def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.activated[int].connect(self.select_file)
box.layout().addWidget(self.file_combo)
layout.addWidget(box, 0, 1)
file_button = gui.button(None,
self,
'...',
callback=self.browse_file,
autoDefault=False)
file_button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon))
file_button.setSizePolicy(Policy.Maximum, Policy.Fixed)
layout.addWidget(file_button, 0, 2)
reload_button = gui.button(None,
self,
"Reload",
callback=self.load_data,
autoDefault=False)
reload_button.setIcon(self.style().standardIcon(
QStyle.SP_BrowserReload))
reload_button.setSizePolicy(Policy.Fixed, Policy.Fixed)
layout.addWidget(reload_button, 0, 3)
self.sheet_box = gui.hBox(None, addToLayout=False, margin=0)
self.sheet_combo = gui.comboBox(
None,
self,
"xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True,
)
self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(self.sheet_label, Qt.AlignLeft)
self.sheet_box.layout().addWidget(self.sheet_combo, Qt.AlignVCenter)
layout.addWidget(self.sheet_box, 2, 1)
self.sheet_box.hide()
rb_button = gui.appendRadioButton(vbox, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.Ignored, Policy.Fixed)
url_combo.setEditable(True)
url_combo.setInsertPolicy(url_combo.InsertAtTop)
url_edit = url_combo.lineEdit()
l, t, r, b = url_edit.getTextMargins()
url_edit.setTextMargins(l + 5, t, r, b)
layout.addWidget(url_combo, 3, 1, 3, 3)
url_combo.activated.connect(self._url_set)
# whit completer we set that combo box is case sensitive when
# matching the history
completer = QCompleter()
completer.setCaseSensitivity(Qt.CaseSensitive)
url_combo.setCompleter(completer)
box = gui.vBox(self.controlArea, "Info")
self.infolabel = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)")
self.domain_editor = DomainEditor(self)
self.editor_model = self.domain_editor.model()
box.layout().addWidget(self.domain_editor)
box = gui.hBox(self.controlArea)
gui.button(box,
self,
"Browse documentation datasets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
gui.button(box, self, "Reset", callback=self.reset_domain_edit)
self.apply_button = gui.button(box,
self,
"Apply",
callback=self.apply_domain_edit)
self.apply_button.setEnabled(False)
self.apply_button.setFixedWidth(170)
self.editor_model.dataChanged.connect(
lambda: self.apply_button.setEnabled(True))
self.set_file_list()
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
self.setAcceptDrops(True)
if self.source == self.LOCAL_FILE:
last_path = self.last_path()
if last_path and os.path.exists(last_path) and \
os.path.getsize(last_path) > self.SIZE_LIMIT:
self.Warning.file_too_big()
return
QTimer.singleShot(0, self.load_data)
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
readers = [
f for f in FileFormat.formats
if getattr(f, 'read', None) and getattr(f, "EXTENSIONS", None)
]
def group_readers_per_addon_key(w):
# readers from Orange.data.io should go first
def package(w):
package = w.qualified_name().split(".")[:-1]
package = package[:2]
if ".".join(package) == "Orange.data":
return ["0"] # force "Orange" to come first
return package
return package(w), w.DESCRIPTION
self.available_readers = sorted(set(readers),
key=group_readers_per_addon_key)
layout = QGridLayout()
layout.setSpacing(4)
gui.widgetBox(self.controlArea, orientation=layout, box='Source')
vbox = gui.radioButtons(None,
self,
"source",
box=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.activated[int].connect(self.select_file)
box.layout().addWidget(self.file_combo)
layout.addWidget(box, 0, 1)
file_button = gui.button(None,
self,
'...',
callback=self.browse_file,
autoDefault=False)
file_button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon))
file_button.setSizePolicy(Policy.Maximum, Policy.Fixed)
layout.addWidget(file_button, 0, 2)
reload_button = gui.button(None,
self,
"Reload",
callback=self.load_data,
autoDefault=False)
reload_button.setIcon(self.style().standardIcon(
QStyle.SP_BrowserReload))
reload_button.setSizePolicy(Policy.Fixed, Policy.Fixed)
layout.addWidget(reload_button, 0, 3)
self.sheet_box = gui.hBox(None, addToLayout=False, margin=0)
self.sheet_combo = QComboBox()
self.sheet_combo.activated[str].connect(self.select_sheet)
self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(self.sheet_label, Qt.AlignLeft)
self.sheet_box.layout().addWidget(self.sheet_combo, Qt.AlignVCenter)
layout.addWidget(self.sheet_box, 2, 1)
self.sheet_box.hide()
rb_button = gui.appendRadioButton(vbox, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.Ignored, Policy.Fixed)
url_combo.setEditable(True)
url_combo.setInsertPolicy(url_combo.InsertAtTop)
url_edit = url_combo.lineEdit()
l, t, r, b = url_edit.getTextMargins()
url_edit.setTextMargins(l + 5, t, r, b)
layout.addWidget(url_combo, 3, 1, 1, 3)
url_combo.activated.connect(self._url_set)
# whit completer we set that combo box is case sensitive when
# matching the history
completer = QCompleter()
completer.setCaseSensitivity(Qt.CaseSensitive)
url_combo.setCompleter(completer)
layout = QGridLayout()
layout.setSpacing(4)
gui.widgetBox(self.controlArea, orientation=layout, box='File Type')
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.reader_combo = QComboBox(self)
self.reader_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.reader_combo.activated[int].connect(self.select_reader)
box.layout().addWidget(self.reader_combo)
layout.addWidget(box, 0, 1)
box = gui.vBox(self.controlArea, "Info")
self.infolabel = gui.widgetLabel(box, 'No data loaded.')
