def setBioMartConfiguration(self, configuration):
assert QThread.currentThread() is self.thread()
self.setEnabled(True)
# parse the xml in the main thread (a long time ago this step was
# done in a thread but would frequently cause `expat` to segfault.
doc = biomart.parseXML(io.BytesIO(configuration))
config = list(doc.elements("DatasetConfig"))[0]
configuration = biomart.DatasetConfig(self.registry, config.tag, config.attributes, config.children)
self.clearConfiguration()
self.configuration = configuration
def hidden(tree):
return getattr(tree, "hidden", "false") != "false" or getattr(tree, "hideDisplay", "false") != "false"
self.attributePagesTabWidget = tabs = gui.tabWidget(self.attributesConfigurationBox)
for page in configuration.elements("AttributePage"):
if not hidden(page):
page_widget = PageWidget(page, self.dataset, self)
gui.createTabPage(tabs, getattr(page, "displayName", ""), widgetToAdd=page_widget, canScroll=True)
if self.SHOW_FILTERS:
self.filterPagesTabWidget = tabs = gui.tabWidget(self.filtersConfigurationBox)
for page in configuration.elements("FilterPage"):
if not hidden(page):
page_widget = PageWidget(page, self.dataset, self)
gui.createTabPage(tabs, getattr(page, "displayName", ""), widgetToAdd=page_widget, canScroll=True)
self.afterInit()
self.commitButton.setEnabled(True)
def __init__(self):
super().__init__()
self.graph = None
self.items = None # items set by Items signal
self.items_graph = None # items set by graph.items by Network signal
self.items_analysis = None # items to output and merge with analysis result
self.known = {}
self.running_jobs = {}
# Indicates that node level statistics have changed or are pending to
self._nodelevel_invalidated = False
self.controlArea = QWidget(self.controlArea)
self.layout().addWidget(self.controlArea)
layout = QGridLayout()
self.controlArea.setLayout(layout)
layout.setContentsMargins(4, 4, 4, 4)
tabs = gui.tabWidget(self.controlArea)
tabs.setMinimumWidth(450)
graph_indices = gui.createTabPage(tabs,
"Graph-level indices",
orientation=Qt.Horizontal)
node_indices = gui.createTabPage(tabs,
"Node-level indices",
orientation=Qt.Horizontal)
graph_methods = gui.vBox(graph_indices)
gui.rubber(graph_indices)
graph_labels = gui.vBox(graph_indices)
node_methods = gui.vBox(node_indices)
gui.rubber(node_indices)
node_labels = gui.vBox(node_indices)
graph_labels.layout().setAlignment(Qt.AlignRight)
self.method_cbs = {}
for method in METHODS.values():
if method.level == INTERNAL:
continue
setattr(self, method.name, method.name in self.enabled_methods)
setattr(self, "lbl_" + method.name, "")
methods = node_methods if method.level == NODELEVEL else graph_methods
labels = node_labels if method.level == NODELEVEL else graph_labels
cb = gui.checkBox(
methods,
self,
method.name,
method.label,
callback=lambda attr=method.name: self.method_clicked(attr))
self.method_cbs[method.name] = cb
lbl = gui.label(labels, self, f"%(lbl_{method.name})s")
labels.layout().setAlignment(lbl, Qt.AlignRight)
setattr(self, "tool_" + method.name, lbl)
# todo: is this accessible through controls?
graph_indices.layout().addStretch(1)
node_indices.layout().addStretch(1)
def clearConfiguration(self):
self.mainTab.deleteLater()
self.mainTab = QTabWidget()
self.mainWidget.layout().addWidget(self.mainTab)
self.mainWidget.layout().setCurrentWidget(self.mainTab)
self.attributesConfigurationBox = gui.createTabPage(self.mainTab, "Attributes")
if self.SHOW_FILTERS:
self.filtersConfigurationBox = gui.createTabPage(self.mainTab, "Filters")
def clearConfiguration(self):
self.mainTab.deleteLater()
self.mainTab = QTabWidget()
self.mainWidget.layout().addWidget(self.mainTab)
self.mainWidget.layout().setCurrentWidget(self.mainTab)
self.attributesConfigurationBox = gui.createTabPage(self.mainTab, "Attributes")
if self.SHOW_FILTERS:
self.filtersConfigurationBox = gui.createTabPage(self.mainTab, "Filters")
def create_control_panel(self):
self.control_tabs = gui.tabWidget(self.controlArea)
self.general_tab = gui.createTabPage(self.control_tabs, "Main")
self.settings_tab = gui.createTabPage(self.control_tabs, "Settings")
self.add_attribute_selection_area(self.general_tab)
self.add_zoom_select_toolbar(self.general_tab)
self.add_visual_settings(self.settings_tab)
self.add_annotation_settings(self.settings_tab)
self.add_color_settings(self.settings_tab)
self.settings_tab.layout().addStretch(100)
self.icons = attributeIconDict
def create_control_panel(self):
self.control_tabs = gui.tabWidget(self.controlArea)
self.general_tab = gui.createTabPage(self.control_tabs, "Main")
self.settings_tab = gui.createTabPage(self.control_tabs, "Settings")
self.add_attribute_selection_area(self.general_tab)
self.add_zoom_select_toolbar(self.general_tab)
self.add_visual_settings(self.settings_tab)
self.add_annotation_settings(self.settings_tab)
self.add_color_settings(self.settings_tab)
self.settings_tab.layout().addStretch(100)
self.icons = attributeIconDict
def setBioMartConfiguration(self, configuration):
assert (QThread.currentThread() is self.thread())
self.setEnabled(True)
# parse the xml in the main thread (a long time ago this step was
# done in a thread but would frequently cause `expat` to segfault.
doc = biomart.parseXML(io.BytesIO(configuration))
config = list(doc.elements("DatasetConfig"))[0]
configuration = biomart.DatasetConfig(self.registry, config.tag,
config.attributes,
config.children)
self.clearConfiguration()
self.configuration = configuration
def hidden(tree):
return getattr(tree, "hidden", "false") != "false" or \
getattr(tree, "hideDisplay", "false") != "false"
self.attributePagesTabWidget = tabs = gui.tabWidget(
self.attributesConfigurationBox)
for page in configuration.elements("AttributePage"):
if not hidden(page):
page_widget = PageWidget(page, self.dataset, self)
gui.createTabPage(tabs,
getattr(page, "displayName", ""),
widgetToAdd=page_widget,
canScroll=True)
if self.SHOW_FILTERS:
self.filterPagesTabWidget = tabs = gui.tabWidget(
self.filtersConfigurationBox)
for page in configuration.elements("FilterPage"):
if not hidden(page):
page_widget = PageWidget(page, self.dataset, self)
gui.createTabPage(tabs,
getattr(page, "displayName", ""),
widgetToAdd=page_widget,
canScroll=True)
self.afterInit()
self.commitButton.setEnabled(True)
def __init__(self):
super().__init__()
self.graph = None
self.items = None # items set by Items signal
self.items_graph = None # items set by graph.items by Network signal
self.items_analysis = None # items to output and merge with analysis result
self.known = {}
self.running_jobs = {}
self.controlArea = QWidget(self.controlArea)
self.layout().addWidget(self.controlArea)
layout = QGridLayout()
self.controlArea.setLayout(layout)
layout.setContentsMargins(4, 4, 4, 4)
tabs = gui.tabWidget(self.controlArea)
tabs.setMinimumWidth(450)
graph_indices = gui.createTabPage(tabs, "Graph-level indices")
node_indices = gui.createTabPage(tabs, "Node-level indices")
self.method_cbs = {}
for method in METHODS.values():
if method.level == INTERNAL:
continue
setattr(self, method.name, method.name in self.enabled_methods)
setattr(self, "lbl_" + method.name, "")
box = gui.hBox(node_indices if method.level ==
NODELEVEL else graph_indices)
cb = gui.checkBox(
box,
self,
method.name,
method.label,
callback=lambda attr=method.name: self.method_clicked(attr))
self.method_cbs[method.name] = cb
box.layout().addStretch(1)
lbl = gui.label(box, self, f"%(lbl_{method.name})s")
setattr(self, "tool_" + method.name, lbl)
# todo: is this accessible through controls?
graph_indices.layout().addStretch(1)
node_indices.layout().addStretch(1)
def initializeTabs(self):
size = len(self.tab)
indexes = range(0, size)
for index in indexes:
self.tabs.removeTab(size-1-index)
self.tab = [gui.createTabPage(self.tabs, "X,Z"),
gui.createTabPage(self.tabs, "X',Z'"),
gui.createTabPage(self.tabs, "X,X'"),
gui.createTabPage(self.tabs, "Z,Z'"),
gui.createTabPage(self.tabs, "Energy")]
for tab in self.tab:
tab.setFixedHeight(self.IMAGE_HEIGHT)
tab.setFixedWidth(self.IMAGE_WIDTH)
self.plot_canvas = [None, None, None, None, None]
self.plot_upper_canvas = [None, None, None, None, None]
self.plot_right_canvas = [None, None, None, None, None]
def createTabPage(cls, tabWidget, name, widgetToAdd=None, canScroll=False, height=None, width=None):
tab = gui.createTabPage(tabWidget, name, widgetToAdd, canScroll)
tab.layout().setAlignment(Qt.AlignTop)
if not height is None:
tab.setFixedHeight(height)
if not width is None:
tab.setFixedWidth(width)
return tab
def createTabPage(cls,
tabWidget,
name,
widgetToAdd=None,
canScroll=False,
height=None,
width=None,
isImage=False):
tab = orange_gui.createTabPage(tabWidget, name, widgetToAdd, canScroll)
tab.layout().setAlignment(Qt.AlignTop)
if not height is None:
tab.setFixedHeight(height)
if not width is None:
tab.setFixedWidth(width)
if isImage: tab.setStyleSheet("background-color: #FFFFFF;")
return tab
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):
super().__init__()
