def __init__(self):
super().__init__()
# Init data
self.data = None
self.selected_data = None
self.selected_data_transformed = None # used for transforming the 'selected data' into the 'data' domain
self.words = []
self.p_values = []
self.fdr_values = []
# Info section
fbox = gui.widgetBox(self.controlArea, "Info")
self.info_all = gui.label(fbox, self, 'Cluster words:')
self.info_sel = gui.label(fbox, self, 'Selected words:')
self.info_fil = gui.label(fbox, self, 'After filtering:')
# Filtering settings
fbox = gui.widgetBox(self.controlArea, "Filter")
hbox = gui.widgetBox(fbox, orientation=0)
self.chb_p = gui.checkBox(hbox, self, "filter_by_p", "p-value",
callback=self.filter_and_display,
tooltip="Filter by word p-value")
self.spin_p = gui.doubleSpin(hbox, self, 'filter_p_value',
1e-4, 1, step=1e-4, labelWidth=15,
callback=self.filter_and_display,
callbackOnReturn=True,
tooltip="Max p-value for word")
self.spin_p.setEnabled(self.filter_by_p)
hbox = gui.widgetBox(fbox, orientation=0)
self.chb_fdr = gui.checkBox(hbox, self, "filter_by_fdr", "FDR",
callback=self.filter_and_display,
tooltip="Filter by word FDR")
self.spin_fdr = gui.doubleSpin(hbox, self, 'filter_fdr_value',
1e-4, 1, step=1e-4, labelWidth=15,
callback=self.filter_and_display,
callbackOnReturn=True,
tooltip="Max p-value for word")
self.spin_fdr.setEnabled(self.filter_by_fdr)
gui.rubber(self.controlArea)
# Word's list view
self.cols = ['Word', 'p-value', 'FDR']
self.sig_words = QTreeWidget()
self.sig_words.setColumnCount(len(self.cols))
self.sig_words.setHeaderLabels(self.cols)
self.sig_words.setSortingEnabled(True)
self.sig_words.setSelectionMode(QTreeView.ExtendedSelection)
self.sig_words.sortByColumn(2, 0) # 0 is ascending order
for i in range(len(self.cols)):
self.sig_words.resizeColumnToContents(i)
self.mainArea.layout().addWidget(self.sig_words)
def __init__(self):
OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
# Init data
self.data = None
self.selected_data = None
# used for transforming the 'selected data' into the 'data' domain
self.selected_data_transformed = None
self.results = Result()
# info box
fbox = gui.widgetBox(self.controlArea, "Info")
self.info_fil = gui.label(fbox, self, 'Words displayed: 0')
# Filtering settings
fbox = gui.widgetBox(self.controlArea, "Filter")
hbox = gui.widgetBox(fbox, orientation=0)
self.chb_p = gui.checkBox(hbox, self, "filter_by_p", "p-value",
callback=self.filter_and_display,
tooltip="Filter by word p-value")
self.spin_p = gui.doubleSpin(hbox, self, 'filter_p_value',
1e-4, 1, step=1e-4, labelWidth=15,
callback=self.filter_and_display,
tooltip="Max p-value for word")
self.spin_p.setEnabled(self.filter_by_p)
hbox = gui.widgetBox(fbox, orientation=0)
self.chb_fdr = gui.checkBox(hbox, self, "filter_by_fdr", "FDR",
callback=self.filter_and_display,
tooltip="Filter by word FDR")
self.spin_fdr = gui.doubleSpin(hbox, self, 'filter_fdr_value',
1e-4, 1, step=1e-4, labelWidth=15,
callback=self.filter_and_display,
tooltip="Max p-value for word")
self.spin_fdr.setEnabled(self.filter_by_fdr)
gui.rubber(self.controlArea)
gui.auto_send(self.buttonsArea, self, "auto_apply")
# Word's list view
self.cols = ['Word', 'p-value', 'FDR']
self.sig_words = QTreeWidget()
self.sig_words.setColumnCount(len(self.cols))
self.sig_words.setHeaderLabels(self.cols)
self.sig_words.setSortingEnabled(True)
self.sig_words.setSelectionMode(QTreeView.NoSelection)
self.sig_words.sortByColumn(1, 0) # 0 is ascending order
for i in range(len(self.cols)):
self.sig_words.resizeColumnToContents(i)
self.mainArea.layout().addWidget(self.sig_words)
def __init__(self, box, parent, settings_var, **kwargs):
# type: (Union[QGroupBox, QWidget], QWidget, str) -> None
super().__init__(**kwargs)
self.parent = parent
self.stored_selection = settings_var
# gene sets object
self.gs_object = GeneSets() # type: GeneSets
self.hierarchy_tree_widget = QTreeWidget(self)
self.hierarchy_tree_widget.setHeaderHidden(True)
self.hierarchy_tree_widget.setEditTriggers(QTreeView.NoEditTriggers)
