def __init__(self, parent=None):
super().__init__(parent)
self.servers = [
('https://dictyexpress.research.bcm.edu/', 'dictyExpress'),
('https://cloud.genialis.com/', 'Genialis'),
]
self.selectedExperiments = []
self.buffer = dicty.CacheSQLite(bufferfile)
self.searchString = ""
self.items = []
self.result_types = []
self.controlArea.setMaximumWidth(250)
self.controlArea.setMinimumWidth(250)
box = gui.widgetBox(self.controlArea, 'Project')
self.projectCB = gui.comboBox(box,
self,
"projecti",
items=[],
callback=self.ProjectChosen)
self.projects = []
b = gui.widgetBox(self.controlArea, "Selection bookmarks")
self.selectionSetsWidget = SelectionSetsWidget(self)
self.selectionSetsWidget.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Maximum)
def store_selections(modified):
if not modified:
self.storedSelections = self.selectionSetsWidget.selections
self.selectionSetsWidget.selectionModified.connect(store_selections)
b.layout().addWidget(self.selectionSetsWidget)
gui.separator(self.controlArea)
b = gui.widgetBox(self.controlArea, "Sort output columns")
self.columnsSortingWidget = SortedListWidget(self)
self.columnsSortingWidget.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Maximum)
box = gui.widgetBox(self.controlArea, 'Experiment name')
self.experimentNameCB = gui.comboBox(box,
self,
"exnamei",
items=SORTING_MODEL_LIST)
b.layout().addWidget(self.columnsSortingWidget)
sorting_model = QStringListModel(SORTING_MODEL_LIST)
self.columnsSortingWidget.setModel(sorting_model)
self.columnsSortingWidget.sortingOrder = self.storedSortOrder
def store_sort_order():
self.storedSortOrder = self.columnsSortingWidget.sortingOrder
self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Expression Type')
self.expressionTypesCB = gui.comboBox(box,
self,
"rtypei",
items=[],
callback=self.UpdateResultsList)
gui.checkBox(self.controlArea, self, "excludeconstant",
"Exclude labels with constant values")
gui.checkBox(self.controlArea, self, "joinreplicates",
"Average replicates (use median)")
gui.checkBox(self.controlArea, self, "log2",
"Logarithmic (base 2) transformation")
gui.checkBox(self.controlArea, self, "transpose", "Genes as columns")
self.commit_button = gui.button(self.controlArea,
self,
"&Commit",
callback=self.Commit)
self.commit_button.setDisabled(True)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Server')
gui.comboBox(box,
self,
"serveri",
items=[title for url, title in self.servers],
callback=self.ServerChosen)
gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"Clear cache",
callback=self.clear_cache)
gui.lineEdit(self.mainArea,
self,
"searchString",
"Search",
callbackOnType=True,
callback=self.SearchUpdate)
self.headerLabels = [t[1] for t in HEADER]
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.experimentsWidget, self.experimentsWidget)
self.experimentsWidget.header().installEventFilter(contextEventFilter)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.setAlternatingRowColors(True)
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.selectionSetsWidget.setSelectionModel(
self.experimentsWidget.selectionModel())
self.selectionSetsWidget.setSelections(self.storedSelections)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.restoreHeaderState()
self.experimentsWidget.header().geometriesChanged.connect(
self.saveHeaderState)
self.dbc = None
self.AuthSet()
QTimer.singleShot(100, self.ConnectAndUpdate)
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)