self.output_corpus = None
self.pubmed_api = None
self.progress = None
self.email_is_valid = False
self.record_count = 0
self.download_running = False
# To hold all the controls. Makes access easier.
self.pubmed_controls = []
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Email:')
label.setMaximumSize(label.sizeHint())
# Drop-down for recent emails.
self.email_combo = QComboBox(h_box)
self.email_combo.setMinimumWidth(150)
self.email_combo.setEditable(True)
self.email_combo.lineEdit().textChanged.connect(self.sync_email)
h_box.layout().addWidget(self.email_combo)
self.email_combo.activated[int].connect(self.select_email)
# RECORD SEARCH
self.search_tabs = gui.tabWidget(self.controlArea)
# --- Regular search ---
regular_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Author
self.author_input = gui.lineEdit(regular_search_box,
self,
'author',
'Author:',
orientation=Qt.Horizontal)
self.pubmed_controls.append(self.author_input)
h_box = gui.hBox(regular_search_box)
year_box = gui.widgetBox(h_box, orientation=Qt.Horizontal)
min_date = QDate.fromString(
self.MIN_DATE.strftime(self.PY_DATE_FORMAT), self.QT_DATE_FORMAT)
if not self.pub_date_from:
self.pub_date_from = self.MIN_DATE.strftime(self.PY_DATE_FORMAT)
if not self.pub_date_to:
self.pub_date_to = date.today().strftime(self.PY_DATE_FORMAT)
self.date_from = QDateEdit(QDate.fromString(self.pub_date_from,
self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True)
self.date_to = QDateEdit(QDate.fromString(self.pub_date_to,
self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True)
self.date_from.dateChanged.connect(lambda date: setattr(
self, 'pub_date_from', date.toString(self.QT_DATE_FORMAT)))
self.date_to.dateChanged.connect(lambda date: setattr(
self, 'pub_date_to', date.toString(self.QT_DATE_FORMAT)))
self.pubmed_controls.append(self.date_from)
self.pubmed_controls.append(self.date_to)
gui.label(year_box, self, 'From:')
year_box.layout().addWidget(self.date_from)
gui.label(year_box, self, 'to:')
year_box.layout().addWidget(self.date_to)
# Keywords.
h_box = gui.hBox(regular_search_box)
label = gui.label(h_box, self, 'Query:')
label.setMaximumSize(label.sizeHint())
self.keyword_combo = QComboBox(h_box)
self.keyword_combo.setMinimumWidth(150)
self.keyword_combo.setEditable(True)
h_box.layout().addWidget(self.keyword_combo)
self.keyword_combo.activated[int].connect(self.select_keywords)
self.pubmed_controls.append(self.keyword_combo)
tab_height = regular_search_box.sizeHint()
regular_search_box.setMaximumSize(tab_height)
# --- Advanced search ---
advanced_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Advanced search query.
h_box = gui.hBox(advanced_search_box)
self.advanced_query_input = QTextEdit(h_box)
h_box.layout().addWidget(self.advanced_query_input)
self.advanced_query_input.setMaximumSize(tab_height)
self.pubmed_controls.append(self.advanced_query_input)
gui.createTabPage(self.search_tabs, 'Regular search',
regular_search_box)
gui.createTabPage(self.search_tabs, 'Advanced search',
advanced_search_box)
# Search info label.
self.search_info_label = gui.label(self.controlArea, self,
'Number of records found: /')
# Search for records button.
self.run_search_button = gui.button(
self.controlArea,
self,
'Find records',
callback=self.run_search,
tooltip='Performs a search for articles that fit the '
'specified parameters.')
self.pubmed_controls.append(self.run_search_button)
h_line = QFrame()
h_line.setFrameShape(QFrame.HLine)
h_line.setFrameShadow(QFrame.Sunken)
self.controlArea.layout().addWidget(h_line)
# RECORD RETRIEVAL
# Text includes box.
text_includes_box = gui.widgetBox(self.controlArea,
'Text includes',
addSpace=True)
self.authors_checkbox = gui.checkBox(text_includes_box, self,
'includes_authors', 'Authors')
self.title_checkbox = gui.checkBox(text_includes_box, self,
'includes_title', 'Article title')
self.mesh_checkbox = gui.checkBox(text_includes_box, self,
'includes_mesh', 'Mesh headings')
self.abstract_checkbox = gui.checkBox(text_includes_box, self,
'includes_abstract', 'Abstract')
self.url_checkbox = gui.checkBox(text_includes_box, self,
'includes_url', 'URL')
self.pubmed_controls.append(self.authors_checkbox)
self.pubmed_controls.append(self.title_checkbox)
self.pubmed_controls.append(self.mesh_checkbox)
self.pubmed_controls.append(self.abstract_checkbox)
self.pubmed_controls.append(self.url_checkbox)
# Num. records.
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Retrieve')
label.setMaximumSize(label.sizeHint())
self.num_records_input = gui.spin(h_box,
self,
'num_records',
minv=1,
maxv=10000)
self.max_records_label = gui.label(h_box, self, 'records from /.')
self.max_records_label.setMaximumSize(
self.max_records_label.sizeHint())
self.pubmed_controls.append(self.num_records_input)
# Download articles.
# Search for records button.
self.retrieve_records_button = gui.button(
self.controlArea,
self,
'Retrieve records',
callback=self.retrieve_records,
tooltip='Retrieves the specified documents.')
self.pubmed_controls.append(self.retrieve_records_button)
# Num. retrieved records info label.
self.retrieval_info_label = gui.label(
self.controlArea, self, 'Number of records retrieved: /')
# Load the most recent emails.
self.set_email_list()
# Load the most recent queries.
self.set_keyword_list()
# Check the email and enable controls accordingly.
if self.recent_emails:
email = self.recent_emails[0]
self.email_is_valid = validate_email(email)
self.enable_controls()
def __init__(self):
super().__init__()
self.controlArea = QWidget(self.controlArea)
self.layout().addWidget(self.controlArea)
layout = QGridLayout()
self.controlArea.setLayout(layout)
layout.setContentsMargins(4, 4, 4, 4)
self.methods = [method for method in METHODS if method[-1] is not None]
self.tab_index = 0
self.mutex = QMutex()
self.graph = None
self.items = None # items set by Items signal
self.items_graph = None # items set by graph.items by Network signal
self.items_analysis = None # items to output and merge with analysis result
self.job_queue = []
self.job_working = []
self.analfeatures = []
self.analdata = {}
for method in self.methods:
setattr(self, method[0], method[0] in self.enabled_methods)
setattr(self, "lbl_" + method[0], "")
self.tabs = gui.tabWidget(self.controlArea)
self.tabs.setMinimumWidth(450)
self.graphIndices = gui.createTabPage(self.tabs, "Graph-level indices")
self.nodeIndices = gui.createTabPage(self.tabs, "Node-level indices")
self.tabs.setCurrentIndex(self.tab_index)
self.tabs.currentChanged.connect(
lambda index: setattr(self, 'tab_index', index))
a = {NODELEVEL: self.nodeIndices, GRAPHLEVEL: self.graphIndices}
for name, _, label, type, algorithm in self.methods:
box = gui.widgetBox(a[type], orientation="horizontal")
gui.checkBox(box,
self,
name,
label=label,
callback=lambda n=name: self.method_clicked(n))
box.layout().addStretch(1)
lbl = gui.label(box, self, "%(lbl_" + name + ")s")
setattr(self, "tool_" + name, lbl)
self.graphIndices.layout().addStretch(1)
self.nodeIndices.layout().addStretch(1)
autobox = gui.auto_commit(None,
self,
"auto_commit",
"Commit",
commit=self.analyze)
layout.addWidget(autobox, 3, 0, 1, 1)
cancel = gui.button(None,
self,
"Cancel",
callback=lambda: self.stop_job(current=False))
autobox.layout().insertWidget(3, cancel)
autobox.layout().insertSpacing(2, 10)
cancel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Preferred)
def __init__(self):
super().__init__()
self.methods = [
("number_of_nodes", True, "Number of nodes", GRAPHLEVEL, lambda G: G.number_of_nodes()),
("number_of_edges", True, "Number of edges", GRAPHLEVEL, lambda G: G.number_of_edges()),
("average_degree", True, "Average degree", GRAPHLEVEL, lambda G: np.average(list(G.degree().values()))),
("diameter", False, "Diameter", GRAPHLEVEL, nx.diameter),
("radius", False, "Radius", GRAPHLEVEL, nx.radius),
("average_shortest_path_length", False, "Average shortest path length", GRAPHLEVEL, nx.average_shortest_path_length),
("density", True, "Density", GRAPHLEVEL, nx.density),
("degree_assortativity_coefficient", False, \
"Degree assortativity coefficient", GRAPHLEVEL, \
nx.degree_assortativity_coefficient if \
hasattr(nx, "degree_assortativity_coefficient") else None),
# additional attr needed
#("attribute_assortativity_coefficient", False, "Attribute assortativity coefficient", GRAPHLEVEL, nx.attribute_assortativity_coefficient),
#("numeric_assortativity_coefficient", False, "Numeric assortativity coefficient", GRAPHLEVEL, nx.numeric_assortativity_coefficient),
("degree_pearson_correlation_coefficient", False, \
"Degree pearson correlation coefficient", GRAPHLEVEL, \
nx.degree_pearson_correlation_coefficient if\
hasattr(nx, "degree_pearson_correlation_coefficient") else None),
("estrada_index", False, "Estrada index", GRAPHLEVEL, \
nx.estrada_index if hasattr(nx, "estrada_index") else None),
("graph_clique_number", False, "Graph clique number", GRAPHLEVEL, nx.graph_clique_number),
("graph_number_of_cliques", False, "Graph number of cliques", GRAPHLEVEL, nx.graph_number_of_cliques),
("transitivity", False, "Graph transitivity", GRAPHLEVEL, nx.transitivity),