box.layout().addWidget(self.hierarchy_tree_widget)
self.custom_set_hier = None
self.default_selection = [('GO', 'molecular_function'),
('GO', 'biological_process'),
('GO', 'cellular_component')]
def setup_gui(self):
# control area
info_box = vBox(self.controlArea, 'Input info')
self.input_info = widgetLabel(info_box)
hierarchy_box = widgetBox(self.controlArea, "Entity Sets")
self.hierarchy_widget = QTreeWidget(self)
self.hierarchy_widget.setEditTriggers(QTreeView.NoEditTriggers)
self.hierarchy_widget.setHeaderLabels(HIERARCHY_HEADER_LABELS)
self.hierarchy_widget.itemClicked.connect(self.display_gene_sets)
hierarchy_box.layout().addWidget(self.hierarchy_widget)
self.commit_button = auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# rubber(self.controlArea)
# main area
self.filter_proxy_model = QSortFilterProxyModel(self.data_view)
self.filter_proxy_model.setFilterKeyColumn(3)
self.data_view = QTreeView()
self.data_view.setModel(self.filter_proxy_model)
self.data_view.setAlternatingRowColors(True)
self.data_view.sortByColumn(2, Qt.DescendingOrder)
self.data_view.setSortingEnabled(True)
self.data_view.setSelectionMode(QTreeView.ExtendedSelection)
self.data_view.setEditTriggers(QTreeView.NoEditTriggers)
self.data_view.viewport().setMouseTracking(True)
self.data_view.setItemDelegateForColumn(
TERM, LinkStyledItemDelegate(self.data_view))
self.data_view.selectionModel().selectionChanged.connect(self.commit)
self.lineEdit_filter = lineEdit(self.mainArea, self, 'search_pattern',
'Filter gene sets:')
self.lineEdit_filter.setPlaceholderText('search pattern ...')
self.lineEdit_filter.textChanged.connect(
self.filter_proxy_model.setFilterRegExp)
self.mainArea.layout().addWidget(self.data_view)
def setup_control_area(self):
info_box = vBox(self.controlArea, 'Info')
self.input_info = widgetLabel(info_box)
box = vBox(self.controlArea, "Custom Gene Sets")
self.gs_label_combobox = comboBox(box,
self,
"gene_set_label",
sendSelectedValue=True,
model=self.feature_model,
callback=self.invalidate)
self.gs_label_combobox.setDisabled(True)
self.reference_radio_box = radioButtonsInBox(
self.controlArea,
self,
"use_reference_data",
["Entire genome", "Reference gene set (input)"],
tooltips=[
"Use entire genome (for gene set enrichment)",
"Use reference set of genes"
],
box="Reference",
callback=self.invalidate)
self.reference_radio_box.setEnabled(False)
hierarchy_box = widgetBox(self.controlArea, "Gene Set Categories")
self.hierarchy_widget = QTreeWidget(self)
self.hierarchy_widget.setEditTriggers(QTreeView.NoEditTriggers)
self.hierarchy_widget.setHeaderLabels([' '])
self.hierarchy_widget.itemClicked.connect(self.update_tree_view)
hierarchy_box.layout().addWidget(self.hierarchy_widget)
self.commit_button = auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
def __init__(self, parent=None):
super().__init__(self, parent)
self.input_data = 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.ShowInfo,
tooltip="Show information on loaded ontology and annotations")
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)
# 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.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.header().setSortIndicator(self.DAGcolumns.index('p-value'), Qt.AscendingOrder)
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
filename = ... # type:str
@staticmethod
def parse_tax_id(f_name):
return f_name.split('.')[1]
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, 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, signalManager=None,
name="Databases update"):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
self.retryButton = gui.button(
box, self, "Reconnect", callback=self.RetrieveFilesList
)
self.retryButton.hide()
gui.rubber(box)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
def __init__(self):
super().__init__()
self.res = None
self.organism = '44689'
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.progress_bar = None
# threads
self.threadpool = QThreadPool()
