader().setStretchLastSection(True)
table.horizontalHeader().hide()
table.setShowGrid(False)
box.layout().addWidget(table)
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.selectionChanged = False
self.filterString = ""
self.datasetName = ""
## GUI
box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoBox = gui.widgetLabel(box, "Initializing\n\n")
box = gui.widgetBox(self.controlArea, "Output", addSpace=True)
gui.radioButtonsInBox(box,
self,
"outputRows",
["Genes in rows", "Samples in rows"],
"Rows",
callback=self.commitIf)
gui.checkBox(box,
self,
"mergeSpots",
"Merge spots of same gene",
callback=self.commitIf)
gui.separator(box)
self.nameEdit = gui.lineEdit(
box,
self,
"datasetName",
"Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited)
self.nameEdit.setPlaceholderText("")
if sys.version_info < (3, ):
box = gui.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = gui.button(box,
self,
"Commit",
callback=self.commit)
cb = gui.checkBox(box, self, "autoCommit", "Commit on any change")
gui.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
else:
gui.auto_commit(self.controlArea,
self,
"autoCommit",
"Commit",
box="Commit")
self.commitIf = self.commit
gui.rubber(self.controlArea)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(textChanged=self.filter)
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.completer)
self.mainArea.layout().addWidget(self.filterLineEdit)
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QTreeView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = gui.LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = gui.widgetBox(splitterH, "Description")
self.infoGDS = gui.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
gui.rubber(box)
box = gui.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"])
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = [
"dataset_id", "title", "platform_organism", "description"
]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float, )))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
def __init__(self):
super().__init__()
# sets self.curvePoints, self.steps equidistant points from
# 1/self.steps to 1
self.updateCurvePoints()
self.scoring = [
("Classification Accuracy", Orange.evaluation.scoring.CA),
("AUC", Orange.evaluation.scoring.AUC),
("Precision", Orange.evaluation.scoring.Precision),
("Recall", Orange.evaluation.scoring.Recall),
]
#: input data on which to construct the learning curve
self.data = None
#: optional test data
self.testdata = None
#: A {input_id: Learner} mapping of current learners from input channel
self.learners = OrderedDict()
#: A {input_id: List[Results]} mapping of input id to evaluation
#: results list, one for each curve point
self.results = OrderedDict()
#: A {input_id: List[float]} mapping of input id to learning curve
#: point scores
self.curves = OrderedDict()
# [start-snippet-3]
#: The current evaluating task (if any)
self._task = None # type: Optional[Task]
#: An executor we use to submit learner evaluations into a thread pool
self._executor = ThreadExecutor()
# [end-snippet-3]
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoa = gui.widgetLabel(box, "No data on input.")
self.infob = gui.widgetLabel(box, "No learners.")
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Evaluation Scores")
gui.comboBox(
box,
self,
"scoringF",
items=[x[0] for x in self.scoring],
callback=self._invalidate_curves,
)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Options")
gui.spin(
box,
self,
"folds",
2,
100,
step=1,
label="Cross validation folds: ",
keyboardTracking=False,
callback=lambda: self._invalidate_results()
if self.commitOnChange else None,
)
gui.spin(
box,
self,
"steps",
2,
100,
step=1,
label="Learning curve points: ",
keyboardTracking=False,
callback=[
self.updateCurvePoints,
lambda: self._invalidate_results()
if self.commitOnChange else None,
],
)
gui.checkBox(box, self, "commitOnChange",
"Apply setting on any change")
self.commitBtn = gui.button(box,
self,
"Apply Setting",
callback=self._invalidate_results,
disabled=True)
gui.rubber(self.controlArea)
# table widget
self.table = gui.table(self.mainArea,
selectionMode=QTableWidget.NoSelection)
def __init__(self, parent=None):
super().__init__(parent)
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 = gui.widgetBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, "No data on input\n")
box = gui.widgetBox(self.controlArea, "Organism")
self.organism_cb = gui.comboBox(box,
self,
"current_taxid_index",
items=map(taxonomy.name, self.taxids),
callback=self._update_organism)
box = gui.widgetBox(self.controlArea, "Genes")
self.genes_cb = gui.comboBox(box,
self,
"gene_var_index",
callback=self._update_query_genes)
self.varmodel = itemmodels.VariableListModel()
self.genes_cb.setModel(self.varmodel)
gui.checkBox(box,
self,
"use_attr_names",
"Use attribute names",
callback=self._update_query_genes)
box = gui.widgetBox(self.controlArea, "Network")
gui.comboBox(box,
self,
"network_source",
items=[s.name for s in SOURCES],
callback=self._on_source_db_changed)
gui.checkBox(box,
self,
"include_neighborhood",
"Include immediate gene neighbors",
callback=self.invalidate)
self.score_spin = gui.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 = gui.widgetBox(self.controlArea, "Commit")
gui.button(box, self, "Retrieve", callback=self.commit, default=True)
self.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
self.layout().setSizeConstraint(QLayout.SetFixedSize)
self.executor = ThreadExecutor()