("average_clustering", False, "Average clustering coefficient", GRAPHLEVEL, nx.average_clustering),
("number_connected_components", False, "Number of connected components", GRAPHLEVEL, nx.number_connected_components),
("number_strongly_connected_components", False, "Number of strongly connected components", GRAPHLEVEL, nx.number_strongly_connected_components),
("number_weakly_connected_components", False, "Number of weakly connected components", GRAPHLEVEL, nx.number_weakly_connected_components),
("number_attracting_components", False, "Number of attracting components", GRAPHLEVEL, nx.number_attracting_components),
# TODO: input parameters
#("max_flow", False, "Maximum flow", GRAPHLEVEL, nx.max_flow),
#("min_cut", False, "Minimum cut", GRAPHLEVEL, nx.min_cut),
#("ford_fulkerson", False, "Maximum single-commodity flow (Ford-Fulkerson)", GRAPHLEVEL, nx.ford_fulkerson),
#("min_cost_flow_cost", False, "min_cost_flow_cost", GRAPHLEVEL, nx.min_cost_flow_cost),
# returns dict of dict
#("shortest_path_length", False, "Shortest path length", GRAPHLEVEL, nx.shortest_path_length),
("degree", False, "Degree", NODELEVEL, nx.degree),
("in_degree", False, "In-degree", NODELEVEL, lambda G: G.in_degree()),
("out_degree", False, "Out-degree", NODELEVEL, lambda G: G.out_degree()),
("average_neighbor_degree", False, "Average neighbor degree", NODELEVEL, nx.average_neighbor_degree),
("clustering", False, "Clustering coefficient", NODELEVEL, nx.clustering),
("triangles", False, "Number of triangles", NODELEVEL, nx.triangles),
("square_clustering", False, "Squares clustering coefficient", NODELEVEL, nx.square_clustering),
("number_of_cliques", False, "Number of cliques", NODELEVEL, nx.number_of_cliques),
("degree_centrality", False, "Degree centrality", NODELEVEL, nx.degree_centrality),
("in_degree_centrality", False, "In-egree centrality", NODELEVEL, nx.in_degree_centrality),
("out_degree_centrality", False, "Out-degree centrality", NODELEVEL, nx.out_degree_centrality),
("closeness_centrality", False, "Closeness centrality", NODELEVEL, nx.closeness_centrality),
("betweenness_centrality", False, "Betweenness centrality", NODELEVEL, nx.betweenness_centrality),
("current_flow_closeness_centrality", False, "Information centrality", NODELEVEL, nx.current_flow_closeness_centrality),
("current_flow_betweenness_centrality", False, "Random-walk betweenness centrality", NODELEVEL, nx.current_flow_betweenness_centrality),
("approximate_current_flow_betweenness_centrality", False, \
"Approx. random-walk betweenness centrality", NODELEVEL, \
nx.approximate_current_flow_betweenness_centrality if \
hasattr(nx, "approximate_current_flow_betweenness_centrality") \
else None),
("eigenvector_centrality", False, "Eigenvector centrality", NODELEVEL, nx.eigenvector_centrality),
("eigenvector_centrality_numpy", False, "Eigenvector centrality (NumPy)", NODELEVEL, nx.eigenvector_centrality_numpy),
("load_centrality", False, "Load centrality", NODELEVEL, nx.load_centrality),
("core_number", False, "Core number", NODELEVEL, nx.core_number),
("eccentricity", False, "Eccentricity", NODELEVEL, nx.eccentricity),
("closeness_vitality", False, "Closeness vitality", NODELEVEL, nx.closeness_vitality),
]
"""
TODO: add
average-degree_connectivity
is_bipartite
is_chordal
katz_centrality
katz_centrality_numpy
communicability
communicability_exp
communicability_centrality
communicability_centrality_exp
communicability_betweenness_centrality
average_node_connectivity
is_directed_acyclic_graph
center
??
"""
self.methods = [method for method in self.methods if method[-1] is not None]
self.auto_commit = False
self.tab_index = 0
self.mutex = QtCore.QMutex()
self.graph = None
self.items = None # items set by Items signal
self.items_graph = None # items set by graph.items by Network signal
self.items_analysis = None # items to output and merge with analysis result
self.job_queue = []
self.job_working = []
self.analfeatures = []
self.analdata = {}
for method in self.methods:
setattr(self, method[0], method[1])
setattr(self, "lbl_" + method[0], "")
self.tabs = gui.tabWidget(self.controlArea)
self.tabs.setMinimumWidth(450)
self.graphIndices = gui.createTabPage(self.tabs, "Graph-level indices")
self.nodeIndices = gui.createTabPage(self.tabs, "Node-level indices")
self.tabs.setCurrentIndex(self.tab_index)
self.tabs.currentChanged.connect(lambda index: setattr(self, 'tab_index', index))
for name, default, label, type, algorithm in self.methods:
if type == NODELEVEL:
box = gui.widgetBox(self.nodeIndices, orientation="horizontal")
elif type == GRAPHLEVEL:
box = gui.widgetBox(self.graphIndices, orientation="horizontal")
gui.checkBox(box, self, name, label=label, callback=lambda n=name: self.method_clicked(n))
box.layout().addStretch(1)
lbl = gui.label(box, self, "%(lbl_" + name + ")s")
setattr(self, "tool_" + name, lbl)
self.graphIndices.layout().addStretch(1)
self.nodeIndices.layout().addStretch(1)
gui.checkBox(self.controlArea, self, "auto_commit", label="Commit automatically")
hb = gui.widgetBox(self.controlArea, None, orientation='horizontal')
self.btnCommit = gui.button(hb, self, "Commit", callback=self.analyze, toggleButton=1)
self.btnStopA = gui.button(hb, self, "Cancel", callback=lambda: self.stop_job(current=False))
self.btnStopA.setEnabled(False)
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):
super().__init__()
#self.contextHandlers = {"": DomainContextHandler("", [ContextField("attributes", selected="node_label_attrs"), ContextField("attributes", selected="tooltipAttributes"), "color"])}
self.view = GraphView(self)
self.mainArea.layout().addWidget(self.view)
self.graph_attrs = []
self.acceptingEnterKeypress = False
self.node_label_attrs = []
self.tooltipAttributes = []
self.searchStringTimer = QTimer(self)
self.markInputItems = None
self.node_color_attr = 0
self.node_size_attr = 0
self.nHighlighted = 0
self.nSelected = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self.lastVertexSizeColumn = ''
self.lastColorColumn = ''
self.lastLabelColumns = set()
self.lastTooltipColumns = set()
self.items_matrix = None
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.graph = None
self.setMinimumWidth(600)
self.tabs = gui.tabWidget(self.controlArea)
self.displayTab = gui.createTabPage(self.tabs, "Display")
self.markTab = gui.createTabPage(self.tabs, "Marking")
def on_tab_changed(index):
self.tabIndex = index
self.set_selection_mode()
self.tabs.currentChanged.connect(on_tab_changed)
self.tabs.setCurrentIndex(self.tabIndex)
ib = gui.widgetBox(self.displayTab, "Info")
gui.label(
ib, self,
"Nodes: %(number_of_nodes_label)i (%(verticesPerEdge).2f per edge)"
)
gui.label(
ib, self,
"Edges: %(number_of_edges_label)i (%(edgesPerVertex).2f per node)")
box = gui.widgetBox(self.displayTab, "Nodes")
self.relayout_button = gui.button(box,
self,
'Re-layout',
callback=self.relayout,
autoDefault=False)
self.view.positionsChanged.connect(
lambda _: self.progressbar.advance())
def animationFinished():
self.relayout_button.setEnabled(True)
self.progressbar.finish()
self.view.animationFinished.connect(animationFinished)
self.colorCombo = gui.comboBox(box,
self,
"node_color_attr",
label='Color:',
orientation='horizontal',
callback=self.set_node_colors)
self.invertNodeSizeCheck = self.maxNodeSizeSpin = QWidget(
) # Forward declaration
self.nodeSizeCombo = gui.comboBox(box,
self,
"node_size_attr",
label='Size:',
orientation='horizontal',
callback=self.set_node_sizes)
hb = gui.widgetBox(box, orientation="horizontal")
hb.layout().addStretch(1)
self.minNodeSizeSpin = gui.spin(hb,
self,
"minNodeSize",
1,
50,
step=1,
label="Min:",
callback=self.set_node_sizes)
self.minNodeSizeSpin.setValue(8)
gui.separator(hb)
self.maxNodeSizeSpin = gui.spin(hb,
self,
"maxNodeSize",
10,
200,
step=5,
label="Max:",
callback=self.set_node_sizes)
self.maxNodeSizeSpin.setValue(50)
gui.separator(hb)
self.invertNodeSizeCheck = gui.checkBox(hb,
self,
"invertNodeSize",
"Invert",
callback=self.set_node_sizes)
hb = gui.widgetBox(self.displayTab,
box="Node labels | tooltips",
orientation="horizontal",
addSpace=False)
self.attListBox = gui.listBox(
hb,
self,
"node_label_attrs",
"graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._on_node_label_attrs_changed)
self.tooltipListBox = gui.listBox(
hb,
self,
"tooltipAttributes",
"graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._clicked_tooltip_lstbox)
eb = gui.widgetBox(self.displayTab, "Edges", orientation="vertical")
self.checkbox_relative_edges = gui.checkBox(
eb,
self,
'relativeEdgeWidths',
'Relative edge widths',
callback=self.set_edge_sizes)
self.checkbox_show_weights = gui.checkBox(
eb,
self,
'showEdgeWeights',
'Show edge weights',
callback=self.set_edge_labels)
ib = gui.widgetBox(self.markTab, "Info", orientation="vertical")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i")
gui.label(ib, self, "Selected: %(nSelected)i")
gui.label(ib, self, "Highlighted: %(nHighlighted)i")
def on_selection_change():
self.nSelected = len(self.view.getSelected())
self.nHighlighted = len(self.view.getHighlighted())
self.set_selection_mode()
self.commit()
self.view.selectionChanged.connect(on_selection_change)
ib = gui.widgetBox(self.markTab, "Highlight nodes ...")
