def add_row(self):
def sync_combos():
combo = self.sender()
index = combo.currentIndex()
model = combo.model()
other = ({row_items.left_combo, row_items.right_combo}
- {combo}).pop()
other_index = other.currentIndex()
other_model = other.model()
if 0 <= index < len(combo.model()):
var = model[index]
if isinstance(var, str):
other.setCurrentText(model[index])
elif isinstance(other_model[other_index], str):
for other_var in other_model:
if isinstance(other_var, Variable) \
and var.name == other_var.name \
and (type(other_var) is type(var)
or (not var.is_continuous
and not other_var.is_continuous)):
other.setCurrentText(var.name)
break
self.emit_list()
def get_combo(model):
combo = QComboBox(self)
combo.setModel(model)
# We use signal activated because it is triggered only on user
# interaction, not programmatically.
combo.activated.connect(sync_combos)
return combo
def get_button(label, callback):
button = QPushButton(label, self)
button.setFlat(True)
button.setFixedWidth(12)
button.clicked.connect(callback)
return button
row = self.layout().count()
row_items = self.RowItems(
QLabel("and" if row else self.pre_label),
get_combo(self.model_left),
QLabel(self.in_label),
get_combo(self.model_right),
get_button("×", self.on_remove_row),
get_button("+", self.on_add_row)
)
layout = QHBoxLayout()
layout.setSpacing(10)
self.layout().addLayout(layout)
layout.addStretch(10)
for item in row_items:
layout.addWidget(item)
self.rows.append(row_items)
self._reset_buttons()
def _setup_gui_labels(self):
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
vlayout.setSpacing(1)
self.labels_edit = QTreeView()
self.labels_edit.setEditTriggers(QTreeView.CurrentChanged)
self.labels_edit.setRootIsDecorated(False)
self.labels_model = DictItemsModel()
self.labels_edit.setModel(self.labels_model)
self.labels_edit.selectionModel().selectionChanged.connect(
self.on_label_selection_changed)
# Necessary signals to know when the labels change
self.labels_model.dataChanged.connect(self.on_labels_changed)
self.labels_model.rowsInserted.connect(self.on_labels_changed)
self.labels_model.rowsRemoved.connect(self.on_labels_changed)
vlayout.addWidget(self.labels_edit)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.setSpacing(1)
self.add_label_action = QAction(
"+",
self,
toolTip="Add a new label.",
triggered=self.on_add_label,
enabled=False,
shortcut=QKeySequence(QKeySequence.New),
)
self.remove_label_action = QAction(
unicodedata.lookup("MINUS SIGN"),
self,
toolTip="Remove selected label.",
triggered=self.on_remove_label,
enabled=False,
shortcut=QKeySequence(QKeySequence.Delete),
)
button_size = gui.toolButtonSizeHint()
button_size = QSize(button_size, button_size)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.add_label_action)
hlayout.addWidget(button)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.remove_label_action)
hlayout.addWidget(button)
hlayout.addStretch(10)
vlayout.addLayout(hlayout)
self.main_form.addRow("Labels:", vlayout)
def _setup_gui_labels(self):
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
vlayout.setSpacing(1)
self.labels_edit = QTreeView()
self.labels_edit.setEditTriggers(QTreeView.CurrentChanged)
self.labels_edit.setRootIsDecorated(False)
self.labels_model = DictItemsModel()
self.labels_edit.setModel(self.labels_model)
self.labels_edit.selectionModel().selectionChanged.connect(
self.on_label_selection_changed)
# Necessary signals to know when the labels change
self.labels_model.dataChanged.connect(self.on_labels_changed)
self.labels_model.rowsInserted.connect(self.on_labels_changed)
self.labels_model.rowsRemoved.connect(self.on_labels_changed)
vlayout.addWidget(self.labels_edit)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.setSpacing(1)
self.add_label_action = QAction(
"+", self,
toolTip="Add a new label.",
triggered=self.on_add_label,
enabled=False,
shortcut=QKeySequence(QKeySequence.New))
self.remove_label_action = QAction(
unicodedata.lookup("MINUS SIGN"), self,
toolTip="Remove selected label.",
triggered=self.on_remove_label,
enabled=False,
