def on_done(self, _):
# update info box
self._update_info_box()
# set output options
self.toggle_radio_options()
# set known genes
self.table_model.initialize(self.gene_matcher.genes)
self.table_view.setModel(self.table_model)
self.table_view.selectionModel().selectionChanged.connect(self.commit)
self.table_view.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table_view.setItemDelegateForColumn(
self.table_model.entrez_column_index,
LinkStyledItemDelegate(self.table_view))
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)
self.table_view.horizontalHeader().setStretchLastSection(True)
# set unknown genes
self.unknown_model.initialize(self.gene_matcher.genes)
self.unknown_view.verticalHeader().setStretchLastSection(True)
self._apply_filter()
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_gui(self):
# control area
self.setup_control_area()
# main area
self.data_view = QTreeView()
self.setup_filter_model()
self.setup_filter_area()
self.data_view.setAlternatingRowColors(True)
self.data_view.sortByColumn(self.COUNT, Qt.DescendingOrder)
self.data_view.setSortingEnabled(True)
self.data_view.setSelectionMode(QTreeView.ExtendedSelection)
self.data_view.setEditTriggers(QTreeView.NoEditTriggers)
self.data_view.viewport().setMouseTracking(False)
self.data_view.setItemDelegateForColumn(self.TERM, LinkStyledItemDelegate(self.data_view))
self.mainArea.layout().addWidget(self.data_view)
self.data_view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.assign_delegates()
def _handle_matcher_results(self):
assert threading.current_thread() == threading.main_thread()
if self.progress_bar:
self.progress_bar.finish()
self.setStatusMessage('')
# update info box
self._update_info_box()
# set output options
self.toggle_radio_options()
# set known genes
self.table_model.initialize(self.gene_matcher.genes)
self.table_view.setModel(self.table_model)
self.table_view.selectionModel().selectionChanged.connect(self.commit)
self.table_view.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table_view.setItemDelegateForColumn(
self.table_model.entrez_column_index,
LinkStyledItemDelegate(self.table_view))
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)
self.table_view.horizontalHeader().setStretchLastSection(True)
# set unknown genes
self.unknown_model.initialize(self.gene_matcher.genes)
self.unknown_view.verticalHeader().setStretchLastSection(True)
self._apply_filter()
def setup_gui(self):
# control area
info_box = vBox(self.controlArea, 'Input info')
self.input_info = widgetLabel(info_box)
organism_box = vBox(self.controlArea, 'Organisms')
self.organism_select_combobox = comboBox(
organism_box,
self,
'selected_organism',
callback=self.on_input_option_change)
# Selection of genes attribute
box = widgetBox(self.controlArea, 'Gene attribute')
self.gene_columns = itemmodels.VariableListModel(parent=self)
self.gene_column_combobox = comboBox(
box, self, 'gene_col_index', callback=self.on_input_option_change)
self.gene_column_combobox.setModel(self.gene_columns)
self.attr_names_checkbox = checkBox(
box,
self,
'use_attr_names',
'Use attribute names',
disables=[(-1, self.gene_column_combobox)],
callback=self.on_input_option_change)
self.gene_column_combobox.setDisabled(bool(self.use_attr_names))
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.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 __init__(self):
super().__init__()
# OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
# Control area
box = vBox(self.controlArea, True, margin=0)
self.gs_selection_component: GeneSetSelection = GeneSetSelection(
self, box)
self.gs_selection_component.selection_changed.connect(
self._on_selection_changed)
# Main area
self.filter_proxy_model = FilterProxyModel()
self.filter_proxy_model.setFilterKeyColumn(Header.term)
self.tree_view = QTreeView()
self.tree_view.setAlternatingRowColors(True)
self.tree_view.setSortingEnabled(True)
self.tree_view.sortByColumn(Header.count, Qt.DescendingOrder)
self.tree_view.setSelectionMode(QTreeView.ExtendedSelection)
self.tree_view.setEditTriggers(QTreeView.NoEditTriggers)
self.tree_view.viewport().setMouseTracking(True)
self.tree_view.setItemDelegateForColumn(
Header.term, LinkStyledItemDelegate(self.tree_view))
self.tree_view.setItemDelegateForColumn(Header.genes,
NumericalColumnDelegate(self))
self.tree_view.setItemDelegateForColumn(Header.count,
NumericalColumnDelegate(self))
self.tree_view.setModel(self.filter_proxy_model)
h_layout = QHBoxLayout()
h_layout.setSpacing(100)
h_widget = widgetBox(self.mainArea, orientation=h_layout)
spin(
h_widget,
self,
'min_count',
0,
1000,
label='Count',
tooltip='Minimum genes count',
checked='use_min_count',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
self.line_edit_filter = lineEdit(h_widget, self, 'search_pattern')
self.line_edit_filter.setPlaceholderText('Filter gene sets ...')