ribg = gui.radioButtonsInBox(ib,
self,
"selectionMode",
callback=self.set_selection_mode)
gui.appendRadioButton(ribg, "None")
gui.appendRadioButton(ribg, "... whose attributes contain:")
self.ctrlMarkSearchString = gui.lineEdit(
gui.indentedBox(ribg),
self,
"markSearchString",
callback=self._set_search_string_timer,
callbackOnType=True)
self.searchStringTimer.timeout.connect(self.set_selection_mode)
gui.appendRadioButton(ribg,
"... neighbours of selected, ≤ N hops away")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkDistance = gui.spin(
ib,
self,
"markDistance",
1,
100,
1,
label="Hops:",
callback=lambda: self.set_selection_mode(SelectionMode.NEIGHBORS))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with at least N connections")
gui.appendRadioButton(ribg, "... with at most N connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNConnections = gui.spin(
ib,
self,
"markNConnections",
0,
1000000,
1,
label="Connections:",
callback=lambda: self.set_selection_mode(
SelectionMode.AT_MOST_N if self.selectionMode == SelectionMode.
AT_MOST_N else SelectionMode.AT_LEAST_N))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg,
"... with more connections than any neighbor")
gui.appendRadioButton(
ribg, "... with more connections than average neighbor")
gui.appendRadioButton(ribg, "... with most connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNumber = gui.spin(
ib,
self,
"markNBest",
1,
1000000,
1,
label="Number of nodes:",
callback=lambda: self.set_selection_mode(SelectionMode.MOST_CONN))
ib.layout().addStretch(1)
self.markInputRadioButton = gui.appendRadioButton(
ribg, "... from Node Subset input signal")
self.markInputRadioButton.setEnabled(True)
gui.auto_commit(ribg, self, 'do_auto_commit', 'Output changes')
self.markTab.layout().addStretch(1)
self.set_graph(None)
self.set_selection_mode()
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):
super().__init__()
self.methods = [
("number_of_nodes", True, "Number of nodes", GRAPHLEVEL, lambda G: G.number_of_nodes()),
("number_of_edges", True, "Number of edges", GRAPHLEVEL, lambda G: G.number_of_edges()),
("average_degree", True, "Average degree", GRAPHLEVEL, lambda G: np.average(list(G.degree().values()))),
("diameter", False, "Diameter", GRAPHLEVEL, nx.diameter),
("radius", False, "Radius", GRAPHLEVEL, nx.radius),
("average_shortest_path_length", False, "Average shortest path length", GRAPHLEVEL, nx.average_shortest_path_length),
("density", True, "Density", GRAPHLEVEL, nx.density),
("degree_assortativity_coefficient", False, \
"Degree assortativity coefficient", GRAPHLEVEL, \
nx.degree_assortativity_coefficient if \
hasattr(nx, "degree_assortativity_coefficient") else None),
# additional attr needed
#("attribute_assortativity_coefficient", False, "Attribute assortativity coefficient", GRAPHLEVEL, nx.attribute_assortativity_coefficient),
#("numeric_assortativity_coefficient", False, "Numeric assortativity coefficient", GRAPHLEVEL, nx.numeric_assortativity_coefficient),
("degree_pearson_correlation_coefficient", False, \
"Degree pearson correlation coefficient", GRAPHLEVEL, \
nx.degree_pearson_correlation_coefficient if\
hasattr(nx, "degree_pearson_correlation_coefficient") else None),
("estrada_index", False, "Estrada index", GRAPHLEVEL, \
nx.estrada_index if hasattr(nx, "estrada_index") else None),
("graph_clique_number", False, "Graph clique number", GRAPHLEVEL, nx.graph_clique_number),
("graph_number_of_cliques", False, "Graph number of cliques", GRAPHLEVEL, nx.graph_number_of_cliques),
("transitivity", False, "Graph transitivity", GRAPHLEVEL, nx.transitivity),
("average_clustering", False, "Average clustering coefficient", GRAPHLEVEL, nx.average_clustering),
("number_connected_components", False, "Number of connected components", GRAPHLEVEL, nx.number_connected_components),
("number_strongly_connected_components", False, "Number of strongly connected components", GRAPHLEVEL, nx.number_strongly_connected_components),
("number_weakly_connected_components", False, "Number of weakly connected components", GRAPHLEVEL, nx.number_weakly_connected_components),
("number_attracting_components", False, "Number of attracting components", GRAPHLEVEL, nx.number_attracting_components),
# TODO: input parameters
#("max_flow", False, "Maximum flow", GRAPHLEVEL, nx.max_flow),
#("min_cut", False, "Minimum cut", GRAPHLEVEL, nx.min_cut),
#("ford_fulkerson", False, "Maximum single-commodity flow (Ford-Fulkerson)", GRAPHLEVEL, nx.ford_fulkerson),
#("min_cost_flow_cost", False, "min_cost_flow_cost", GRAPHLEVEL, nx.min_cost_flow_cost),
# returns dict of dict
#("shortest_path_length", False, "Shortest path length", GRAPHLEVEL, nx.shortest_path_length),
("degree", False, "Degree", NODELEVEL, nx.degree),
("in_degree", False, "In-degree", NODELEVEL, lambda G: G.in_degree()),
("out_degree", False, "Out-degree", NODELEVEL, lambda G: G.out_degree()),
("average_neighbor_degree", False, "Average neighbor degree", NODELEVEL, nx.average_neighbor_degree),
("clustering", False, "Clustering coefficient", NODELEVEL, nx.clustering),
("triangles", False, "Number of triangles", NODELEVEL, nx.triangles),
("square_clustering", False, "Squares clustering coefficient", NODELEVEL, nx.square_clustering),
("number_of_cliques", False, "Number of cliques", NODELEVEL, nx.number_of_cliques),
("degree_centrality", False, "Degree centrality", NODELEVEL, nx.degree_centrality),
("in_degree_centrality", False, "In-egree centrality", NODELEVEL, nx.in_degree_centrality),
("out_degree_centrality", False, "Out-degree centrality", NODELEVEL, nx.out_degree_centrality),
("closeness_centrality", False, "Closeness centrality", NODELEVEL, nx.closeness_centrality),
("betweenness_centrality", False, "Betweenness centrality", NODELEVEL, nx.betweenness_centrality),
("current_flow_closeness_centrality", False, "Information centrality", NODELEVEL, nx.current_flow_closeness_centrality),
("current_flow_betweenness_centrality", False, "Random-walk betweenness centrality", NODELEVEL, nx.current_flow_betweenness_centrality),
("approximate_current_flow_betweenness_centrality", False, \
"Approx. random-walk betweenness centrality", NODELEVEL, \
nx.approximate_current_flow_betweenness_centrality if \
hasattr(nx, "approximate_current_flow_betweenness_centrality") \
else None),
("eigenvector_centrality", False, "Eigenvector centrality", NODELEVEL, nx.eigenvector_centrality),
("eigenvector_centrality_numpy", False, "Eigenvector centrality (NumPy)", NODELEVEL, nx.eigenvector_centrality_numpy),
("load_centrality", False, "Load centrality", NODELEVEL, nx.load_centrality),
("core_number", False, "Core number", NODELEVEL, nx.core_number),
("eccentricity", False, "Eccentricity", NODELEVEL, nx.eccentricity),
("closeness_vitality", False, "Closeness vitality", NODELEVEL, nx.closeness_vitality),
]
"""
TODO: add
average-degree_connectivity
is_bipartite
is_chordal
katz_centrality
katz_centrality_numpy
communicability
communicability_exp
communicability_centrality
communicability_centrality_exp
communicability_betweenness_centrality
average_node_connectivity
is_directed_acyclic_graph
center
??