shortcut=QKeySequence(QKeySequence.Delete))
button_size = gui.toolButtonSizeHint()
button_size = QSize(button_size, button_size)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.add_label_action)
hlayout.addWidget(button)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.remove_label_action)
hlayout.addWidget(button)
hlayout.addStretch(10)
vlayout.addLayout(hlayout)
self.main_form.addRow("Labels:", vlayout)
def setup_filter_area(self):
h_layout = QHBoxLayout()
h_layout.setSpacing(100)
h_widget = widgetBox(self.mainArea, orientation=h_layout)
spin(
h_widget,
self,
'min_count',
0,
100,
label='Count',
tooltip='Minimum genes count',
checked='use_min_count',
callback=self.filter_data_view,
callbackOnReturn=True,
checkCallback=self.filter_data_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_data_view,
callbackOnReturn=True,
checkCallback=self.filter_data_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_data_view,
callbackOnReturn=True,
checkCallback=self.filter_data_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_data_view)
def _setup_gui_values(self):
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
vlayout.setSpacing(1)
self.values_edit = QListView()
self.values_edit.setEditTriggers(QTreeView.CurrentChanged)
self.values_model = itemmodels.PyListModel(flags=Qt.ItemIsSelectable | \
Qt.ItemIsEnabled | Qt.ItemIsEditable)
self.values_edit.setModel(self.values_model)
self.values_edit.selectionModel().selectionChanged.connect(
self.on_value_selection_changed)
self.values_model.dataChanged.connect(self.on_values_changed)
vlayout.addWidget(self.values_edit)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.setSpacing(1)
self.move_value_up = QAction(unicodedata.lookup("UPWARDS ARROW"),
self,
toolTip="Move up.",
triggered=self.move_up,
enabled=False,
shortcut=QKeySequence(QKeySequence.New))
self.move_value_down = QAction(unicodedata.lookup("DOWNWARDS ARROW"),
self,
toolTip="Move down.",
triggered=self.move_down,
enabled=False,
shortcut=QKeySequence(
QKeySequence.Delete))
button_size = gui.toolButtonSizeHint()
button_size = QSize(button_size, button_size)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.move_value_up)
hlayout.addWidget(button)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.move_value_down)
hlayout.addWidget(button)
hlayout.addStretch(10)
vlayout.addLayout(hlayout)
self.main_form.addRow("Values:", vlayout)
def insertRow(self, index, actions, background="light-orange"):
"""Insert a row with `actions` at `index`.
"""
widget = QWidget(objectName="icon-row")
layout = QHBoxLayout()
layout.setContentsMargins(40, 0, 40, 0)
layout.setSpacing(65)
widget.setLayout(layout)
self.__mainLayout.insertWidget(index, widget, stretch=10,
alignment=Qt.AlignCenter)
for i, action in enumerate(actions):
self.insertAction(index, i, action, background)
def insertRow(self, index, actions, background="light-orange"):
"""Insert a row with `actions` at `index`.
"""
widget = QWidget(objectName="icon-row")
layout = QHBoxLayout()
layout.setContentsMargins(40, 0, 40, 0)
layout.setSpacing(65)
widget.setLayout(layout)
self.__mainLayout.insertWidget(
index, widget, stretch=10, alignment=Qt.AlignCenter
)
for i, action in enumerate(actions):
self.insertAction(index, i, action, background)
def __init__(self, state=AVAILABLE, parent=None):
QWidget.__init__(self, parent)
layout = QHBoxLayout()
layout.setSpacing(1)
layout.setContentsMargins(1, 1, 1, 1)
self.checkButton = QCheckBox()
layout.addWidget(self.checkButton)
self.setLayout(layout)
self.setMinimumHeight(20)
self.setMaximumHeight(20)
self.state = -1
self.setState(state)
def __init__(self, state=AVAILABLE, parent=None):
QWidget.__init__(self, parent)
layout = QHBoxLayout()
layout.setSpacing(1)
layout.setContentsMargins(1, 1, 1, 1)
self.checkButton = QCheckBox()
layout.addWidget(self.checkButton)
self.setLayout(layout)
self.setMinimumHeight(20)
self.setMaximumHeight(20)
self._state = state
self._update()
def __init__(self, parent=None, **kwargs):
QWidget.__init__(self, parent, **kwargs)
self.__pages = []
self.__currentIndex = -1