box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)")
self.domain_editor = DomainEditor(self)
self.editor_model = self.domain_editor.model()
box.layout().addWidget(self.domain_editor)
box = gui.hBox(box)
gui.button(box,
self,
"Reset",
callback=self.reset_domain_edit,
autoDefault=False)
gui.rubber(box)
self.apply_button = gui.button(box,
self,
"Apply",
callback=self.apply_domain_edit)
self.apply_button.setEnabled(False)
self.apply_button.setFixedWidth(170)
self.editor_model.dataChanged.connect(
lambda: self.apply_button.setEnabled(True))
hBox = gui.hBox(self.controlArea)
gui.rubber(hBox)
gui.button(hBox,
self,
"Browse documentation datasets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(hBox)
self.set_file_list()
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
self.setAcceptDrops(True)
if self.source == self.LOCAL_FILE:
last_path = self.last_path()
if last_path and os.path.exists(last_path) and \
os.path.getsize(last_path) > self.SIZE_LIMIT:
self.Warning.file_too_big()
return
QTimer.singleShot(0, self.load_data)
class OWSetEnrichment(widget.OWWidget):
name = "Set Enrichment"
description = ""
icon = "../widgets/icons/GeneSetEnrichment.svg"
priority = 5000
inputs = [("Data", Orange.data.Table, "setData", widget.Default),
("Reference", Orange.data.Table, "setReference")]
outputs = [("Data subset", Orange.data.Table)]
settingsHandler = settings.DomainContextHandler()
taxid = settings.ContextSetting(None)
speciesIndex = settings.ContextSetting(0)
genesinrows = settings.ContextSetting(False)
geneattr = settings.ContextSetting(0)
categoriesCheckState = settings.ContextSetting({})
useReferenceData = settings.Setting(False)
useMinCountFilter = settings.Setting(True)
useMaxPValFilter = settings.Setting(True)
useMaxFDRFilter = settings.Setting(True)
minClusterCount = settings.Setting(3)
maxPValue = settings.Setting(0.01)
maxFDR = settings.Setting(0.01)
autocommit = settings.Setting(False)
Ready, Initializing, Loading, RunningEnrichment = 0, 1, 2, 4
def __init__(self, parent=None):
super().__init__(parent)
self.geneMatcherSettings = [False, False, True, False]
self.data = None
self.referenceData = None
self.taxid_list = []
self.__genematcher = (None, fulfill(gene.matcher([])))
self.__invalidated = False
self.currentAnnotatedCategories = []
self.state = None
self.__state = OWSetEnrichment.Initializing
box = gui.widgetBox(self.controlArea, "Info")
self.infoBox = gui.widgetLabel(box, "Info")
self.infoBox.setText("No data on input.\n")
self.speciesComboBox = gui.comboBox(
self.controlArea, self,
"speciesIndex", "Species",
callback=self.__on_speciesIndexChanged)
box = gui.widgetBox(self.controlArea, "Entity names")
self.geneAttrComboBox = gui.comboBox(
box, self, "geneattr", "Entity feature", sendSelectedValue=0,
callback=self.updateAnnotations)
cb = gui.checkBox(
box, self, "genesinrows", "Use feature names",
callback=self.updateAnnotations,
disables=[(-1, self.geneAttrComboBox)])
cb.makeConsistent()
# gui.button(box, self, "Gene matcher settings",
# callback=self.updateGeneMatcherSettings,
# tooltip="Open gene matching settings dialog")
self.referenceRadioBox = gui.radioButtonsInBox(
self.controlArea,
self, "useReferenceData",
["All entities", "Reference set (input)"],
tooltips=["Use entire genome (for gene set enrichment) or all " +
"available entities for reference",
"Use entities from Reference Examples input signal " +
"as reference"],
box="Reference", callback=self.updateAnnotations)
box = gui.widgetBox(self.controlArea, "Entity Sets")
self.groupsWidget = QTreeWidget(self)
self.groupsWidget.setHeaderLabels(["Category"])
box.layout().addWidget(self.groupsWidget)
hLayout = QHBoxLayout()
hLayout.setSpacing(10)
hWidget = gui.widgetBox(self.mainArea, orientation=hLayout)
gui.spin(hWidget, self, "minClusterCount",
0, 100, label="Entities",
tooltip="Minimum entity count",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
checked="useMinCountFilter",
checkCallback=self.filterAnnotationsChartView)
pvalfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(
pvalfilterbox, self, "useMaxPValFilter", "p-value",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
pvalfilterbox, self, "maxPValue", 0.0, 1.0, 0.0001,
tooltip="Maximum p-value",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
pvalfilterbox.layout().setAlignment(cb, Qt.AlignRight)
pvalfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
fdrfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(
fdrfilterbox, self, "useMaxFDRFilter", "FDR",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
fdrfilterbox, self, "maxFDR", 0.0, 1.0, 0.0001,
tooltip="Maximum False discovery rate",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
fdrfilterbox.layout().setAlignment(cb, Qt.AlignRight)
fdrfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
self.filterLineEdit = QLineEdit(
self, placeholderText="Filter ...")
self.filterCompleter = QCompleter(self.filterLineEdit)
self.filterCompleter.setCaseSensitivity(Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.filterCompleter)
hLayout.addWidget(self.filterLineEdit)
self.mainArea.layout().addWidget(hWidget)
self.filterLineEdit.textChanged.connect(
self.filterAnnotationsChartView)
self.annotationsChartView = QTreeView(
alternatingRowColors=True,
sortingEnabled=True,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
self.annotationsChartView.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.annotationsChartView)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.annotationsChartView)
self.annotationsChartView.header().installEventFilter(contextEventFilter)
self.groupsWidget.itemClicked.connect(self.subsetSelectionChanged)
gui.auto_commit(self.controlArea, self, "autocommit", "Commit")
self.setBlocking(True)
task = EnsureDownloaded(
[(taxonomy.Taxonomy.DOMAIN, taxonomy.Taxonomy.FILENAME),
(geneset.sfdomain, "index.pck")]
)
task.finished.connect(self.__initialize_finish)
self.setStatusMessage("Initializing")
self._executor = ThreadExecutor(
parent=self, threadPool=QThreadPool(self))
self._executor.submit(task)
def sizeHint(self):
return QSize(1024, 600)
def __initialize_finish(self):
# Finalize the the widget's initialization (preferably after
# ensuring all required databases have been downloaded.
sets = geneset.list_all()
taxids = set(taxonomy.common_taxids() +
list(filter(None, [tid for _, tid, _ in sets])))
organisms = [(tid, name_or_none(tid)) for tid in taxids]
organisms = [(tid, name) for tid, name in organisms
if name is not None]
organisms = [(None, "None")] + sorted(organisms)
taxids = [tid for tid, _ in organisms]
names = [name for _, name in organisms]
self.taxid_list = taxids
self.speciesComboBox.clear()
self.speciesComboBox.addItems(names)
self.genesets = sets
if self.taxid in self.taxid_list:
taxid = self.taxid
else:
taxid = self.taxid_list[0]
self.taxid = None
self.setCurrentOrganism(taxid)
self.setBlocking(False)
self.__state = OWSetEnrichment.Ready
self.setStatusMessage("")
def setCurrentOrganism(self, taxid):
"""Set the current organism `taxid`."""