# Login Section
box = gui.widgetBox(self.controlArea, 'Login')
self.namefield = gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"Output", addSpace=True)
gui.radioButtonsInBox(box,
self,
"gene_as_attr_name",
["Genes in rows", "Genes in columns"],
callback=self.invalidate)
self.controlArea.layout().addWidget(h_line())
self.refresh_button = gui.button(self.controlArea,
self,
"Refresh",
callback=self.refresh)
self.handle_cache_button(True)
gui.rubber(self.controlArea)
self.commit_button = gui.auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.mainArea.layout().addWidget(h_line())
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.on_selection_changed)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.auth_set()
self.connect()
self.sizeHint()
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, 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 = 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,
parent=None,
signalManager=None,
name="Databases update"):
OWWidget.__init__(self,
parent,
signalManager,
name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.search_update)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(header_labels)
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(header.Title, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.search_update)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box,
self,
"Update all",
callback=self.update_all,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box,
self,
"Download all",
callback=self.download_filtered,
tooltip="Download all filtered files shown")
self.cancelButton = gui.button(
box,
self,
"Cancel",
callback=self.cancel_active_threads,
tooltip="Cancel scheduled downloads/updates.")
# add empty label to separate button.
# TODO: is there better way of doing this?
box.layout().addWidget(QLabel(), Qt.AlignRight)
self.addButton = gui.button(box,
self,
"Add ...",
callback=self.__handle_dialog,
tooltip="Add files for personal use.")
self.retryButton = gui.button(box,
self,
"Reconnect",
callback=self.initialize_files_view)
self.retryButton.hide()
# gui.rubber(box)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.resize(800, 600)
self.update_items = []
self._dialog = None
self.progress_bar = None
# threads
self.threadpool = QThreadPool(self)
#self.threadpool.setMaxThreadCount(1)
self.workers = list()
self.initialize_files_view()
def __init__(self):
OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
self.gds_info: Optional[GDSInfo] = GDSInfo(
) # TODO: handle possible exceptions
self.gds_data: Optional[Table] = None
# Control area
box = widgetBox(self.controlArea, 'Info', addSpace=True)
self.infoBox = widgetLabel(box, 'Initializing\n\n')
box = widgetBox(self.controlArea, 'Output', addSpace=True)
radioButtonsInBox(box,
self,
'genes_as_rows',
['Samples in rows', 'Genes in rows'],
callback=self._run)
separator(box)
rubber(self.controlArea)
auto_commit(self.controlArea,
self,
'auto_commit',
'&Commit',
box=False)
# Main Area
# Filter widget
self.filter = lineEdit(self.mainArea,
self,
'search_pattern',
'Filter:',
callbackOnType=True,
callback=self._apply_filter)
self.mainArea.layout().addWidget(self.filter)
splitter_vertical = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter_vertical)
# set table view
self.table_view = QTableView(splitter_vertical)
self.table_view.setShowGrid(False)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(1, Qt.AscendingOrder)
self.table_view.setAlternatingRowColors(True)
self.table_view.verticalHeader().setVisible(False)
self.table_view.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table_view.setSelectionMode(QAbstractItemView.SingleSelection)
self.table_view.viewport().setMouseTracking(True)
self.table_view.setSizeAdjustPolicy(
QAbstractScrollArea.AdjustToContents)
self.table_model = GEODatasetsModel()
self.table_model.initialize(self.gds_info)
self.table_view.setModel(self.table_model)
self.table_model.show_table()
self.table_view.horizontalHeader().setStretchLastSection(True)