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(6)
self.__tab = TabBarWidget(self)
self.__tab.currentChanged.connect(self.setCurrentIndex)
self.__tab.setChangeOnHover(True)
self.__stack = MenuStackWidget(self)
layout.addWidget(self.__tab, alignment=Qt.AlignTop)
layout.addWidget(self.__stack)
self.setLayout(layout)
def __init__(self, parent=None, **kwargs):
# type: (Optional[QWidget], Any) -> None
super().__init__(parent, **kwargs)
self.__currentIndex = -1
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(6)
self.__tab = TabBarWidget(self)
self.__tab.currentChanged.connect(self.setCurrentIndex)
self.__tab.setChangeOnHover(True)
self.__stack = MenuStackWidget(self)
layout.addWidget(self.__tab, alignment=Qt.AlignTop)
layout.addWidget(self.__stack)
self.setLayout(layout)
def setup_filter_area(self):
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_data_view,
callbackOnReturn=True,
checkCallback=self.filter_data_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_data_view)
def __init__(self, parent, highlighting_scheme, font):
super().__init__(parent, highlighting_scheme, font)
self.indentation_level = 1
self.signal_labels = {}
self._prefix = None
layout = QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
# `return `
ret_lbl = QLabel('<b style="color: ' + \
highlighting_scheme[Keyword].split(' ')[-1] + \
';">return </b>', self)
ret_lbl.setFont(self.font())
ret_lbl.setContentsMargins(0, 0, 0, 0)
layout.addWidget(ret_lbl)
# `out_data[, ]` * 4
self.make_signal_labels('out_')
layout.addStretch()
self.setLayout(layout)
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
class PreprocessorModule(gui.OWComponent, QWidget):
"""The base widget for the pre-processing modules."""
change_signal = pyqtSignal() # Emitted when the settings are changed.
title = NotImplemented
attribute = NotImplemented
methods = NotImplemented
single_method = True
toggle_enabled = True
enabled = settings.Setting(True)
disabled_value = None
Layout = QGridLayout
def __init__(self, master):
QWidget.__init__(self)
gui.OWComponent.__init__(self, master)
self.master = master
# Title bar.
title_holder = QWidget()
title_holder.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed)
title_holder.setStyleSheet("""
.QWidget {
background: qlineargradient( x1:0 y1:0, x2:0 y2:1,
stop:0 #F8F8F8, stop:1 #C8C8C8);
border-bottom: 1px solid #B3B3B3;
}
""")
self.titleArea = QHBoxLayout()
self.titleArea.setContentsMargins(10, 5, 10, 5)
self.titleArea.setSpacing(0)
title_holder.setLayout(self.titleArea)
self.title_label = QLabel(self.title)
self.title_label.mouseDoubleClickEvent = self.on_toggle
self.title_label.setStyleSheet(
'font-size: 12px; border: 2px solid red;')
self.titleArea.addWidget(self.title_label)
self.off_label = QLabel('[disabled]')
self.off_label.setStyleSheet('color: #B0B0B0; margin-left: 5px;')
self.titleArea.addWidget(self.off_label)
self.off_label.hide()
self.titleArea.addStretch()
# Root.
self.rootArea = QVBoxLayout()
self.rootArea.setContentsMargins(0, 0, 0, 0)
self.rootArea.setSpacing(0)
self.setLayout(self.rootArea)
self.rootArea.addWidget(title_holder)
self.contents = QWidget()
contentArea = QVBoxLayout()
contentArea.setContentsMargins(15, 10, 15, 10)
self.contents.setLayout(contentArea)
self.rootArea.addWidget(self.contents)
self.method_layout = self.Layout()
self.setup_method_layout()
self.contents.layout().addLayout(self.method_layout)
if self.toggle_enabled:
self.on_off_button = OnOffButton(enabled=self.enabled)
self.on_off_button.stateChanged.connect(self.on_toggle)
self.on_off_button.setContentsMargins(0, 0, 0, 0)
self.titleArea.addWidget(self.on_off_button)
self.display_widget()
@staticmethod
def get_tooltip(method):
return ' '.join([l.strip() for l in method.__doc__.split('\n')]).strip('.') \
if method.__doc__ else None
@staticmethod
def textify(text):
return text.replace('&', '&&')
@property
def value(self):
if self.enabled:
return self.get_value()
return self.disabled_value
def setup_method_layout(self):
raise NotImplementedError
def on_toggle(self, event=None):