"""
self.methods = [
method for method in self.methods if method[-1] is not None
]
self.auto_commit = False
self.tab_index = 0
self.mutex = QtCore.QMutex()
self.graph = None
self.items = None # items set by Items signal
self.items_graph = None # items set by graph.items by Network signal
self.items_analysis = None # items to output and merge with analysis result
self.job_queue = []
self.job_working = []
self.analfeatures = []
self.analdata = {}
for method in self.methods:
setattr(self, method[0], method[1])
setattr(self, "lbl_" + method[0], "")
self.tabs = gui.tabWidget(self.controlArea)
self.tabs.setMinimumWidth(450)
self.graphIndices = gui.createTabPage(self.tabs, "Graph-level indices")
self.nodeIndices = gui.createTabPage(self.tabs, "Node-level indices")
self.tabs.setCurrentIndex(self.tab_index)
self.tabs.currentChanged.connect(
lambda index: setattr(self, 'tab_index', index))
for name, default, label, type, algorithm in self.methods:
if type == NODELEVEL:
box = gui.widgetBox(self.nodeIndices, orientation="horizontal")
elif type == GRAPHLEVEL:
box = gui.widgetBox(self.graphIndices,
orientation="horizontal")
gui.checkBox(box,
self,
name,
label=label,
callback=lambda n=name: self.method_clicked(n))
box.layout().addStretch(1)
lbl = gui.label(box, self, "%(lbl_" + name + ")s")
setattr(self, "tool_" + name, lbl)
self.graphIndices.layout().addStretch(1)
self.nodeIndices.layout().addStretch(1)
gui.checkBox(self.controlArea,
self,
"auto_commit",
label="Commit automatically")
hb = gui.widgetBox(self.controlArea, None, orientation='horizontal')
self.btnCommit = gui.button(hb,
self,
"Commit",
callback=self.analyze,
toggleButton=1)
self.btnStopA = gui.button(
hb, self, "Cancel", callback=lambda: self.stop_job(current=False))
self.btnStopA.setEnabled(False)
def __init__(self):
super().__init__()
self.output_corpus = None
self.pubmed_api = None
self.progress = None
self.email_is_valid = False
self.record_count = 0
self.download_running = False
# To hold all the controls. Makes access easier.
self.pubmed_controls = []
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Email:')
label.setMaximumSize(label.sizeHint())
# Drop-down for recent emails.
self.email_combo = QComboBox(h_box)
self.email_combo.setMinimumWidth(150)
self.email_combo.setEditable(True)
self.email_combo.lineEdit().textChanged.connect(self.sync_email)
h_box.layout().addWidget(self.email_combo)
self.email_combo.activated[int].connect(self.select_email)
# RECORD SEARCH
self.search_tabs = gui.tabWidget(self.controlArea)
# --- Regular search ---
regular_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Author
self.author_input = gui.lineEdit(regular_search_box, self, 'author',
'Author:', orientation=Qt.Horizontal)
self.pubmed_controls.append(self.author_input)
h_box = gui.hBox(regular_search_box)
year_box = gui.widgetBox(h_box, orientation=Qt.Horizontal)
min_date = QDate.fromString(
self.MIN_DATE.strftime(self.PY_DATE_FORMAT),
self.QT_DATE_FORMAT
)
if not self.pub_date_from:
self.pub_date_from = self.MIN_DATE.strftime(self.PY_DATE_FORMAT)
if not self.pub_date_to:
self.pub_date_to = date.today().strftime(self.PY_DATE_FORMAT)
self.date_from = QDateEdit(
QDate.fromString(self.pub_date_from, self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True
)
self.date_to = QDateEdit(
QDate.fromString(self.pub_date_to, self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True
)
self.date_from.dateChanged.connect(
lambda date: setattr(self, 'pub_date_from',
date.toString(self.QT_DATE_FORMAT)))
self.date_to.dateChanged.connect(
lambda date: setattr(self, 'pub_date_to',
date.toString(self.QT_DATE_FORMAT)))
self.pubmed_controls.append(self.date_from)
self.pubmed_controls.append(self.date_to)
gui.label(year_box, self, 'From:')
year_box.layout().addWidget(self.date_from)
gui.label(year_box, self, 'to:')
year_box.layout().addWidget(self.date_to)
# Keywords.
h_box = gui.hBox(regular_search_box)
label = gui.label(h_box, self, 'Query:')
label.setMaximumSize(label.sizeHint())
self.keyword_combo = QComboBox(h_box)
self.keyword_combo.setMinimumWidth(150)
self.keyword_combo.setEditable(True)
h_box.layout().addWidget(self.keyword_combo)
self.keyword_combo.activated[int].connect(self.select_keywords)
self.pubmed_controls.append(self.keyword_combo)
tab_height = regular_search_box.sizeHint()
regular_search_box.setMaximumSize(tab_height)
# --- Advanced search ---
advanced_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Advanced search query.
h_box = gui.hBox(advanced_search_box)
self.advanced_query_input = QTextEdit(h_box)
h_box.layout().addWidget(self.advanced_query_input)
self.advanced_query_input.setMaximumSize(tab_height)
self.pubmed_controls.append(self.advanced_query_input)
gui.createTabPage(self.search_tabs, 'Regular search',
regular_search_box)
gui.createTabPage(self.search_tabs, 'Advanced search',
advanced_search_box)
# Search info label.
self.search_info_label = gui.label(
self.controlArea, self,
'Number of records found: /')
# Search for records button.
self.run_search_button = gui.button(
self.controlArea,
self,
'Find records',
callback=self.run_search,
tooltip='Performs a search for articles that fit the '
'specified parameters.')
self.pubmed_controls.append(self.run_search_button)
h_line = QFrame()
h_line.setFrameShape(QFrame.HLine)
h_line.setFrameShadow(QFrame.Sunken)
self.controlArea.layout().addWidget(h_line)
# RECORD RETRIEVAL
# Text includes box.
text_includes_box = gui.widgetBox(self.controlArea,
'Text includes', addSpace=True)
self.authors_checkbox = gui.checkBox(text_includes_box, self,
'includes_authors', 'Authors')
self.title_checkbox = gui.checkBox(text_includes_box, self,
'includes_title', 'Article title')
self.mesh_checkbox = gui.checkBox(text_includes_box, self,
'includes_mesh', 'Mesh headings')
self.abstract_checkbox = gui.checkBox(text_includes_box, self,
'includes_abstract', 'Abstract')
self.url_checkbox = gui.checkBox(text_includes_box, self,
'includes_url', 'URL')
self.pubmed_controls.append(self.authors_checkbox)
self.pubmed_controls.append(self.title_checkbox)
self.pubmed_controls.append(self.mesh_checkbox)
self.pubmed_controls.append(self.abstract_checkbox)
self.pubmed_controls.append(self.url_checkbox)
# Num. records.
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Retrieve')
label.setMaximumSize(label.sizeHint())
self.num_records_input = gui.spin(h_box, self, 'num_records',
minv=1, maxv=100000)
self.max_records_label = gui.label(h_box, self, 'records from /.')
self.max_records_label.setMaximumSize(self.max_records_label
.sizeHint())
self.pubmed_controls.append(self.num_records_input)
# Download articles.
# Search for records button.
self.retrieve_records_button = gui.button(
self.controlArea,
self,
'Retrieve records',
callback=self.retrieve_records,
tooltip='Retrieves the specified documents.')
