class EditableTreeView(QWidget):
dataChanged = Signal()
selectionChanged = Signal()
def __init__(self, parent=None):
super().__init__(parent=parent)
self.__stack: List = []
self.__stack_index: int = -1
def push_on_data_changed(_, __, roles):
if Qt.EditRole in roles:
self._push_data()
self.__model = QStandardItemModel()
self.__model.dataChanged.connect(self.dataChanged)
self.__model.dataChanged.connect(push_on_data_changed)
self.__root: QStandardItem = self.__model.invisibleRootItem()
self.__tree = TreeView(self.dataChanged)
self.__tree.drop_finished.connect(self.dataChanged)
self.__tree.drop_finished.connect(self._push_data)
self.__tree.setModel(self.__model)
self.__tree.selectionModel().selectionChanged.connect(
self.selectionChanged)
actions_widget = ModelActionsWidget()
actions_widget.layout().setSpacing(1)
action = QAction("+", self, toolTip="Add a new word")
action.triggered.connect(self.__on_add)
actions_widget.addAction(action)
action = QAction("\N{MINUS SIGN}", self, toolTip="Remove word")
action.triggered.connect(self.__on_remove)
actions_widget.addAction(action)
action = QAction("\N{MINUS SIGN}R", self,
toolTip="Remove word recursively (incl. children)")
action.triggered.connect(self.__on_remove_recursive)
actions_widget.addAction(action)
gui.rubber(actions_widget)
self.__undo_action = action = QAction("Undo", self, toolTip="Undo")
action.triggered.connect(self.__on_undo)
actions_widget.addAction(action)
self.__redo_action = action = QAction("Redo", self, toolTip="Redo")
action.triggered.connect(self.__on_redo)
actions_widget.addAction(action)
self._enable_undo_redo()
layout = QVBoxLayout()
layout.setSpacing(1)
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self.__tree)
layout.addWidget(actions_widget)
self.setLayout(layout)
def __on_add(self):
parent: QStandardItem = self.__root
selection: List = self.__tree.selectionModel().selectedIndexes()
if selection:
sel_index: QModelIndex = selection[0]
parent: QStandardItem = self.__model.itemFromIndex(sel_index)
item = QStandardItem("")
parent.appendRow(item)
index: QModelIndex = item.index()
with disconnected(self.__model.dataChanged, self.dataChanged):
self.__model.setItemData(index, {Qt.EditRole: ""})
self.__tree.setCurrentIndex(index)
self.__tree.edit(index)
def __on_remove_recursive(self):
sel_model: QItemSelectionModel = self.__tree.selectionModel()
if len(sel_model.selectedIndexes()):
while sel_model.selectedIndexes():
index: QModelIndex = sel_model.selectedIndexes()[0]
self.__model.removeRow(index.row(), index.parent())
self._push_data()
self.dataChanged.emit()
def __on_remove(self):
sel_model: QItemSelectionModel = self.__tree.selectionModel()
if len(sel_model.selectedIndexes()):
while sel_model.selectedIndexes():
index: QModelIndex = sel_model.selectedIndexes()[0]
# move children to item's parent
item: QStandardItem = self.__model.itemFromIndex(index)
children = [item.takeChild(i) for i in range(item.rowCount())]
parent = item.parent() or self.__root
self.__model.removeRow(index.row(), index.parent())
for child in children[::-1]:
parent.insertRow(index.row(), child)
self.__tree.expandAll()
self._push_data()
self.dataChanged.emit()
def __on_undo(self):
self.__stack_index -= 1
self._set_from_stack()
def __on_redo(self):
self.__stack_index += 1
self._set_from_stack()
def get_words(self) -> List:
return _model_to_words(self.__root)
def get_selected_words(self) -> Set:
return set(self.__model.itemFromIndex(index).text() for index in
self.__tree.selectionModel().selectedIndexes())
def get_selected_words_with_children(self) -> Set:
words = set()
for index in self.__tree.selectionModel().selectedIndexes():
item: QStandardItem = self.__model.itemFromIndex(index)
words.update(_model_to_words(item))
return words
def get_data(self, with_selection=False) -> Union[Dict, OntoType]:
selection = self.__tree.selectionModel().selectedIndexes()
return _model_to_tree(self.__root, selection, with_selection)
def set_data(self, data: Dict, keep_history: bool = False):
if not keep_history:
self.__stack = []
self.__stack_index = -1
self._set_data(data)
self._push_data()
def _set_data(self, data: Dict):
self.clear()
_tree_to_model(data, self.__root, self.__tree.selectionModel())
self.__tree.expandAll()
def clear(self):
if self.__model.hasChildren():
self.__model.removeRows(0, self.__model.rowCount())
def _enable_undo_redo(self):
index = self.__stack_index
self.__undo_action.setEnabled(index >= 1)
self.__redo_action.setEnabled(index < len(self.__stack) - 1)
def _push_data(self):
self.__stack_index += 1
self.__stack = self.__stack[:self.__stack_index]
self.__stack.append(self.get_data())
self._enable_undo_redo()
def _set_from_stack(self):
assert self.__stack_index < len(self.__stack)
assert self.__stack_index >= 0
self._set_data(self.__stack[self.__stack_index])
self._enable_undo_redo()
self.dataChanged.emit()
class OWBatchNorm(OWWidget):
name = "Batch Effect Removal"
description = "Batch effect normalization on Single Cell data set."
icon = "icons/BatchEffectRemoval.svg"
priority = 230
class Inputs:
data = Input("Data", Table)
class Outputs:
data = Output("Data", Table)
class Error(OWWidget.Error):
general_error = Msg({})
discrete_attributes = Msg("Data with discrete attributes "
"can not be processed.")
class Warning(OWWidget.Warning):
missing_values = Msg("Missing values have been replaced with 0.")
negative_values = Msg("Unable to use current settings due "
"to negative values in data.")
resizing_enabled = False
want_main_area = False
settingsHandler = PerfectDomainContextHandler()
batch_vars = ContextSetting([])
link_method = Setting(LinkMethod.IDENTITY_LINK)
skip_zeros = Setting(False)
auto_commit = Setting(True)
def __init__(self, parent=None):
super().__init__(parent)
self.data = None
# Info
infobox = gui.widgetBox(self.controlArea, "Info")
self.info_label = gui.widgetLabel(infobox, "No data on input.")