# Activated when the widget is enabled/disabled.
self.enabled = not self.enabled
self.display_widget()
self.update_value()
def display_widget(self):
if self.enabled:
self.off_label.hide()
self.contents.show()
self.title_label.setStyleSheet('color: #000000;')
else:
self.off_label.show()
self.contents.hide()
self.title_label.setStyleSheet('color: #B0B0B0;')
def get_value(self):
raise NotImplemented
def update_value(self):
self.change_signal.emit()
def __init__(self,
parent=None,
icon=QIcon(),
title="",
text="",
wordWrap=False,
textFormat=Qt.PlainText,
standardButtons=NoButton,
acceptLabel="Ok",
rejectLabel="No",
**kwargs):
super().__init__(parent, **kwargs)
self._title = title
self._text = text
self._icon = QIcon()
self._wordWrap = wordWrap
self._standardButtons = NotificationMessageWidget.NoButton
self._buttons = []
self._acceptLabel = acceptLabel
self._rejectLabel = rejectLabel
self._iconlabel = QLabel(objectName="icon-label")
self._titlelabel = QLabel(objectName="title-label",
text=title,
wordWrap=wordWrap,
textFormat=textFormat)
self._textlabel = QLabel(objectName="text-label",
text=text,
wordWrap=wordWrap,
textFormat=textFormat)
self._textlabel.setTextInteractionFlags(Qt.TextBrowserInteraction)
self._textlabel.setOpenExternalLinks(True)
if sys.platform == "darwin":
self._titlelabel.setAttribute(Qt.WA_MacSmallSize)
self._textlabel.setAttribute(Qt.WA_MacSmallSize)
layout = QHBoxLayout()
self._iconlabel.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
layout.addWidget(self._iconlabel)
layout.setAlignment(self._iconlabel, Qt.AlignTop)
message_layout = QVBoxLayout()
self._titlelabel.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Fixed)
if sys.platform == "darwin":
self._titlelabel.setContentsMargins(0, 1, 0, 0)
else:
self._titlelabel.setContentsMargins(0, 0, 0, 0)
message_layout.addWidget(self._titlelabel)
self._textlabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
message_layout.addWidget(self._textlabel)
self.button_layout = QHBoxLayout()
self.button_layout.setAlignment(Qt.AlignLeft)
message_layout.addLayout(self.button_layout)
layout.addLayout(message_layout)
layout.setSpacing(7)
self.setLayout(layout)
self.setIcon(icon)
self.setStandardButtons(standardButtons)
class PreprocessorModule(gui.OWComponent, QWidget):
"""The base widget for the pre-processing modules."""
change_signal = pyqtSignal() # Emitted when the settings are changed.
title = NotImplemented
attribute = NotImplemented
methods = NotImplemented
single_method = True
toggle_enabled = True
enabled = settings.Setting(True)
disabled_value = None
Layout = QGridLayout
def __init__(self, master):
QWidget.__init__(self)
gui.OWComponent.__init__(self, master)
self.master = master
# Title bar.
title_holder = QWidget()
title_holder.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed)
title_holder.setStyleSheet("""
.QWidget {
background: qlineargradient( x1:0 y1:0, x2:0 y2:1,
stop:0 #F8F8F8, stop:1 #C8C8C8);
border-bottom: 1px solid #B3B3B3;
}
""")
self.titleArea = QHBoxLayout()
self.titleArea.setContentsMargins(10, 5, 10, 5)
self.titleArea.setSpacing(0)
title_holder.setLayout(self.titleArea)
self.title_label = QLabel(self.title)
self.title_label.mouseDoubleClickEvent = self.on_toggle
self.title_label.setStyleSheet('font-size: 12px; border: 2px solid red;')
self.titleArea.addWidget(self.title_label)
self.off_label = QLabel('[disabled]')
self.off_label.setStyleSheet('color: #B0B0B0; margin-left: 5px;')
self.titleArea.addWidget(self.off_label)
self.off_label.hide()
self.titleArea.addStretch()
# Root.
self.rootArea = QVBoxLayout()
self.rootArea.setContentsMargins(0, 0, 0, 0)
self.rootArea.setSpacing(0)
self.setLayout(self.rootArea)
self.rootArea.addWidget(title_holder)
self.contents = QWidget()
contentArea = QVBoxLayout()
contentArea.setContentsMargins(15, 10, 15, 10)
self.contents.setLayout(contentArea)
self.rootArea.addWidget(self.contents)
self.method_layout = self.Layout()
self.setup_method_layout()
self.contents.layout().addLayout(self.method_layout)
if self.toggle_enabled:
self.on_off_button = OnOffButton(enabled=self.enabled)
self.on_off_button.stateChanged.connect(self.on_toggle)
self.on_off_button.setContentsMargins(0, 0, 0, 0)
self.titleArea.addWidget(self.on_off_button)
self.display_widget()
@staticmethod
def get_tooltip(method):
return ' '.join([l.strip() for l in method.__doc__.split('\n')]).strip('.') \
if method.__doc__ else None
@staticmethod
def textify(text):
return text.replace('&', '&&')
@property
def value(self):
if self.enabled:
return self.get_value()
return self.disabled_value
def setup_method_layout(self):
raise NotImplementedError
def on_toggle(self, event=None):