self.pubmed_controls.append(self.retrieve_records_button)
# Num. retrieved records info label.
self.retrieval_info_label = gui.label(
self.controlArea,
self,
'Number of records retrieved: /')
# Load the most recent emails.
self.set_email_list()
# Load the most recent queries.
self.set_keyword_list()
# Check the email and enable controls accordingly.
if self.recent_emails:
email = self.recent_emails[0]
self.email_is_valid = validate_email(email)
self.enable_controls()
def __init__(self):
super().__init__()
#self.contextHandlers = {"": DomainContextHandler("", [ContextField("attributes", selected="node_label_attrs"), ContextField("attributes", selected="tooltipAttributes"), "color"])}
self.view = GraphView(self)
self.mainArea.layout().addWidget(self.view)
self.graph_attrs = []
self.acceptingEnterKeypress = False
self.node_label_attrs = []
self.tooltipAttributes = []
self.searchStringTimer = QTimer(self)
self.markInputItems = None
self.node_color_attr = 0
self.node_size_attr = 0
self.nHighlighted = 0
self.nSelected = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self.lastVertexSizeColumn = ''
self.lastColorColumn = ''
self.lastLabelColumns = set()
self.lastTooltipColumns = set()
self.items_matrix = None
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.graph = None
self.setMinimumWidth(600)
self.tabs = gui.tabWidget(self.controlArea)
self.displayTab = gui.createTabPage(self.tabs, "Display")
self.markTab = gui.createTabPage(self.tabs, "Marking")
def on_tab_changed(index):
self.tabIndex = index
self.set_selection_mode()
self.tabs.currentChanged.connect(on_tab_changed)
self.tabs.setCurrentIndex(self.tabIndex)
ib = gui.widgetBox(self.displayTab, "Info")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i (%(verticesPerEdge).2f per edge)")
gui.label(ib, self, "Edges: %(number_of_edges_label)i (%(edgesPerVertex).2f per node)")
box = gui.widgetBox(self.displayTab, "Nodes")
self.relayout_button = gui.button(box, self, 'Re-layout',
callback=self.relayout, autoDefault=False)
self.view.positionsChanged.connect(lambda _: self.progressbar.advance())
def animationFinished():
self.relayout_button.setEnabled(True)
self.progressbar.finish()
self.view.animationFinished.connect(animationFinished)
self.colorCombo = gui.comboBox(
box, self, "node_color_attr", label='Color:',
orientation='horizontal', callback=self.set_node_colors)
self.invertNodeSizeCheck = self.maxNodeSizeSpin = QWidget() # Forward declaration
self.nodeSizeCombo = gui.comboBox(
box, self, "node_size_attr",
label='Size:',
orientation='horizontal',
callback=self.set_node_sizes)
hb = gui.widgetBox(box, orientation="horizontal")
hb.layout().addStretch(1)
self.minNodeSizeSpin = gui.spin(
hb, self, "minNodeSize", 1, 50, step=1, label="Min:",
callback=self.set_node_sizes)
self.minNodeSizeSpin.setValue(8)
gui.separator(hb)
self.maxNodeSizeSpin = gui.spin(
hb, self, "maxNodeSize", 10, 200, step=5, label="Max:",
callback=self.set_node_sizes)
self.maxNodeSizeSpin.setValue(50)
gui.separator(hb)
self.invertNodeSizeCheck = gui.checkBox(
hb, self, "invertNodeSize", "Invert",
callback=self.set_node_sizes)
hb = gui.widgetBox(self.displayTab, box="Node labels | tooltips",
orientation="horizontal", addSpace=False)
self.attListBox = gui.listBox(
hb, self, "node_label_attrs", "graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._on_node_label_attrs_changed)
self.tooltipListBox = gui.listBox(
hb, self, "tooltipAttributes", "graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._clicked_tooltip_lstbox)
eb = gui.widgetBox(self.displayTab, "Edges", orientation="vertical")
self.checkbox_relative_edges = gui.checkBox(
eb, self, 'relativeEdgeWidths', 'Relative edge widths',
callback=self.set_edge_sizes)
self.checkbox_show_weights = gui.checkBox(
eb, self, 'showEdgeWeights', 'Show edge weights',
callback=self.set_edge_labels)
ib = gui.widgetBox(self.markTab, "Info", orientation="vertical")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i")
gui.label(ib, self, "Selected: %(nSelected)i")
gui.label(ib, self, "Highlighted: %(nHighlighted)i")
def on_selection_change():
self.nSelected = len(self.view.getSelected())
self.nHighlighted = len(self.view.getHighlighted())
self.set_selection_mode()
self.commit()
self.view.selectionChanged.connect(on_selection_change)
ib = gui.widgetBox(self.markTab, "Highlight nodes ...")
ribg = gui.radioButtonsInBox(ib, self, "selectionMode", callback=self.set_selection_mode)
gui.appendRadioButton(ribg, "None")
gui.appendRadioButton(ribg, "... whose attributes contain:")
self.ctrlMarkSearchString = gui.lineEdit(gui.indentedBox(ribg), self, "markSearchString", callback=self._set_search_string_timer, callbackOnType=True)
self.searchStringTimer.timeout.connect(self.set_selection_mode)
gui.appendRadioButton(ribg, "... neighbours of selected, ≤ N hops away")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkDistance = gui.spin(ib, self, "markDistance", 1, 100, 1, label="Hops:",
callback=lambda: self.set_selection_mode(SelectionMode.NEIGHBORS))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with at least N connections")
gui.appendRadioButton(ribg, "... with at most N connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNConnections = gui.spin(ib, self, "markNConnections", 0, 1000000, 1, label="Connections:",
callback=lambda: self.set_selection_mode(SelectionMode.AT_MOST_N if self.selectionMode == SelectionMode.AT_MOST_N else SelectionMode.AT_LEAST_N))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with more connections than any neighbor")
gui.appendRadioButton(ribg, "... with more connections than average neighbor")
gui.appendRadioButton(ribg, "... with most connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNumber = gui.spin(ib, self, "markNBest", 1, 1000000, 1,
label="Number of nodes:",
callback=lambda: self.set_selection_mode(SelectionMode.MOST_CONN))
ib.layout().addStretch(1)
self.markInputRadioButton = gui.appendRadioButton(ribg, "... given in the ItemSubset input signal")
self.markInput = 0
ib = gui.indentedBox(ribg)
self.markInputCombo = gui.comboBox(ib, self, 'markInput',
callback=lambda: self.set_selection_mode(SelectionMode.FROM_INPUT))
self.markInputRadioButton.setEnabled(False)
gui.auto_commit(ribg, self, 'do_auto_commit', 'Output changes')
self.markTab.layout().addStretch(1)
self.set_graph(None)
self.set_selection_mode()
def __init__(self, parent=None):
super().__init__(parent)
self.selectedDatabase = 0
self.uniqueRows = True
gui.button(gui.widgetBox(self.controlArea, "Cache", addSpace=True),
self, "Clear cache",
tooltip="Clear saved query results",
callback=self.clearCache)
self.serviceindex = 0
self.serviceCombo = gui.comboBox(
self.controlArea, self, "serviceindex", "Mart Service",
callback=self._setServiceUrl
)
for name, url in MartServices:
self.serviceCombo.addItem(name, userData=url)
idx = self.serviceCombo.findData(self.selectedService, Qt.UserRole)
self.serviceCombo.setCurrentIndex(idx)
# self.selectedService = self.serviceCombo.itemData(self.serviceCombo.currentItem())
self.martsCombo = gui.comboBox(
self.controlArea, self, "selectedDatabase", "Database",
callback=self.setSelectedMart,
addSpace=True)
self.martsCombo.setMaximumWidth(250)
self.datasetsCombo = gui.comboBox(
self.controlArea, self, "selectedDataset", "Dataset",
callback=self.setSelectedDataset,
addSpace=True)
self.datasetsCombo.setMaximumWidth(250)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Results")
gui.checkBox(
box, self, "uniqueRows", "Unique results only",
tooltip="Return unique results only.",)
self.commitButton = gui.button(
box, self, "Get Results", callback=self.commit,
tooltip="Query the BioMart server and output the results",
autoDefault=True)
self.commitButton.setEnabled(False)
self.mainWidget = gui.widgetBox(
self.mainArea, orientation=QStackedLayout())
self.mainTab = QTabWidget()
self.mainWidget.layout().addWidget(self.mainTab)
self.attributesConfigurationBox = gui.createTabPage(self.mainTab, "Attributes")
if self.SHOW_FILTERS: # ??
self.filtersConfigurationBox = gui.createTabPage(self.mainTab, "Filters")
self.error(0)
self.setEnabled(False)
self._task = None
self._executor = concurrent.ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
service = self.selectedService
self._task = task = concurrent.Task(
function=partial(self._get_registry, url=service))
task.resultReady.connect(self.setBioMartRegistry)
task.exceptionReady.connect(self._handleException)
self._executor.submit(task)
self._setServiceUrl()
self._afterInitQueue = []
try:
from Bio import SeqIO
self.hasBiopython = True
except ImportError:
self.warning(100, "Biopython package not found.\nTo retrieve FASTA sequence data from BioMart install Biopython.")
self.hasBiopython = False
def __init__(self, parent=None):
super().__init__(parent)
self.selectedDatabase = 0
self.uniqueRows = True
gui.button(gui.widgetBox(self.controlArea, "Cache", addSpace=True),
self, "Clear cache",
tooltip="Clear saved query results",
callback=self.clearCache)
self.serviceindex = 0
self.serviceCombo = gui.comboBox(
self.controlArea, self, "serviceindex", "Mart Service",
callback=self._setServiceUrl
)
for name, url in MartServices:
self.serviceCombo.addItem(name, userData=url)
idx = self.serviceCombo.findData(self.selectedService, Qt.UserRole)
self.serviceCombo.setCurrentIndex(idx)
# self.selectedService = self.serviceCombo.itemData(self.serviceCombo.currentItem())
self.martsCombo = gui.comboBox(
self.controlArea, self, "selectedDatabase", "Database",
callback=self.setSelectedMart,
addSpace=True)
self.martsCombo.setMaximumWidth(250)
self.datasetsCombo = gui.comboBox(
self.controlArea, self, "selectedDataset", "Dataset",
callback=self.setSelectedDataset,
addSpace=True)
self.datasetsCombo.setMaximumWidth(250)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Results")
gui.checkBox(
box, self, "uniqueRows", "Unique results only",
tooltip="Return unique results only.",)
self.commitButton = gui.button(
box, self, "Get Results", callback=self.commit,
tooltip="Query the BioMart server and output the results",
autoDefault=True)
self.commitButton.setEnabled(False)
self.mainWidget = gui.widgetBox(
self.mainArea, orientation=QStackedLayout())
self.mainTab = QTabWidget()
self.mainWidget.layout().addWidget(self.mainTab)
self.attributesConfigurationBox = gui.createTabPage(self.mainTab, "Attributes")
if self.SHOW_FILTERS: # ??