if taxid not in self.taxid_list:
taxid = self.taxid_list[min(self.speciesIndex,
len(self.taxid_list) - 1)]
if self.taxid != taxid:
self.taxid = taxid
self.speciesIndex = self.taxid_list.index(taxid)
self.refreshHierarchy()
self._invalidateGeneMatcher()
self._invalidate()
def currentOrganism(self):
"""Return the current organism taxid"""
return self.taxid
def __on_speciesIndexChanged(self):
taxid = self.taxid_list[self.speciesIndex]
self.taxid = "< Do not look >"
self.setCurrentOrganism(taxid)
if self.__invalidated and self.data is not None:
self.updateAnnotations()
def clear(self):
"""Clear/reset the widget state."""
self._cancelPending()
self.state = None
self.__state = self.__state & ~OWSetEnrichment.RunningEnrichment
self._clearView()
if self.annotationsChartView.model() is not None:
self.annotationsChartView.model().clear()
self.geneAttrComboBox.clear()
self.geneAttrs = []
self._updatesummary()
def _cancelPending(self):
"""Cancel pending tasks."""
if self.state is not None:
self.state.results.cancel()
self.state.namematcher.cancel()
self.state.cancelled = True
def _clearView(self):
"""Clear the enrichment report view (main area)."""
if self.annotationsChartView.model() is not None:
self.annotationsChartView.model().clear()
def setData(self, data=None):
"""Set the input dataset with query gene names"""
if self.__state & OWSetEnrichment.Initializing:
self.__initialize_finish()
self.error(0)
self.closeContext()
self.clear()
self.groupsWidget.clear()
self.data = data
if data is not None:
varlist = [var for var in data.domain.variables + data.domain.metas
if isinstance(var, Orange.data.StringVariable)]
self.geneAttrs = varlist
for var in varlist:
self.geneAttrComboBox.addItem(*gui.attributeItem(var))
oldtaxid = self.taxid
self.geneattr = min(self.geneattr, len(self.geneAttrs) - 1)
taxid = data_hints.get_hint(data, "taxid", "")
if taxid in self.taxid_list:
self.speciesIndex = self.taxid_list.index(taxid)
self.taxid = taxid
self.genesinrows = data_hints.get_hint(
data, "genesinrows", self.genesinrows)
self.openContext(data)
if oldtaxid != self.taxid:
self.taxid = "< Do not look >"
self.setCurrentOrganism(taxid)
self.refreshHierarchy()
self._invalidate()
def setReference(self, data=None):
"""Set the (optional) input dataset with reference gene names."""
self.referenceData = data
self.referenceRadioBox.setEnabled(bool(data))
if self.useReferenceData:
self._invalidate()
def handleNewSignals(self):
if self.__invalidated:
self.updateAnnotations()
def _invalidateGeneMatcher(self):
_, f = self.__genematcher
f.cancel()
self.__genematcher = (None, fulfill(gene.matcher([])))
def _invalidate(self):
self.__invalidated = True
def genesFromTable(self, table):
if self.genesinrows:
genes = [attr.name for attr in table.domain.attributes]
else:
geneattr = self.geneAttrs[self.geneattr]
genes = [str(ex[geneattr]) for ex in table]
return genes
def getHierarchy(self, taxid):
def recursive_dict():
return defaultdict(recursive_dict)
collection = recursive_dict()
def collect(col, hier):
if hier:
collect(col[hier[0]], hier[1:])
for hierarchy, t_id, _ in self.genesets:
collect(collection[t_id], hierarchy)
return (taxid, collection[taxid]), (None, collection[None])
def setHierarchy(self, hierarchy, hierarchy_noorg):
self.groupsWidgetItems = {}
def fill(col, parent, full=(), org=""):
for key, value in sorted(col.items()):
full_cat = full + (key,)
item = QTreeWidgetItem(parent, [key])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable |
Qt.ItemIsSelectable | Qt.ItemIsEnabled)
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
checked = self.categoriesCheckState.get(
(full_cat, org), Qt.Checked)
item.setData(0, Qt.CheckStateRole, checked)
item.setExpanded(True)
item.category = full_cat
item.organism = org
self.groupsWidgetItems[full_cat] = item
fill(value, item, full_cat, org=org)
self.groupsWidget.clear()
fill(hierarchy[1], self.groupsWidget, org=hierarchy[0])
fill(hierarchy_noorg[1], self.groupsWidget, org=hierarchy_noorg[0])
def refreshHierarchy(self):
self.setHierarchy(*self.getHierarchy(taxid=self.taxid_list[self.speciesIndex]))
def selectedCategories(self):
"""
Return a list of currently selected hierarchy keys.
A key is a tuple of identifiers from the root to the leaf of
the hierarchy tree.
