class GeneSetsSelection(QWidget):
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 clear_custom_sets(self):
# delete any custom sets if they exists
self.gs_object.delete_sets_by_hierarchy(self.custom_set_hier)
def add_custom_sets(self,
gene_sets_names,
gene_names,
hierarchy_title=None,
select_customs_flag=False):
# type: (np.ndarray, np.ndarray) -> None
self.custom_set_hier = hierarchy_title
self.clear_custom_sets()
temp_dict = defaultdict(list)
for set_name, gene_name in zip(gene_sets_names, gene_names):
temp_dict[set_name].append(gene_name)
g_sets = []
for key, value in temp_dict.items():
g_sets.append(
GeneSet(gs_id=key,
hierarchy=self.custom_set_hier,
organism=self.gs_object.common_org(),
name=key,
genes=set(value)))
self.gs_object.update(g_sets)
self.update_gs_hierarchy(select_customs_flag=select_customs_flag)
def load_gene_sets(self, tax_id):
# type: (str) -> None
self.gs_object = GeneSets()
self.clear()
gene_sets = list_all(organism=tax_id)
self.set_hierarchy_model(self.hierarchy_tree_widget,
self.hierarchy_tree(gene_sets))
for gene_set in gene_sets:
g_sets = load_gene_sets(gene_set, tax_id)
self.gs_object.update([g_set for g_set in g_sets])
self.set_selected_hierarchies()
def clear_gene_sets(self):
self.gs_object = GeneSets()
def clear(self):
# reset hierarchy widget state
self.hierarchy_tree_widget.clear()
def update_gs_hierarchy(self, select_customs_flag=False):
self.clear()
self.set_hierarchy_model(
self.hierarchy_tree_widget,
self.hierarchy_tree(self.gs_object.hierarchies()))
if select_customs_flag:
self.set_custom_sets()
else:
self.set_selected_hierarchies()
def set_hierarchy_model(self, tree_widget, sets):
def beautify_displayed_text(text):
if '_' in text:
return text.replace('_', ' ').title()
else:
return text
# TODO: maybe optimize this code?
for key, value in sets.items():
item = QTreeWidgetItem(tree_widget, [beautify_displayed_text(key)])
item.setFlags(item.flags()
& (Qt.ItemIsUserCheckable | Qt.ItemIsSelectable
| Qt.ItemIsEnabled))
item.setExpanded(True)
item.hierarchy = key
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
self.set_hierarchy_model(item, value)
else:
if item.parent():
item.hierarchy = (item.parent().hierarchy, key)
if not item.childCount() and not item.parent():
item.hierarchy = (key, )
def get_hierarchies(self, **kwargs):
""" return selected hierarchy
"""
only_selected = kwargs.get('only_selected', None)
sets_to_display = list()
if only_selected:
iterator = QTreeWidgetItemIterator(self.hierarchy_tree_widget,
QTreeWidgetItemIterator.Checked)
else:
iterator = QTreeWidgetItemIterator(self.hierarchy_tree_widget)
while iterator.value():
# note: if hierarchy value is not a tuple, then this is just top level qTreeWidgetItem that
# holds subcategories. We don't want to display all sets from category
if type(iterator.value().hierarchy) is not str:
if not only_selected:
sets_to_display.append(iterator.value().hierarchy)
else:
if not iterator.value().isDisabled():
sets_to_display.append(iterator.value().hierarchy)
iterator += 1
return sets_to_display
def set_selected_hierarchies(self):
iterator = QTreeWidgetItemIterator(self.hierarchy_tree_widget,
QTreeWidgetItemIterator.All)
defaults = []
while iterator.value():
# note: if hierarchy value is not a tuple, then this is just top level qTreeWidgetItem that
# holds subcategories. We don't want to display all sets from category
if type(iterator.value().hierarchy) is not str:
if iterator.value().hierarchy in self.parent.__getattribute__(
self.stored_selection):
iterator.value().setCheckState(0, Qt.Checked)
else:
iterator.value().setCheckState(0, Qt.Unchecked)
# if no items are checked, set defaults
if iterator.value().hierarchy in self.default_selection:
defaults.append(iterator.value())
iterator += 1
if len(self.get_hierarchies(only_selected=True)) == 0:
[item.setCheckState(0, Qt.Checked) for item in defaults]
def set_custom_sets(self):
iterator = QTreeWidgetItemIterator(self.hierarchy_tree_widget,
QTreeWidgetItemIterator.All)
while iterator.value():
# note: if hierarchy value is not a tuple, then this is just top level qTreeWidgetItem that
# holds subcategories. We don't want to display all sets from category
if type(iterator.value().hierarchy) is not str:
if iterator.value().hierarchy == self.custom_set_hier:
iterator.value().setCheckState(0, Qt.Checked)
else:
iterator.value().setCheckState(0, Qt.Unchecked)
iterator += 1
@staticmethod
def hierarchy_tree(gene_sets):
def tree():
return defaultdict(tree)
collection = tree()
def collect(col, set_hierarchy):
if set_hierarchy:
collect(col[set_hierarchy[0]], set_hierarchy[1:])
for hierarchy in gene_sets:
collect(collection, hierarchy)
return collection