self.filtersConfigurationBox = gui.createTabPage(self.mainTab, "Filters")
self.error(0)
self.setEnabled(False)
self._task = None
self._executor = concurrent.ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
service = self.selectedService
self._task = task = concurrent.Task(
function=partial(self._get_registry, url=service))
task.resultReady.connect(self.setBioMartRegistry)
task.exceptionReady.connect(self._handleException)
self._executor.submit(task)
self._setServiceUrl()
self._afterInitQueue = []
try:
from Bio import SeqIO
self.hasBiopython = True
except ImportError:
self.warning(100, "Biopython package not found.\nTo retrieve FASTA sequence data from BioMart install Biopython.")
self.hasBiopython = False
def __init__(self, parent=None):
super().__init__(parent)
self.selectedDatabase = 0
self.idAttr = 0
self.useAttrNames = False
self.uniqueRows = True
gui.button(
gui.widgetBox(self.controlArea, "Cache", addSpace=True),
self,
"Clear cache",
tooltip="Clear saved query results",
callback=self.clearCache,
)
self.martsCombo = gui.comboBox(
self.controlArea, self, "selectedDatabase", "Database", callback=self.setSelectedMart, addSpace=True
)
self.martsCombo.setMaximumWidth(250)
self.datasetsCombo = gui.comboBox(
self.controlArea, self, "selectedDataset", "Dataset", callback=self.setSelectedDataset, addSpace=True
)
self.datasetsCombo.setMaximumWidth(250)
box = gui.widgetBox(self.controlArea, "Input Ids")
cb = gui.checkBox(
box,
self,
"useAttrNames",
"Use attribute names",
tooltip="Use attribute names for ids",
callback=self.updateInputIds,
)
self.idAttrCB = gui.comboBox(
box, self, "idAttr", tooltip="Use attribute values from ...", callback=self.updateInputIds
)
cb.disables = [(-1, self.idAttrCB)]
cb.makeConsistent()
self.idText = QPlainTextEdit()
self.idText.setReadOnly(True)
box.layout().addWidget(self.idText)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Results")
gui.checkBox(box, self, "uniqueRows", "Unique results only", tooltip="Return unique results only.")
self.commitButton = gui.button(
box,
self,
"Get Results",
callback=self.commit,
tooltip="Query the BioMart server and output the results",
autoDefault=True,
)
self.commitButton.setEnabled(False)
self.mainWidget = gui.widgetBox(self.mainArea, orientation=QStackedLayout())
self.mainTab = QTabWidget()
self.mainWidget.layout().addWidget(self.mainTab)
self.attributesConfigurationBox = gui.createTabPage(self.mainTab, "Attributes")
if self.SHOW_FILTERS: # ??
self.filtersConfigurationBox = gui.createTabPage(self.mainTab, "Filters")
self.error(0)
self.setEnabled(False)
self._executor = concurrent.ThreadExecutor(threadPool=QThreadPool(maxThreadCount=2))
self._task = task = concurrent.Task(function=self._get_registry)
task.resultReady.connect(self.setBioMartRegistry)
task.exceptionReady.connect(self._handleException)
self._executor.submit(task)
self.candidateIdAttrs = []
self._afterInitQueue = []
self.data = None
try:
from Bio import SeqIO
self.hasBiopython = True
except ImportError:
self.warning(
100, "Biopython package not found.\nTo retrieve FASTA sequence data from BioMart install Biopython."
)
self.hasBiopython = False
def __init__(self):
super().__init__()
#self.contextHandlers = {"": DomainContextHandler("", [ContextField("attributes", selected="node_label_attrs"), ContextField("attributes", selected="tooltipAttributes"), "color"])}
self.networkCanvas = networkCanvas = OWNxCanvas(self)
self.graph_attrs = []
self.edges_attrs = []
self.node_label_attrs = []
self.tooltipAttributes = []
self.edgeLabelAttributes = []
self.autoSendSelection = False
self.graphShowGrid = 1 # show gridlines in the graph
self.markNConnections = 2
self.markNumber = 0
self.markProportion = 0
self.markSearchString = ""
self.markDistance = 2
self.frSteps = 1
self.hubs = 0
self.node_color_attr = 0
self.edgeColor = 0
self.node_size_attr = 0
self.nShown = self.nHidden = self.nHighlighted = self.nSelected = self.verticesPerEdge = self.edgesPerVertex = 0
self.optimizeWhat = 1
self.maxNodeSize = 50
self.labelsOnMarkedOnly = 0
self.invertNodeSize = 0
self.optMethod = 0
self.lastVertexSizeColumn = ''
self.lastColorColumn = ''
self.lastLabelColumns = set()
self.lastTooltipColumns = set()
self.showWeights = 0
self.selectedEdgeSchemaIndex = 0
self.items_matrix = None
self.showDistances = 0
self.showMissingValues = 0
self.fontSize = 12
self.fontWeight = 1
self.mdsTorgerson = 0
self.mdsAvgLinkage = 1
self.mdsSteps = 10000
self.mdsRefresh = 50
self.mdsStressDelta = 0.0000001
self.showTextMiningInfo = 0
self.toolbarSelection = 0
self.minComponentEdgeWidth = 10
self.maxComponentEdgeWidth = 70
self.mdsFromCurrentPos = 0
self.tabIndex = 0
self.number_of_nodes_label = -1
self.number_of_edges_label = -1
self.opt_from_curr = False
self.checkSendMarkedNodes = True
self.checkSendSelectedNodes = True
self.marked_nodes = []
self._network_view = None
self.graph = None
self.graph_base = None
self.networkCanvas.showMissingValues = self.showMissingValues
class ViewBox(pg.ViewBox):
def __init__(self):
super().__init__()
def mouseDragEvent(self, ev):
if not ev.isFinish():
return super().mouseDragEvent(ev)
if self.state['mouseMode'] != self.RectMode:
return
# Tap into pg.ViewBox's rbScaleBox ... it'll be fine.
self.rbScaleBox.hide()
ax = QRectF(pg.Point(ev.buttonDownPos(ev.button())),
pg.Point(ev.pos()))
ax = self.childGroup.mapRectFromParent(ax)
networkCanvas.selectNodesInRect(ax)
self.setMouseMode(self.PanMode)
ev.accept()
def mouseClickEvent(self, ev):
if ev.button() == Qt.LeftButton:
if networkCanvas.is_animating:
networkCanvas.is_animating = False
ev.accept()
else:
networkCanvas.mouseClickEvent(ev)
super().mouseClickEvent(ev)
class PlotItem(pg.PlotItem):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
for axis in ('bottom', 'left'):
self.hideAxis(axis)
def _path(filename):
return os.path.join(os.path.dirname(__file__), 'icons', filename + '.png')
self.rectBtn = pg.ButtonItem(_path('button_rect'), parentItem=self)
self.rectBtn.clicked.connect(self.rectBtnClicked)
self._qtBaseClass.setParentItem(self.autoBtn, None)
self.autoBtn.hide()
self.autoBtn = pg.ButtonItem(_path('button_autoscale'), parentItem=self)
self.autoBtn.mode = 'auto'
self.autoBtn.clicked.connect(self.autoBtnClicked)
self.textEnterToSelect = pg.TextItem(
html='<div style="background-color:#f0f0f0; padding:5px;">'
'<font color="#444444"><b>Press <tt>Enter</tt> to add '
'<i><font color="{}">highlighted</font></i> nodes to '
'<i><font color="{}">selection</font></i> ...</font></b></div>'
.format(NodePenColor.HIGHLIGHTED, NodePenColor.SELECTED))
self.textEnterToSelect.setParentItem(self)
self.textEnterToSelect.hide()
def rectBtnClicked(self, ev):
self.vb.setMouseMode(self.vb.RectMode)
def updateButtons(self):
self.autoBtn.show()
def resizeEvent(self, ev):
super().resizeEvent(ev)
btnRect = self.mapRectFromItem(self.rectBtn, self.rectBtn.boundingRect())
LEFT_OFFSET, BOTTOM_OFFSET = 3, 5
y = self.size().height() - btnRect.height() - BOTTOM_OFFSET
self.autoBtn.setPos(LEFT_OFFSET, y)
self.rectBtn.setPos(2*LEFT_OFFSET + btnRect.width(), y)
self.textEnterToSelect.setPos(LEFT_OFFSET, BOTTOM_OFFSET)
class PlotWidget(pg.PlotWidget):
def __init__(self, *args, **kwargs):
pg.GraphicsView.__init__(self, *args, **kwargs)
plot = PlotWidget(self, background='w')
plot.plotItem = PlotItem(enableAutoRange=True, viewBox=ViewBox())
plot.setCentralItem(plot.plotItem)
# Required, copied from pg.PlotWidget constructor
for m in ['addItem', 'removeItem', 'autoRange', 'clear', 'setXRange',
'setYRange', 'setRange', 'setAspectLocked', 'setMouseEnabled',
'setXLink', 'setYLink', 'enableAutoRange', 'disableAutoRange',
'setLimits', 'register', 'unregister', 'viewRect']:
setattr(plot, m, getattr(plot.plotItem, m))
plot.plotItem.sigRangeChanged.connect(plot.viewRangeChanged)
self.textEnterToSelect = plot.plotItem.textEnterToSelect
plot.setFrameStyle(QFrame.StyledPanel)
plot.setMinimumSize(500, 500)
plot.setAspectLocked(True)
plot.addItem(self.networkCanvas)
self.mainArea.layout().addWidget(plot)
self.tabs = gui.tabWidget(self.controlArea)
self.displayTab = gui.createTabPage(self.tabs, "Display")
self.markTab = gui.createTabPage(self.tabs, "Marking")
def showTextOnMarkingTab(index):
if self.tabs.widget(index) == self.markTab:
self.set_mark_mode()
else:
self.acceptingEnterKeypress = False
self.tabs.currentChanged.connect(showTextOnMarkingTab)
self.tabs.setCurrentIndex(self.tabIndex)
self.connect(self.tabs, SIGNAL("currentChanged(int)"), lambda index: setattr(self, 'tabIndex', index))
ib = gui.widgetBox(self.displayTab, "Info")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i (%(verticesPerEdge).2f per edge)")
gui.label(ib, self, "Edges: %(number_of_edges_label)i (%(edgesPerVertex).2f per node)")
box = gui.widgetBox(self.displayTab, "Nodes")
self.optCombo = gui.comboBox(
box, self, "optMethod", label='Layout:',
orientation='horizontal', callback=self.graph_layout_method)
for layout in Layout.all: self.optCombo.addItem(layout)
self.optMethod = Layout.all.index(Layout.FHR)
self.optCombo.setCurrentIndex(self.optMethod)
self.colorCombo = gui.comboBox(
box, self, "node_color_attr", label='Color by:',
orientation='horizontal', callback=self.set_node_colors)
hb = gui.widgetBox(box, orientation="horizontal", addSpace=False)
hb.layout().addWidget(QLabel('Size by:', hb))
self.nodeSizeCombo = gui.comboBox(
hb, self, "node_size_attr", callback=self.set_node_sizes)
self.maxNodeSizeSpin = gui.spin(
hb, self, "maxNodeSize", 5, 200, step=10, label="Max:",
callback=self.set_node_sizes)
self.maxNodeSizeSpin.setValue(50)
self.invertNodeSizeCheck = gui.checkBox(
hb, self, "invertNodeSize", "Invert",
callback=self.set_node_sizes)
lb = gui.widgetBox(box, "Node labels | tooltips", orientation="vertical", addSpace=False)
hb = gui.widgetBox(lb, orientation="horizontal", addSpace=False)
self.attListBox = gui.listBox(
hb, self, "node_label_attrs", "graph_attrs",
selectionMode=QListWidget.MultiSelection,
callback=self._on_node_label_attrs_changed)
self.tooltipListBox = gui.listBox(
hb, self, "tooltipAttributes", "graph_attrs",
selectionMode=QListWidget.MultiSelection,
callback=self._clicked_tooltip_lstbox)
eb = gui.widgetBox(self.displayTab, "Edges", orientation="vertical")
self.checkbox_relative_edges = gui.checkBox(
eb, self, 'networkCanvas.relative_edge_widths', 'Relative edge widths',
callback=self.networkCanvas.set_edge_sizes)
self.checkbox_show_weights = gui.checkBox(
eb, self, 'networkCanvas.show_edge_weights', 'Show edge weights',
callback=self.networkCanvas.set_edge_labels)
self.edgeColorCombo = gui.comboBox(
eb, self, "edgeColor", label='Color by:', orientation='horizontal',
callback=self.set_edge_colors)
elb = gui.widgetBox(eb, "Edge labels", addSpace=False)
self.edgeLabelListBox = gui.listBox(
elb, self, "edgeLabelAttributes", "edges_attrs",
selectionMode=QListWidget.MultiSelection,
callback=self._clicked_edge_label_listbox)
elb.setEnabled(False)
ib = gui.widgetBox(self.markTab, "Info", orientation="vertical")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i")
gui.label(ib, self, "Selected: %(nSelected)i")
gui.label(ib, self, "Highlighted: %(nHighlighted)i")
ib = gui.widgetBox(self.markTab, "Highlight nodes ...")
ribg = gui.radioButtonsInBox(ib, self, "hubs", [], "Mark", callback=self.set_mark_mode)
gui.appendRadioButton(ribg, "None")
gui.appendRadioButton(ribg, "... whose attributes contain:")
self.ctrlMarkSearchString = gui.lineEdit(gui.indentedBox(ribg), self, "markSearchString", callback=self._set_search_string_timer, callbackOnType=True)
self.searchStringTimer = QTimer(self)
self.connect(self.searchStringTimer, SIGNAL("timeout()"), self.set_mark_mode)
gui.appendRadioButton(ribg, "... neighbours of selected, ≤ N hops away")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkDistance = gui.spin(ib, self, "markDistance", 1, 100, 1, label="Distance:",
callback=lambda: self.set_mark_mode(SelectionMode.NEIGHBORS))
#self.ctrlMarkFreeze = gui.button(ib, self, "&Freeze", value="graph.freezeNeighbours", toggleButton = True)
gui.appendRadioButton(ribg, "... with at least N connections")
gui.appendRadioButton(ribg, "... with at most N connections")
self.ctrlMarkNConnections = gui.spin(gui.indentedBox(ribg), self, "markNConnections", 0, 1000000, 1, label="N:",
callback=lambda: self.set_mark_mode(SelectionMode.AT_MOST_N if self.hubs == SelectionMode.AT_MOST_N else SelectionMode.AT_LEAST_N))
gui.appendRadioButton(ribg, "... with more connections than any neighbor")
gui.appendRadioButton(ribg, "... with more connections than average neighbor")
gui.appendRadioButton(ribg, "... with most connections")
ib = gui.indentedBox(ribg)
#~ self.ctrlMarkNumber = gui.spin(ib, self, "markNumber", 1, 1000000, 1, label="Number of nodes:", callback=(lambda h=7: self.set_mark_mode(h)))
self.ctrlMarkNumber = gui.spin(ib, self, "markNumber", 1, 1000000, 1, label="Number of nodes:", callback=lambda: self.set_mark_mode(SelectionMode.MOST_CONN))
gui.auto_commit(ribg, self, 'do_auto_commit', 'Output changes')
#ib = gui.widgetBox(self.markTab, "General", orientation="vertical")
#self.checkSendMarkedNodes = True
self.toolbar = gui.widgetBox(self.controlArea, orientation='horizontal')
#~ G = self.networkCanvas.gui
#~ self.zoomSelectToolbar = G.zoom_select_toolbar(self.toolbar, nomargin=True, buttons=
#~ G.default_zoom_select_buttons +
#~ [
#~ G.Spacing,
#~ ("buttonM2S", "Marked to selection", None, None, "marked_to_selected", 'Dlg_Mark2Sel'),
#~ ("buttonS2M", "Selection to marked", None, None, "selected_to_marked", 'Dlg_Sel2Mark'),
#~ ("buttonHSEL", "Hide selection", None, None, "hide_selection", 'Dlg_HideSelection'),
#~ ("buttonSSEL", "Show all nodes", None, None, "show_selection", 'Dlg_ShowSelection'),
#~ #("buttonUN", "Hide unselected", None, None, "hideUnSelectedVertices", 'Dlg_SelectedNodes'),
#~ #("buttonSW", "Show all nodes", None, None, "showAllVertices", 'Dlg_clear'),
#~ ])
#~ self.zoomSelectToolbar.buttons[G.SendSelection].clicked.connect(self.send_data)
#~ self.zoomSelectToolbar.buttons[G.SendSelection].clicked.connect(self.send_marked_nodes)
#~ self.zoomSelectToolbar.buttons[("buttonHSEL", "Hide selection", None, None, "hide_selection", 'Dlg_HideSelection')].clicked.connect(self.hide_selection)
#~ self.zoomSelectToolbar.buttons[("buttonSSEL", "Show all nodes", None, None, "show_selection", 'Dlg_ShowSelection')].clicked.connect(self.show_selection)
#self.zoomSelectToolbar.buttons[G.SendSelection].hide()
self.set_mark_mode()
self.displayTab.layout().addStretch(1)
self.markTab.layout().addStretch(1)
self.graph_layout_method()
self.set_graph(None)
self.setMinimumWidth(900)