self.line_edit_filter.textChanged.connect(self.filter_view)
self.mainArea.layout().addWidget(self.tree_view)
self.tree_view.header().setSectionResizeMode(
QHeaderView.ResizeToContents)
self.commit_button = auto_commit(self.controlArea,
self,
'auto_commit',
'&Commit',
box=False)
self.input_data: Optional[Table] = None
self.num_of_selected_genes: int = 0
def __init__(self):
super().__init__()
# OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
# Control area
box = vBox(self.controlArea, True, margin=0)
self.gs_selection_component: GeneSetSelection = GeneSetSelection(self, box)
self.gs_selection_component.selection_changed.connect(self._on_selection_changed)
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._on_selection_changed,
)
self.reference_radio_box.setEnabled(False)
self.reference_genes: Optional[List[str]] = None
# Main area
self.filter_proxy_model = FilterProxyModel()
self.filter_proxy_model.setFilterKeyColumn(Header.term)
self.tree_view = QTreeView()
self.tree_view.setAlternatingRowColors(True)
self.tree_view.setSortingEnabled(True)
self.tree_view.sortByColumn(Header.count, Qt.DescendingOrder)
self.tree_view.setSelectionMode(QTreeView.ExtendedSelection)
self.tree_view.setEditTriggers(QTreeView.NoEditTriggers)
self.tree_view.viewport().setMouseTracking(True)
self.tree_view.setItemDelegateForColumn(Header.term, LinkStyledItemDelegate(self.tree_view))
self.tree_view.setItemDelegateForColumn(Header.genes, NumericalColumnDelegate(self))
self.tree_view.setItemDelegateForColumn(Header.count, NumericalColumnDelegate(self))
self.tree_view.setItemDelegateForColumn(Header.p_val, NumericalColumnDelegate(self, precision=2, notation='e'))
self.tree_view.setItemDelegateForColumn(Header.fdr, NumericalColumnDelegate(self, precision=2, notation='e'))
self.tree_view.setItemDelegateForColumn(Header.enrichment, NumericalColumnDelegate(self, precision=1))
self.tree_view.setItemDelegateForColumn(Header.reference, NumericalColumnDelegate(self))
self.tree_view.setModel(self.filter_proxy_model)
h_layout = QHBoxLayout()
h_layout.setSpacing(100)
h_widget = widgetBox(self.mainArea, orientation=h_layout)
spin(
h_widget,
self,
'min_count',
0,
1000,
label='Count',
tooltip='Minimum genes count',
checked='use_min_count',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
doubleSpin(
h_widget,
self,
'max_p_value',
0.0,
1.0,
0.0001,
label='p-value',
tooltip='Maximum p-value of the enrichment score',
checked='use_p_value',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
doubleSpin(
h_widget,
self,
'max_fdr',
0.0,
1.0,
0.0001,
label='FDR',
tooltip='Maximum false discovery rate',
checked='use_max_fdr',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
self.line_edit_filter = lineEdit(h_widget, self, 'search_pattern')
self.line_edit_filter.setPlaceholderText('Filter gene sets ...')
self.line_edit_filter.textChanged.connect(self.filter_view)
self.mainArea.layout().addWidget(self.tree_view)
self.tree_view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.commit_button = auto_commit(self.controlArea, self, 'auto_commit', '&Commit', box=False)
self.input_data: Optional[Table] = None
self.num_of_selected_genes: int = 0
self.gene_info: Optional[GeneInfo] = None
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()