"""
return [key for key, check in self.getHierarchyCheckState().items()
if check == Qt.Checked]
def getHierarchyCheckState(self):
def collect(item, full=()):
checked = item.checkState(0)
name = str(item.data(0, Qt.DisplayRole))
full_cat = full + (name,)
result = [((full_cat, item.organism), checked)]
for i in range(item.childCount()):
result.extend(collect(item.child(i), full_cat))
return result
items = [self.groupsWidget.topLevelItem(i)
for i in range(self.groupsWidget.topLevelItemCount())]
states = itertools.chain(*(collect(item) for item in items))
return dict(states)
def subsetSelectionChanged(self, item, column):
# The selected geneset (hierarchy) subset has been changed by the
# user. Update the displayed results.
# Update the stored state (persistent settings)
self.categoriesCheckState = self.getHierarchyCheckState()
categories = self.selectedCategories()
if self.data is not None:
if self._nogenematching() or \
not set(categories) <= set(self.currentAnnotatedCategories):
self.updateAnnotations()
else:
self.filterAnnotationsChartView()
def updateGeneMatcherSettings(self):
raise NotImplementedError
from .OWGOEnrichmentAnalysis import GeneMatcherDialog
dialog = GeneMatcherDialog(self, defaults=self.geneMatcherSettings, enabled=[True] * 4, modal=True)
if dialog.exec_():
self.geneMatcherSettings = [getattr(dialog, item[0]) for item in dialog.items]
self._invalidateGeneMatcher()
if self.data is not None:
self.updateAnnotations()
def _genematcher(self):
"""
Return a Future[gene.SequenceMatcher]
"""
taxid = self.taxid_list[self.speciesIndex]
current, matcher_f = self.__genematcher
if taxid == current and \
not matcher_f.cancelled():
return matcher_f
self._invalidateGeneMatcher()
if taxid is None:
self.__genematcher = (None, fulfill(gene.matcher([])))
return self.__genematcher[1]
matchers = [gene.GMGO, gene.GMKEGG, gene.GMNCBI, gene.GMAffy]
matchers = [m for m, use in zip(matchers, self.geneMatcherSettings)
if use]
def create():
return gene.matcher([m(taxid) for m in matchers])
matcher_f = self._executor.submit(create)
self.__genematcher = (taxid, matcher_f)
return self.__genematcher[1]
def _nogenematching(self):
return self.taxid is None or not any(self.geneMatcherSettings)
def updateAnnotations(self):
if self.data is None:
return
assert not self.__state & OWSetEnrichment.Initializing
self._cancelPending()
self._clearView()
self.information(0)
self.warning(0)
self.error(0)
if not self.genesinrows and len(self.geneAttrs) == 0:
self.error(0, "Input data contains no columns with gene names")
return
self.__state = OWSetEnrichment.RunningEnrichment
taxid = self.taxid_list[self.speciesIndex]
self.taxid = taxid
categories = self.selectedCategories()
clusterGenes = self.genesFromTable(self.data)
if self.referenceData is not None and self.useReferenceData:
referenceGenes = self.genesFromTable(self.referenceData)
else:
referenceGenes = None
self.currentAnnotatedCategories = categories
genematcher = self._genematcher()
self.progressBarInit()
## Load collections in a worker thread
# TODO: Use cached collections if already loaded and
# use ensure_genesetsdownloaded with progress report (OWSelectGenes)
collections = self._executor.submit(geneset.collections, *categories)
def refset_null():
"""Return the default background reference set"""
col = collections.result()
return reduce(operator.ior, (set(g.genes) for g in col), set())
def refset_ncbi():
"""Return all NCBI gene names"""
geneinfo = gene.NCBIGeneInfo(taxid)
return set(geneinfo.keys())
def namematcher():
matcher = genematcher.result()
match = matcher.set_targets(ref_set.result())
match.umatch = memoize(match.umatch)
return match
def map_unames():
matcher = namematcher.result()
query = list(filter(None, map(matcher.umatch, querynames)))
reference = list(filter(None, map(matcher.umatch, ref_set.result())))
return query, reference
if self._nogenematching():
if referenceGenes is None:
ref_set = self._executor.submit(refset_null)
else:
ref_set = fulfill(referenceGenes)
else:
if referenceGenes == None:
ref_set = self._executor.submit(refset_ncbi)
else:
ref_set = fulfill(referenceGenes)
namematcher = self._executor.submit(namematcher)
querynames = clusterGenes
state = types.SimpleNamespace()
state.query_set = clusterGenes
state.reference_set = referenceGenes
state.namematcher = namematcher
state.query_count = len(set(clusterGenes))
state.reference_count = (len(set(referenceGenes))
if referenceGenes is not None else None)
state.cancelled = False
progress = methodinvoke(self, "_setProgress", (float,))
info = methodinvoke(self, "_setRunInfo", (str,))
@withtraceback
def run():
info("Loading data")
match = namematcher.result()
query, reference = map_unames()
gscollections = collections.result()
results = []
info("Running enrichment")
p = 0
for i, gset in enumerate(gscollections):
genes = set(filter(None, map(match.umatch, gset.genes)))
enr = set_enrichment(genes, reference, query)
results.append((gset, enr))
if state.cancelled:
raise UserInteruptException
pnew = int(100 * i / len(gscollections))
if pnew != p:
progress(pnew)
p = pnew
progress(100)
info("")
return query, reference, results
task = Task(function=run)
task.resultReady.connect(self.__on_enrichment_finished)
task.exceptionReady.connect(self.__on_enrichment_failed)
result = self._executor.submit(task)
state.results = result
self.state = state
self._updatesummary()
def __on_enrichment_failed(self, exception):
if not isinstance(exception, UserInteruptException):
print("ERROR:", exception, file=sys.stderr)
print(exception._traceback, file=sys.stderr)
self.progressBarFinished()
self.setStatusMessage("")
self.__state &= ~OWSetEnrichment.RunningEnrichment