# Activated when the widget is enabled/disabled.
self.enabled = not self.enabled
self.display_widget()
self.update_value()
def display_widget(self):
if self.enabled:
self.off_label.hide()
self.contents.show()
self.title_label.setStyleSheet('color: #000000;')
else:
self.off_label.show()
self.contents.hide()
self.title_label.setStyleSheet('color: #B0B0B0;')
def get_value(self):
raise NotImplemented
def update_value(self):
self.change_signal.emit()
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):
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__()
# 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
class Screenshot(QDialog):
def __init__(self, parent=None):
super().__init__(parent, Qt.CustomizeWindowHint | Qt.FramelessWindowHint | Qt.Window |
Qt.WindowStaysOnTopHint | Qt.X11BypassWindowManagerHint)
self.setAttribute(Qt.WA_DeleteOnClose)
self.installEventFilter(self)
self.setMouseTracking(True)
self._band = QRubberBand(QRubberBand.Rectangle, self)
self._resize_origin = None
self._drag_mask = 0
self._origin = None
self.selected_image = None
# Window background
desktop = QApplication.desktop()
if is_qt5():
g = desktop.geometry()
self._snapshot = QPixmap(g.width(), g.height())
painter = QPainter(self._snapshot)
for screen in QApplication.screens():
g = screen.geometry()
painter.drawPixmap(g, screen.grabWindow(0, g.x(), g.y(), g.width(), g.height()))
painter.end()
else:
self._snapshot = QPixmap.grabWindow(desktop.winId(), 0, 0, desktop.width(), desktop.height())
self.setGeometry(desktop.geometry())
self._darken = self._snapshot.copy()
painter = QPainter(self._darken)
brush = QBrush(QColor(0, 0, 0, 128))
painter.setBrush(brush)
painter.drawRect(self._darken.rect())
painter.end()
# Buttons
self._buttons = QWidget(self)
self._button_layout = QHBoxLayout(self._buttons)
self._button_layout.setSpacing(0)
self._button_layout.setContentsMargins(0, 0, 0, 0)
self._button_layout.setContentsMargins(0, 0, 0, 0)
self.save_as = QPushButton(self.tr('Save As'))
self.save_as.pressed.connect(self.save_image_as)
self.save_as.setCursor(Qt.ArrowCursor)
self._button_layout.addWidget(self.save_as)
self.copy = QPushButton(self.tr('Copy'))
self.copy.pressed.connect(self.copy_to_clipboard)
self.copy.setCursor(Qt.ArrowCursor)
self._button_layout.addWidget(self.copy)
self.share = QPushButton(self.tr('Share'))
self.share.pressed.connect(self.share_selection)
self.share.setCursor(Qt.ArrowCursor)
self._button_layout.addWidget(self.share)
self._buttons.hide()
def paintEvent(self, _):
painter = QPainter(self)
painter.drawPixmap(0, 0, self._darken)
if self._band.isVisible():
br = self._band.geometry()
r = QRect(br.topLeft(), br.bottomRight())
painter.drawPixmap(r, self._snapshot.copy(r))
def get_selection(self):
return self._snapshot.copy(self._band.geometry())
def save_image_as(self):
img = self.get_selection().toImage()
if img.isNull():
QMessageBox.critical(self, self.tr('Error'), self.tr('No image was selected!'))
return
self.hide()
formats = {
self.tr('Portable Network Graphics (*.png)'): 'png',
self.tr('Joint Photographic Experts Group (*.jpg *.jpeg)'): 'jpg',
self.tr('Graphics Interchange Format (*.gif)'): 'gif',
self.tr('Bitmap (*.bmp)'): 'bmp',
self.tr('All Images (*.png *.jpg *.gif *.bmp)'): 'all'
}
file_format = None
destination = QFileDialog.getSaveFileName(self, 'Save image', '', ';;'.join(formats.keys()))
if isinstance(destination, tuple):
destination, file_format = destination
file_format = formats[file_format]
if file_format == 'all':
file_format = None
if not file_format:
file_format = destination.rsplit('.', 1)[-1]
if destination:
if file_format not in formats.values():
file_format = 'png'
if not destination.endswith('.' + file_format):
destination += '.' + file_format
img.save(destination, file_format, 0 if file_format == 'png' else 90)
self.reject()
def copy_to_clipboard(self):
img = self.get_selection()
if img.isNull():
QMessageBox.critical(self, self.tr('Error'), self.tr('No image was selected!'))