self.table_view.resizeColumnsToContents()
v_header = self.table_view.verticalHeader()
option = self.table_view.viewOptions()
size = self.table_view.style().sizeFromContents(
QStyle.CT_ItemViewItem, option, QSize(20, 20), self.table_view)
v_header.setDefaultSectionSize(size.height() + 2)
v_header.setMinimumSectionSize(5)
# set item delegates
self.table_view.setItemDelegateForColumn(
self.table_model.pubmedid_col,
LinkStyledItemDelegate(self.table_view))
self.table_view.setItemDelegateForColumn(
self.table_model.gds_id_col,
LinkStyledItemDelegate(self.table_view))
self.table_view.setItemDelegateForColumn(
self.table_model.indicator_col,
IndicatorItemDelegate(self.table_view, role=Qt.DisplayRole),
)
splitter_horizontal = QSplitter(Qt.Horizontal, splitter_vertical)
# Description Widget
box = widgetBox(splitter_horizontal, 'Description')
self.description_widget = widgetLabel(box, '')
self.description_widget.setWordWrap(True)
rubber(box)
# Sample Annotations Widget
box = widgetBox(splitter_horizontal, 'Sample Annotations')
self.annotations_widget = QTreeWidget(box)
self.annotations_widget.setHeaderLabels(
['Type (Sample annotations)', 'Sample count'])
self.annotations_widget.setRootIsDecorated(True)
box.layout().addWidget(self.annotations_widget)
self._annotations_updating = False
self.annotations_widget.itemChanged.connect(
self.on_annotation_selection_changed)
self.splitters = splitter_vertical, splitter_horizontal
for sp, setting in zip(self.splitters, self.splitter_settings):
sp.splitterMoved.connect(self._splitter_moved)
sp.restoreState(setting)
self.table_view.selectionModel().selectionChanged.connect(
self.on_gds_selection_changed)
self._apply_filter()
self._run()
def __init__(self):
super().__init__()
ConcurrentWidgetMixin.__init__(self)
self._res: Optional[genapi.GenAPI] = None
self.organism = '44689'
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.genapi_pub_auth = {
'url': genapi.DEFAULT_URL,
'username': genapi.DEFAULT_EMAIL,
'password': genapi.DEFAULT_PASSWD,
}
# Login Section
box = gui.widgetBox(self.controlArea, 'Sign in')
self.user_info = gui.label(box, self, '')
self.server_info = gui.label(box, self, '')
box = gui.widgetBox(box, orientation=Qt.Horizontal)
self.sign_in_btn = gui.button(box,
self,
'Sign In',
callback=self.sign_in,
autoDefault=False)
self.sign_out_btn = gui.button(box,
self,
'Sign Out',
callback=self.sign_out,
autoDefault=False)
box = gui.widgetBox(self.controlArea, "Output")
gui.radioButtonsInBox(box,
self,
"gene_as_attr_name",
["Genes in rows", "Genes in columns"],
callback=self.invalidate)
self.clear_cache_btn = gui.button(self.controlArea,
self,
"Clear cache",
autoDefault=False,
callback=self.clear_cache)
gui.rubber(self.controlArea)
self.commit_button = gui.auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.on_selection_changed)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.sign_in(silent=True)
self.sizeHint()
def __init__(self):
super().__init__()
self.res = None
self.orgnism = 352472
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.lastSelected = None # store last selected customTreeItem
self.progress_bar = None
# threads
self.threadpool = QThreadPool()
# Login Section
box = gui.widgetBox(self.controlArea, 'Login')
self.namefield = gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"setTimeVariable",
"Set Time variable")
self.time_var_checkBox.setToolTip(
'Create new column where each row represents one time point')
self.controlArea.layout().addWidget(h_line())
self.commit_button = gui.button(self.controlArea,
self,
"Commit",
callback=self.commit)
self.handle_commit_button(False)
self.refresh_button = gui.button(self.controlArea,
self,
"Refresh",
callback=self.refresh)
self.handle_cache_button(True)
gui.rubber(self.controlArea)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.mainArea.layout().addWidget(h_line())
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.auth_set()
self.connect()
def __init__(self, parent=None):
super().__init__(self, parent)
self.clusterDataset = None