def __on_enrichment_finished(self, results):
assert QThread.currentThread() is self.thread()
self.__state &= ~OWSetEnrichment.RunningEnrichment
query, reference, results = results
if self.annotationsChartView.model():
self.annotationsChartView.model().clear()
nquery = len(query)
nref = len(reference)
maxcount = max((len(e.query_mapped) for _, e in results),
default=1)
maxrefcount = max((len(e.reference_mapped) for _, e in results),
default=1)
nspaces = int(math.ceil(math.log10(maxcount or 1)))
refspaces = int(math.ceil(math.log(maxrefcount or 1)))
query_fmt = "%" + str(nspaces) + "s (%.2f%%)"
ref_fmt = "%" + str(refspaces) + "s (%.2f%%)"
def fmt_count(fmt, count, total):
return fmt % (count, 100.0 * count / (total or 1))
fmt_query_count = partial(fmt_count, query_fmt)
fmt_ref_count = partial(fmt_count, ref_fmt)
linkFont = QFont(self.annotationsChartView.viewOptions().font)
linkFont.setUnderline(True)
def item(value=None, tooltip=None, user=None):
si = QStandardItem()
if value is not None:
si.setData(value, Qt.DisplayRole)
if tooltip is not None:
si.setData(tooltip, Qt.ToolTipRole)
if user is not None:
si.setData(user, Qt.UserRole)
else:
si.setData(value, Qt.UserRole)
return si
model = QStandardItemModel()
model.setSortRole(Qt.UserRole)
model.setHorizontalHeaderLabels(
["Category", "Term", "Count", "Reference count", "p-value",
"FDR", "Enrichment"])
for i, (gset, enrich) in enumerate(results):
if len(enrich.query_mapped) == 0:
continue
nquery_mapped = len(enrich.query_mapped)
nref_mapped = len(enrich.reference_mapped)
row = [
item(", ".join(gset.hierarchy)),
item(gsname(gset), tooltip=gset.link),
item(fmt_query_count(nquery_mapped, nquery),
tooltip=nquery_mapped, user=nquery_mapped),
item(fmt_ref_count(nref_mapped, nref),
tooltip=nref_mapped, user=nref_mapped),
item(fmtp(enrich.p_value), user=enrich.p_value),
item(), # column 5, FDR, is computed in filterAnnotationsChartView
item(enrich.enrichment_score,
tooltip="%.3f" % enrich.enrichment_score,
user=enrich.enrichment_score)
]
row[0].geneset = gset
row[0].enrichment = enrich
row[1].setData(gset.link, gui.LinkRole)
row[1].setFont(linkFont)
row[1].setForeground(QColor(Qt.blue))
model.appendRow(row)
self.annotationsChartView.setModel(model)
self.annotationsChartView.selectionModel().selectionChanged.connect(
self.commit
)
if not model.rowCount():
self.warning(0, "No enriched sets found.")
else:
self.warning(0)
allnames = set(gsname(geneset)
for geneset, (count, _, _, _) in results if count)
allnames |= reduce(operator.ior,
(set(word_split(name)) for name in allnames),
set())
self.filterCompleter.setModel(None)
self.completerModel = QStringListModel(sorted(allnames))
self.filterCompleter.setModel(self.completerModel)
if results:
max_score = max((e.enrichment_score for _, e in results
if np.isfinite(e.enrichment_score)),
default=1)
self.annotationsChartView.setItemDelegateForColumn(
6, BarItemDelegate(self, scale=(0.0, max_score))
)
self.annotationsChartView.setItemDelegateForColumn(
1, gui.LinkStyledItemDelegate(self.annotationsChartView)
)
header = self.annotationsChartView.header()
for i in range(model.columnCount()):
sh = self.annotationsChartView.sizeHintForColumn(i)
sh = max(sh, header.sectionSizeHint(i))
self.annotationsChartView.setColumnWidth(i, max(min(sh, 300), 30))
# self.annotationsChartView.resizeColumnToContents(i)
self.filterAnnotationsChartView()
self.progressBarFinished()
self.setStatusMessage("")
def _updatesummary(self):
state = self.state
if state is None:
self.error(0,)
self.warning(0)
self.infoBox.setText("No data on input.\n")
return
text = "{.query_count} unique names on input\n".format(state)
if state.results.done() and not state.results.exception():
mapped, _, _ = state.results.result()
ratio_mapped = (len(mapped) / state.query_count
if state.query_count else 0)
text += ("%i (%.1f%%) gene names matched" %
(len(mapped), 100.0 * ratio_mapped))
elif not state.results.done():
text += "..."
else:
text += "<Error {}>".format(str(state.results.exception()))
self.infoBox.setText(text)
# TODO: warn on no enriched sets found (i.e no query genes
# mapped to any set)
def filterAnnotationsChartView(self, filterString=""):
if self.__state & OWSetEnrichment.RunningEnrichment:
return
# TODO: Move filtering to a filter proxy model
# TODO: Re-enable string search
categories = set(", ".join(cat)
for cat, _ in self.selectedCategories())
# filterString = str(self.filterLineEdit.text()).lower()
model = self.annotationsChartView.model()
def ishidden(index):
# Is item at index (row) hidden
item = model.item(index)
item_cat = item.data(Qt.DisplayRole)
return item_cat not in categories
hidemask = [ishidden(i) for i in range(model.rowCount())]
# compute FDR according the selected categories
pvals = [model.item(i, 4).data(Qt.UserRole)
for i, hidden in enumerate(hidemask) if not hidden]
fdrs = utils.stats.FDR(pvals)
# update FDR for the selected collections and apply filtering rules
itemsHidden = []
fdriter = iter(fdrs)
for index, hidden in enumerate(hidemask):
if not hidden:
fdr = next(fdriter)
pval = model.index(index, 4).data(Qt.UserRole)
count = model.index(index, 2).data(Qt.ToolTipRole)
hidden = (self.useMinCountFilter and count < self.minClusterCount) or \
(self.useMaxPValFilter and pval > self.maxPValue) or \
(self.useMaxFDRFilter and fdr > self.maxFDR)
if not hidden:
fdr_item = model.item(index, 5)
fdr_item.setData(fmtpdet(fdr), Qt.ToolTipRole)
fdr_item.setData(fmtp(fdr), Qt.DisplayRole)
fdr_item.setData(fdr, Qt.UserRole)
self.annotationsChartView.setRowHidden(
index, QModelIndex(), hidden)
itemsHidden.append(hidden)
if model.rowCount() and all(itemsHidden):
self.information(0, "All sets were filtered out.")