# Link method
method_box = gui.widgetBox(self.controlArea, "Method")
gui.comboBox(method_box,
self,
"link_method",
items=LinkMethod.items(),
callback=self.__link_method_changed)
gui.separator(method_box)
self.skip_zeros_check = gui.checkBox(
method_box,
self,
"skip_zeros",
"Skip zero expressions",
enabled=self.link_method != LinkMethod.LOG_LINK,
callback=lambda: self.commit())
# Batch Variable Selection
header_shema = (("selected", ""), ("variable", "Variable"),
("count", "#"), ("score", "Score"))
header_labels = labels = [label for _, label in header_shema]
header = namedtuple("header", [tag for tag, _ in header_shema])
self.Header = header(*[index for index, _ in enumerate(labels)])
batch_box = gui.widgetBox(self.controlArea, "Batch Variable Selection")
self.view = QTreeView()
self.model = QStandardItemModel()
self.model.itemChanged.connect(self.__selected_batch_vars_changed)
self.model.setHorizontalHeaderLabels(header_labels)
batch_box.layout().addWidget(self.view)
self._setup_view()
gui.auto_commit(self.controlArea, self, "auto_commit", "Apply",
"Apply Automatically")
def __link_method_changed(self):
enable = self.link_method != LinkMethod.LOG_LINK
self.skip_zeros_check.setEnabled(enable)
if not enable:
self.skip_zeros_check.setChecked(True)
self.commit()
def __selected_batch_vars_changed(self, item):
if item.checkState():
self.batch_vars.append(item.data(VariableRole))
else:
self.batch_vars.remove(item.data(VariableRole))
self.commit()
def _setup_view(self):
self.view.setModel(self.model)
self.view.setSelectionMode(QTreeView.NoSelection)
self.view.setSortingEnabled(True)
self.view.setRootIsDecorated(False)
self.view.setItemDelegateForColumn(self.Header.count,
IntegralDelegate(self))
self.view.setItemDelegateForColumn(self.Header.score,
RealDelegate(self))
self.view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.view.header().setStretchLastSection(False)
self.view.header().setSectionResizeMode(self.Header.variable,
QHeaderView.Stretch)
self.view.setFocus()
@Inputs.data
def set_data(self, data):
self.closeContext()
self.clear()
self.data = data
self._setup_info_label()
self._check_data()
self.openContext(data)
if self.data is not None:
self.batch_vars = [data.domain[v.name] for v in self.batch_vars]
self._setup_model()
self.commit()
def clear(self):
self.batch_vars = []
if self.model:
n_rows = self.model.rowCount()
self.model.removeRows(0, n_rows)
def _setup_info_label(self):
text = "No data on input."
if self.data is not None:
domain, attrs = self.data.domain, self.data.domain.attributes
text = "{} cells, {} genes\n".format(len(self.data), len(attrs))
text += "{} meta features".format(len(domain.metas)) \
if len(domain.metas) else "(no meta features)"
self.info_label.setText(text)
def _check_data(self):
self.clear_messages()
if self.data and self.data.domain.has_discrete_attributes():
self.data = None
self.Error.discrete_attributes()
if self.data and np.isnan(self.data.X).any():
self.data.X = np.nan_to_num(self.data.X)
self.Warning.missing_values()
def _setup_model(self):
estimator = ScBatchScorer()
for var in self.data.domain.class_vars + self.data.domain.metas:
if not var.is_primitive():
continue
try:
score = float(estimator.score_data(self.data, var))
except Exception:
score = np.nan
self.model.appendRow([
self.__selected_item(var),
self.__variable_item(var),
self.__count_item(var),
self.__score_item(score)
])
def __selected_item(self, var):
item = QStandardItem()
item.setData(var, VariableRole)
item.setCheckable(True)
select = var in self.batch_vars
item.setCheckState(Qt.Checked if select else Qt.Unchecked)
item.setEditable(False)
return item
def __variable_item(self, var):
item = QStandardItem()
item.setData(var.name, Qt.DisplayRole)
item.setData(gui.attributeIconDict[var], Qt.DecorationRole)
item.setEditable(False)
return item
def __count_item(self, var):
item = QStandardItem()
if var.is_discrete:
item.setData(len(var.values), Qt.DisplayRole)
item.setEditable(False)
return item
def __score_item(self, score):
item = QStandardItem()
item.setData(score, Qt.DisplayRole)
item.setEditable(False)
return item
def commit(self):
data = None
self.Error.general_error.clear()
self.Warning.negative_values.clear()
if self.data is not None:
if (self.data.X < 0).any() and self.skip_zeros:
self.Warning.negative_values()
data = self.data
else:
try:
data = SCBatchNormalizer(
LinkMethod.items()[self.link_method], self.skip_zeros,
self.batch_vars)(self.data)
except Exception as e:
self.Error.general_error(str(e))
data = None
self.Outputs.data.send(data)
def send_report(self):
method = LinkMethod.items()[self.link_method]
if self.skip_zeros:
method += " (Skip zero expressions)"
variables = ", ".join([v.name for v in self.batch_vars]) \
if self.batch_vars else "None"
self.report_items("", [("Method", method),
("Batch variable selection", variables)])