return
QApplication.clipboard().setPixmap(img)
self.reject()
def share_selection(self):
self.selected_image = self.get_selection()
self.accept()
def eventFilter(self, obj, e):
if e.type() == QEvent.Enter:
self.activateWindow()
if e.type() == QEvent.KeyPress and e.key() == Qt.Key_Escape:
self.reject()
return True
return super().eventFilter(obj, e)
def mousePressEvent(self, event):
if self.update_cursor_shape(event.pos(), event.button() == Qt.LeftButton):
self._resize_origin = event.pos()
else:
self._origin = event.pos()
if not self._band.isVisible():
self._band.setGeometry(QRect(self._origin, self._origin))
self._band.show()
super().mousePressEvent(event)
def mouseMoveEvent(self, event):
p = event.pos()
mouse_down = event.buttons() & Qt.LeftButton
if mouse_down:
m = self._drag_mask
wr = self.rect()
if m:
g = self._band.geometry()
d = p - self._resize_origin
if d.x() or d.y():
if m == RESIZE_DRAG:
g.translate(d)
else:
if m & RESIZE_LEFT:
g.translate(d.x(), 0)
g.setWidth(g.width() - d.x())
elif m & RESIZE_RIGHT:
g.setWidth(g.width() + d.x())
if m & RESIZE_TOP:
g.translate(0, d.y())
g.setHeight(g.height() - d.y())
elif m & RESIZE_BOTTOM:
g.setHeight(g.height() + d.y())
self._resize_origin = p
# Contain in the screen
px = min(max(g.topLeft().x(), 0), wr.width() - g.width())
py = min(max(g.topLeft().y(), 0), wr.height() - g.height())
g.moveTo(px, py)
else:
g = QRect(self._origin, p).normalized()
self._band.setGeometry(g)
br = self._band.geometry()
x = (br.width() / 2 - self._buttons.width() / 2) + br.left() # buttons at center of band
x = max(0, min(x, wr.width() - self._buttons.width())) # prevent going off-screen
if (wr.height() - br.bottom()) > self._buttons.height(): # if at bottom
y = br.bottom()
else:
y = max(0, br.top() - self._buttons.height())
self._buttons.move(x, y)
self._buttons.show()
self.repaint()
else:
self.update_cursor_shape(p, mouse_down)
self._drag_mask = self.get_drag_mask(p)
super().mouseMoveEvent(event)
def mouseReleaseEvent(self, event):
self.update_cursor_shape(event.pos(), False)
super().mouseReleaseEvent(event)
def update_cursor_shape(self, p, mouse_down):
m = self.get_drag_mask(p)
if m == RESIZE_DRAG:
self.setCursor(Qt.ClosedHandCursor if mouse_down else Qt.OpenHandCursor)
elif (m & RESIZE_LEFT and m & RESIZE_TOP) or (m & RESIZE_RIGHT and m & RESIZE_BOTTOM):
self.setCursor(Qt.SizeFDiagCursor)
elif (m & RESIZE_LEFT and m & RESIZE_BOTTOM) or (m & RESIZE_RIGHT and m & RESIZE_TOP):
self.setCursor(Qt.SizeBDiagCursor)
elif m & RESIZE_LEFT or m & RESIZE_RIGHT:
self.setCursor(Qt.SizeHorCursor)
elif m & RESIZE_TOP or m & RESIZE_BOTTOM:
self.setCursor(Qt.SizeVerCursor)
else:
self.setCursor(Qt.ArrowCursor)
return False
return True
def get_drag_mask(self, p):
br = self._band.geometry()
if br.contains(p):
def is_hovering(x):
return 0 <= x <= 10
m = 0
m |= RESIZE_LEFT if is_hovering(p.x() - br.left()) else 0
m |= RESIZE_RIGHT if is_hovering(br.right() - p.x()) else 0
m |= RESIZE_BOTTOM if is_hovering(br.bottom() - p.y()) else 0
m |= RESIZE_TOP if is_hovering(p.y() - br.top()) else 0
if m:
return m
return RESIZE_DRAG
return 0