self.referenceDataset = None
self.ontology = None
self.annotations = None
self.loadedAnnotationCode = "---"
self.treeStructRootKey = None
self.probFunctions = [stats.Binomial(), stats.Hypergeometric()]
self.selectedTerms = []
self.selectionChanging = 0
self.__state = OWGOEnrichmentAnalysis.Initializing
self.annotationCodes = []
#############
## 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=self.annotationCodes,
callback=self._updateEnrichment,
tooltip="Select organism")
genebox = gui.widgetBox(self.inputTab, "Gene Names")
self.geneAttrIndexCombo = gui.comboBox(
genebox,
self,
"geneAttrIndex",
callback=self._updateEnrichment,
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._updateEnrichment)
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._updateEnrichment)
self.referenceRadioBox.buttons[1].setDisabled(True)
gui.radioButtonsInBox(
self.inputTab,
self,
"aspectIndex",
["Biological process", "Cellular component", "Molecular function"],
box="Aspect",
callback=self._updateEnrichment)
## 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._updateEnrichment)
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.inputTab.layout().addStretch(1)
self.filterTab.layout().addStretch(1)
self.selectTab.layout().addStretch(1)
self.setBlocking(True)
self._executor = ThreadExecutor()
self._init = EnsureDownloaded([(taxonomy.Taxonomy.DOMAIN,
taxonomy.Taxonomy.FILENAME),
("GO", "taxonomy.pickle")])
self._init.finished.connect(self.__initialize_finish)
self._executor.submit(self._init)
def __init__(self, parent=None):
super().__init__(parent)
self._changedFlag = False
self.__invalidated = False
self.__runstate = OWKEGGPathwayBrowser.Initializing
self.__in_setProgress = False
self.controlArea.setMaximumWidth(250)
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(box, "No data on input\n")
gui.separator(self.controlArea)
gui.checkBox(self.controlArea,
self,
"useReference",
"From signal",
box="Reference",
callback=self.Update)
gui.separator(self.controlArea)
gui.checkBox(
self.controlArea,
self,
"showOrthology",
"Show pathways in full orthology",
box="Orthology",
callback=self.UpdateListView,
)
gui.checkBox(
self.controlArea,
self,
"autoResize",
"Resize to fit",
box="Image",
callback=self.UpdatePathwayViewTransform,
)
box = gui.widgetBox(self.controlArea, "Cache Control")
gui.button(
box,
self,
"Clear cache",
callback=self.ClearCache,
tooltip="Clear all locally cached KEGG data.",
default=False,
autoDefault=False,
)
gui.separator(self.controlArea)
gui.auto_commit(self.controlArea, self, "autoCommit", "Commit")
gui.rubber(self.controlArea)
spliter = QSplitter(Qt.Vertical, self.mainArea)
self.pathwayView = PathwayView(self, spliter)
self.pathwayView.scene().selectionChanged.connect(
self._onSelectionChanged)
self.mainArea.layout().addWidget(spliter)
self.listView = QTreeWidget(allColumnsShowFocus=True,
selectionMode=QTreeWidget.SingleSelection,
sortingEnabled=True,
maximumHeight=200)
spliter.addWidget(self.listView)
self.listView.setColumnCount(4)
self.listView.setHeaderLabels(
["Pathway", "P value", "Genes", "Reference"])
self.listView.itemSelectionChanged.connect(self.UpdatePathwayView)
select = QAction("Select All", self, shortcut=QKeySequence.SelectAll)
select.triggered.connect(self.selectAll)
self.addAction(select)
self.data = None
self.input_genes = []
self.tax_id = None
self.use_attr_names = None
self.gene_id_attribute = None
self.gene_id_column = None
self.ref_data = None
self.ref_genes = []
self.ref_tax_id = None
self.ref_use_attr_names = None
self.ref_gene_id_attribute = None
self.ref_gene_id_column = None
self.pathways = {}
self.ncbi_gene_map = []
self.org = None
self._executor = concurrent.ThreadExecutor()
self.setEnabled(False)
self.setBlocking(True)
progress = concurrent.methodinvoke(self, "setProgress", (float, ))
def get_genome():
"""Return a KEGGGenome with the common org entries precached."""
genome = kegg.KEGGGenome()
essential = genome.essential_organisms()
common = genome.common_organisms()