else:
self.information(0)
self._updatesummary()
@Slot(float)
def _setProgress(self, value):
assert QThread.currentThread() is self.thread()
self.progressBarSet(value, processEvents=None)
@Slot(str)
def _setRunInfo(self, text):
self.setStatusMessage(text)
def commit(self):
if self.data is None or \
self.__state & OWSetEnrichment.RunningEnrichment:
return
model = self.annotationsChartView.model()
rows = self.annotationsChartView.selectionModel().selectedRows(0)
selected = [model.item(index.row(), 0) for index in rows]
mapped = reduce(operator.ior,
(set(item.enrichment.query_mapped)
for item in selected),
set())
assert self.state.namematcher.done()
matcher = self.state.namematcher.result()
axis = 1 if self.genesinrows else 0
if axis == 1:
mapped = [attr for attr in self.data.domain.attributes
if matcher.umatch(attr.name) in mapped]
newdomain = Orange.data.Domain(
mapped, self.data.domain.class_vars, self.data.domain.metas)
data = self.data.from_table(newdomain, self.data)
else:
geneattr = self.geneAttrs[self.geneattr]
selected = [i for i, ex in enumerate(self.data)
if matcher.umatch(str(ex[geneattr])) in mapped]
data = self.data[selected]
self.send("Data subset", data)
def onDeleteWidget(self):
if self.state is not None:
self._cancelPending()
self.state = None
self._executor.shutdown(wait=False)
class OWSetEnrichment(widget.OWWidget):
name = "Set Enrichment"
description = ""
icon = "../widgets/icons/GeneSetEnrichment.svg"
priority = 5000
inputs = [("Data", Orange.data.Table, "setData", widget.Default),
("Reference", Orange.data.Table, "setReference")]
outputs = [("Data subset", Orange.data.Table)]
settingsHandler = settings.DomainContextHandler()
taxid = settings.ContextSetting(None)
speciesIndex = settings.ContextSetting(0)
genesinrows = settings.ContextSetting(False)
geneattr = settings.ContextSetting(0)
categoriesCheckState = settings.ContextSetting({})
useReferenceData = settings.Setting(False)
useMinCountFilter = settings.Setting(True)
useMaxPValFilter = settings.Setting(True)
useMaxFDRFilter = settings.Setting(True)
minClusterCount = settings.Setting(3)
maxPValue = settings.Setting(0.01)
maxFDR = settings.Setting(0.01)
autocommit = settings.Setting(False)
Ready, Initializing, Loading, RunningEnrichment = 0, 1, 2, 4
def __init__(self, parent=None):
super().__init__(parent)
self.geneMatcherSettings = [False, False, True, False]
self.data = None
self.referenceData = None
self.taxid_list = []
self.__genematcher = (None, fulfill(gene.matcher([])))
self.__invalidated = False
self.currentAnnotatedCategories = []
self.state = None
self.__state = OWSetEnrichment.Initializing
box = gui.widgetBox(self.controlArea, "Info")
self.infoBox = gui.widgetLabel(box, "Info")
self.infoBox.setText("No data on input.\n")
self.speciesComboBox = gui.comboBox(
self.controlArea,
self,
"speciesIndex",
"Species",
callback=self.__on_speciesIndexChanged)
box = gui.widgetBox(self.controlArea, "Entity names")
self.geneAttrComboBox = gui.comboBox(box,
self,
"geneattr",
"Entity feature",
sendSelectedValue=0,
callback=self.updateAnnotations)
cb = gui.checkBox(box,
self,
"genesinrows",
"Use feature names",
callback=self.updateAnnotations,
disables=[(-1, self.geneAttrComboBox)])
cb.makeConsistent()
# gui.button(box, self, "Gene matcher settings",
# callback=self.updateGeneMatcherSettings,
# tooltip="Open gene matching settings dialog")
self.referenceRadioBox = gui.radioButtonsInBox(
self.controlArea,
self,
"useReferenceData", ["All entities", "Reference set (input)"],
tooltips=[
"Use entire genome (for gene set enrichment) or all " +
"available entities for reference",
"Use entities from Reference Examples input signal " +
"as reference"
],
box="Reference",
callback=self.updateAnnotations)
box = gui.widgetBox(self.controlArea, "Entity Sets")
self.groupsWidget = QTreeWidget(self)
self.groupsWidget.setHeaderLabels(["Category"])
box.layout().addWidget(self.groupsWidget)
hLayout = QHBoxLayout()
hLayout.setSpacing(10)
hWidget = gui.widgetBox(self.mainArea, orientation=hLayout)
gui.spin(hWidget,
self,
"minClusterCount",
0,
100,
label="Entities",
tooltip="Minimum entity count",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
checked="useMinCountFilter",
checkCallback=self.filterAnnotationsChartView)
pvalfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(pvalfilterbox,
self,
"useMaxPValFilter",
"p-value",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
pvalfilterbox,
self,
"maxPValue",
0.0,
1.0,
0.0001,
tooltip="Maximum p-value",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
pvalfilterbox.layout().setAlignment(cb, Qt.AlignRight)
pvalfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
fdrfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(fdrfilterbox,
self,
"useMaxFDRFilter",
"FDR",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
fdrfilterbox,
self,
"maxFDR",
0.0,
1.0,
0.0001,
tooltip="Maximum False discovery rate",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
fdrfilterbox.layout().setAlignment(cb, Qt.AlignRight)
fdrfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
self.filterLineEdit = QLineEdit(self, placeholderText="Filter ...")
self.filterCompleter = QCompleter(self.filterLineEdit)
self.filterCompleter.setCaseSensitivity(Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.filterCompleter)
hLayout.addWidget(self.filterLineEdit)
self.mainArea.layout().addWidget(hWidget)
self.filterLineEdit.textChanged.connect(
self.filterAnnotationsChartView)
self.annotationsChartView = QTreeView(
alternatingRowColors=True,
sortingEnabled=True,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
self.annotationsChartView.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.annotationsChartView)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.annotationsChartView)
self.annotationsChartView.header().installEventFilter(
contextEventFilter)
self.groupsWidget.itemClicked.connect(self.subsetSelectionChanged)
gui.auto_commit(self.controlArea, self, "autocommit", "Commit")
self.setBlocking(True)
task = EnsureDownloaded([(taxonomy.Taxonomy.DOMAIN,
taxonomy.Taxonomy.FILENAME),
(geneset.sfdomain, "index.pck")])
task.finished.connect(self.__initialize_finish)
self.setStatusMessage("Initializing")
self._executor = ThreadExecutor(parent=self,
threadPool=QThreadPool(self))
self._executor.submit(task)
def sizeHint(self):
return QSize(1024, 600)
def __initialize_finish(self):
# Finalize the the widget's initialization (preferably after
# ensuring all required databases have been downloaded.
sets = geneset.list_all()
taxids = set(taxonomy.common_taxids() +
list(filter(None, [tid for _, tid, _ in sets])))
organisms = [(tid, name_or_none(tid)) for tid in taxids]
organisms = [(tid, name) for tid, name in organisms
if name is not None]
organisms = [(None, "None")] + sorted(organisms)
taxids = [tid for tid, _ in organisms]
names = [name for _, name in organisms]
self.taxid_list = taxids
self.speciesComboBox.clear()
self.speciesComboBox.addItems(names)
self.genesets = sets
if self.taxid in self.taxid_list:
taxid = self.taxid
else:
taxid = self.taxid_list[0]
self.taxid = None
self.setCurrentOrganism(taxid)
self.setBlocking(False)
self.__state = OWSetEnrichment.Ready
self.setStatusMessage("")
def setCurrentOrganism(self, taxid):
"""Set the current organism `taxid`."""
if taxid not in self.taxid_list:
taxid = self.taxid_list[min(self.speciesIndex,
len(self.taxid_list) - 1)]
if self.taxid != taxid:
self.taxid = taxid
self.speciesIndex = self.taxid_list.index(taxid)
self.refreshHierarchy()
self._invalidateGeneMatcher()
self._invalidate()
def currentOrganism(self):
"""Return the current organism taxid"""
return self.taxid
def __on_speciesIndexChanged(self):
taxid = self.taxid_list[self.speciesIndex]
self.taxid = "< Do not look >"
self.setCurrentOrganism(taxid)
if self.__invalidated and self.data is not None:
self.updateAnnotations()
def clear(self):
"""Clear/reset the widget state."""
self._cancelPending()
self.state = None
self.__state = self.__state & ~OWSetEnrichment.RunningEnrichment
self._clearView()
if self.annotationsChartView.model() is not None:
self.annotationsChartView.model().clear()
self.geneAttrComboBox.clear()
self.geneAttrs = []
self._updatesummary()
def _cancelPending(self):
"""Cancel pending tasks."""
if self.state is not None:
self.state.results.cancel()
self.state.namematcher.cancel()
self.state.cancelled = True
def _clearView(self):
"""Clear the enrichment report view (main area)."""
if self.annotationsChartView.model() is not None:
self.annotationsChartView.model().clear()
def setData(self, data=None):
"""Set the input dataset with query gene names"""
if self.__state & OWSetEnrichment.Initializing:
self.__initialize_finish()
self.error(0)
self.closeContext()
self.clear()
self.groupsWidget.clear()
self.data = data
if data is not None:
varlist = [
var for var in data.domain.variables + data.domain.metas
if isinstance(var, Orange.data.StringVariable)
]
self.geneAttrs = varlist
for var in varlist:
self.geneAttrComboBox.addItem(*gui.attributeItem(var))
oldtaxid = self.taxid
self.geneattr = min(self.geneattr, len(self.geneAttrs) - 1)
taxid = data_hints.get_hint(data, "taxid", "")
if taxid in self.taxid_list:
self.speciesIndex = self.taxid_list.index(taxid)
self.taxid = taxid
self.genesinrows = data_hints.get_hint(data, "genesinrows",
self.genesinrows)
self.openContext(data)
if oldtaxid != self.taxid:
self.taxid = "< Do not look >"
self.setCurrentOrganism(taxid)
self.refreshHierarchy()
self._invalidate()
def setReference(self, data=None):
"""Set the (optional) input dataset with reference gene names."""
self.referenceData = data
self.referenceRadioBox.setEnabled(bool(data))
if self.useReferenceData:
self._invalidate()
def handleNewSignals(self):
if self.__invalidated:
self.updateAnnotations()
def _invalidateGeneMatcher(self):
_, f = self.__genematcher
f.cancel()
self.__genematcher = (None, fulfill(gene.matcher([])))
def _invalidate(self):
self.__invalidated = True
def genesFromTable(self, table):
if self.genesinrows:
genes = [attr.name for attr in table.domain.attributes]
else:
geneattr = self.geneAttrs[self.geneattr]
genes = [str(ex[geneattr]) for ex in table]
return genes
def getHierarchy(self, taxid):
def recursive_dict():
return defaultdict(recursive_dict)
collection = recursive_dict()
def collect(col, hier):
if hier:
collect(col[hier[0]], hier[1:])
for hierarchy, t_id, _ in self.genesets:
collect(collection[t_id], hierarchy)
return (taxid, collection[taxid]), (None, collection[None])
def setHierarchy(self, hierarchy, hierarchy_noorg):
self.groupsWidgetItems = {}
def fill(col, parent, full=(), org=""):
for key, value in sorted(col.items()):
full_cat = full + (key, )
item = QTreeWidgetItem(parent, [key])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable
| Qt.ItemIsSelectable | Qt.ItemIsEnabled)
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
checked = self.categoriesCheckState.get((full_cat, org),
Qt.Checked)
item.setData(0, Qt.CheckStateRole, checked)
item.setExpanded(True)
item.category = full_cat
item.organism = org
self.groupsWidgetItems[full_cat] = item
fill(value, item, full_cat, org=org)
self.groupsWidget.clear()
fill(hierarchy[1], self.groupsWidget, org=hierarchy[0])
fill(hierarchy_noorg[1], self.groupsWidget, org=hierarchy_noorg[0])
def refreshHierarchy(self):
self.setHierarchy(*self.getHierarchy(
taxid=self.taxid_list[self.speciesIndex]))
def selectedCategories(self):
"""
Return a list of currently selected hierarchy keys.
A key is a tuple of identifiers from the root to the leaf of
the hierarchy tree.