# Remove duplicates of essential from common.
# (essential + common list as defined here will be used in the
# GUI.)
common = [c for c in common if c not in essential]
# TODO: Add option to specify additional organisms not
# in the common list.
keys = list(map(genome.org_code_to_entry_key, essential + common))
genome.pre_cache(keys, progress_callback=progress)
return (keys, genome)
self._genomeTask = task = concurrent.Task(function=get_genome)
task.finished.connect(self.__initialize_finish)
self.progressBarInit()
self.infoLabel.setText("Fetching organism definitions\n")
self._executor.submit(task)
def __init__(self,
parent=None,
signalManager=None,
name="Databases update"):
OWWidget.__init__(self,
parent,
signalManager,
name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.search_update)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(header_labels)
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(header.Title, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.search_update)
box.layout().addWidget(self.filesView)
layout = QHBoxLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
self.updateButton = gui.button(
box,
self,
"Update all",
callback=self.update_all,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box,
self,
"Download all",
callback=self.download_filtered,
tooltip="Download all filtered files shown")
self.cancelButton = gui.button(
box,
self,
"Cancel",
callback=self.cancel_active_threads,
tooltip="Cancel scheduled downloads/updates.")
self.addButton = gui.button(box,
self,
"Add ...",
callback=self.__handle_dialog,
tooltip="Add files for personal use.")
layout.addWidget(self.updateButton)
layout.addWidget(self.downloadButton)
layout.addWidget(self.cancelButton)
layout.addStretch()
layout.addWidget(self.addButton)
# Enable retryButton once connection is established
# self.retryButton = gui.button(
# box, self, "Reconnect", callback=self.initialize_files_view
# )
# self.retryButton.hide()
self.resize(800, 600)
self.update_items = []
self._dialog = None
self.progress_bar = None
# threads
self.threadpool = QThreadPool(self)
#self.threadpool.setMaxThreadCount(1)
self.workers = list()
self.initialize_files_view()
def __init__(self):
self.data = None
self.output = None
self._is_running = False
self.isRegexMatch = lambda x: True
self.tree = QTreeWidget(self.mainArea,
columnCount=2,
allColumnsShowFocus=True,
alternatingRowColors=True,
selectionMode=QTreeWidget.ExtendedSelection,
uniformRowHeights=True)
self.tree.setHeaderLabels(["Itemsets", "Support", "%"])
self.tree.header().setStretchLastSection(True)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.mainArea.layout().addWidget(self.tree)
box = gui.widgetBox(self.controlArea, "Info")
self.nItemsets = self.nSelectedExamples = self.nSelectedItemsets = ''
gui.label(box, self, "Number of itemsets: %(nItemsets)s")
gui.label(box, self, "Selected itemsets: %(nSelectedItemsets)s")
gui.label(box, self, "Selected examples: %(nSelectedExamples)s")
hbox = gui.widgetBox(box, orientation='horizontal')
gui.button(hbox, self, "Expand all", callback=self.tree.expandAll)
gui.button(hbox, self, "Collapse all", callback=self.tree.collapseAll)
box = gui.widgetBox(self.controlArea, 'Find itemsets')
gui.valueSlider(box,
self,
'minSupport',
values=[.0001, .0005, .001, .005, .01, .05, .1, .5] +
list(range(1, 101)),
label='Minimal support:',
labelFormat="%g%%",
callback=lambda: self.find_itemsets())
gui.hSlider(box,
self,
'maxItemsets',
minValue=10000,
maxValue=100000,
step=10000,
label='Max. number of itemsets:',
labelFormat="%d",
callback=lambda: self.find_itemsets())
self.button = gui.auto_commit(
box,
self,
'autoFind',
'Find Itemsets',
commit=self.find_itemsets,
callback=lambda: self.autoFind and self.find_itemsets())
box = gui.widgetBox(self.controlArea, 'Filter itemsets')
gui.lineEdit(box,
self,
'filterKeywords',
'Contains:',
callback=self.filter_change,
orientation='horizontal',
tooltip='A comma or space-separated list of regular '
'expressions.')
hbox = gui.widgetBox(box, orientation='horizontal')
gui.spin(hbox,
self,
'filterMinItems',
1,
998,
label='Min. items:',
callback=self.filter_change)
gui.spin(hbox,
self,
'filterMaxItems',
2,
999,
label='Max. items:',
callback=self.filter_change)
gui.checkBox(box,
self,
'filterSearch',
label='Apply these filters in search',
tooltip='If checked, the itemsets are filtered according '
'to these filter conditions already in the search '
'phase. \nIf unchecked, the only filters applied '
'during search are the ones above, '
'and the itemsets are \nfiltered afterwards only for '
'display, i.e. only the matching itemsets are shown.')
gui.rubber(hbox)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, 'autoSend', 'Send selection')
self.filter_change()