"""
return [
key for key, check in self.getHierarchyCheckState().items()
if check == Qt.Checked
]
def getHierarchyCheckState(self):
def collect(item, full=()):
checked = item.checkState(0)
name = str(item.data(0, Qt.DisplayRole))
full_cat = full + (name, )
result = [((full_cat, item.organism), checked)]
for i in range(item.childCount()):
result.extend(collect(item.child(i), full_cat))
return result
items = [
self.groupsWidget.topLevelItem(i)
for i in range(self.groupsWidget.topLevelItemCount())
]
states = itertools.chain(*(collect(item) for item in items))
return dict(states)
def subsetSelectionChanged(self, item, column):
# The selected geneset (hierarchy) subset has been changed by the
# user. Update the displayed results.
# Update the stored state (persistent settings)
self.categoriesCheckState = self.getHierarchyCheckState()
categories = self.selectedCategories()
if self.data is not None:
if self._nogenematching() or \
not set(categories) <= set(self.currentAnnotatedCategories):
self.updateAnnotations()
else:
self.filterAnnotationsChartView()
def updateGeneMatcherSettings(self):
raise NotImplementedError
from .OWGOEnrichmentAnalysis import GeneMatcherDialog
dialog = GeneMatcherDialog(self,
defaults=self.geneMatcherSettings,
enabled=[True] * 4,
modal=True)
if dialog.exec_():
self.geneMatcherSettings = [
getattr(dialog, item[0]) for item in dialog.items
]
self._invalidateGeneMatcher()
if self.data is not None:
self.updateAnnotations()
def _genematcher(self):
"""
Return a Future[gene.SequenceMatcher]
"""
taxid = self.taxid_list[self.speciesIndex]
current, matcher_f = self.__genematcher
if taxid == current and \
not matcher_f.cancelled():
return matcher_f
self._invalidateGeneMatcher()
if taxid is None:
self.__genematcher = (None, fulfill(gene.matcher([])))
return self.__genematcher[1]
matchers = [gene.GMGO, gene.GMKEGG, gene.GMNCBI, gene.GMAffy]
matchers = [
m for m, use in zip(matchers, self.geneMatcherSettings) if use
]
def create():
return gene.matcher([m(taxid) for m in matchers])
matcher_f = self._executor.submit(create)
self.__genematcher = (taxid, matcher_f)
return self.__genematcher[1]
def _nogenematching(self):
return self.taxid is None or not any(self.geneMatcherSettings)
def updateAnnotations(self):
if self.data is None:
return
assert not self.__state & OWSetEnrichment.Initializing
self._cancelPending()
self._clearView()
self.information(0)
self.warning(0)
self.error(0)
if not self.genesinrows and len(self.geneAttrs) == 0:
self.error(0, "Input data contains no columns with gene names")
return
self.__state = OWSetEnrichment.RunningEnrichment
taxid = self.taxid_list[self.speciesIndex]
self.taxid = taxid
categories = self.selectedCategories()
clusterGenes = self.genesFromTable(self.data)
if self.referenceData is not None and self.useReferenceData:
referenceGenes = self.genesFromTable(self.referenceData)
else:
referenceGenes = None
self.currentAnnotatedCategories = categories
genematcher = self._genematcher()
self.progressBarInit()
## Load collections in a worker thread
# TODO: Use cached collections if already loaded and
# use ensure_genesetsdownloaded with progress report (OWSelectGenes)
collections = self._executor.submit(geneset.collections, *categories)
def refset_null():
"""Return the default background reference set"""
col = collections.result()
return reduce(operator.ior, (set(g.genes) for g in col), set())
def refset_ncbi():
"""Return all NCBI gene names"""
geneinfo = gene.NCBIGeneInfo(taxid)
return set(geneinfo.keys())
def namematcher():
matcher = genematcher.result()
match = matcher.set_targets(ref_set.result())
match.umatch = memoize(match.umatch)
return match
def map_unames():
matcher = namematcher.result()
query = list(filter(None, map(matcher.umatch, querynames)))
reference = list(
filter(None, map(matcher.umatch, ref_set.result())))
return query, reference
if self._nogenematching():
if referenceGenes is None:
ref_set = self._executor.submit(refset_null)
else:
ref_set = fulfill(referenceGenes)
else:
if referenceGenes == None:
ref_set = self._executor.submit(refset_ncbi)
else:
ref_set = fulfill(referenceGenes)
namematcher = self._executor.submit(namematcher)
querynames = clusterGenes
state = types.SimpleNamespace()
state.query_set = clusterGenes
state.reference_set = referenceGenes
state.namematcher = namematcher
state.query_count = len(set(clusterGenes))
state.reference_count = (len(set(referenceGenes))
if referenceGenes is not None else None)
state.cancelled = False
progress = methodinvoke(self, "_setProgress", (float, ))
info = methodinvoke(self, "_setRunInfo", (str, ))
@withtraceback
def run():
info("Loading data")
match = namematcher.result()
query, reference = map_unames()
gscollections = collections.result()
results = []
info("Running enrichment")
p = 0
for i, gset in enumerate(gscollections):
genes = set(filter(None, map(match.umatch, gset.genes)))
enr = set_enrichment(genes, reference, query)
results.append((gset, enr))
if state.cancelled:
raise UserInteruptException
pnew = int(100 * i / len(gscollections))
if pnew != p:
progress(pnew)
p = pnew
progress(100)
info("")
return query, reference, results
task = Task(function=run)
task.resultReady.connect(self.__on_enrichment_finished)
task.exceptionReady.connect(self.__on_enrichment_failed)
result = self._executor.submit(task)
state.results = result
self.state = state
self._updatesummary()
def __on_enrichment_failed(self, exception):
if not isinstance(exception, UserInteruptException):
print("ERROR:", exception, file=sys.stderr)
print(exception._traceback, file=sys.stderr)
self.progressBarFinished()
self.setStatusMessage("")
self.__state &= ~OWSetEnrichment.RunningEnrichment
def __on_enrichment_finished(self, results):
assert QThread.currentThread() is self.thread()
self.__state &= ~OWSetEnrichment.RunningEnrichment
query, reference, results = results
if self.annotationsChartView.model():
self.annotationsChartView.model().clear()
nquery = len(query)
nref = len(reference)
maxcount = max((len(e.query_mapped) for _, e in results), default=1)
maxrefcount = max((len(e.reference_mapped) for _, e in results),
default=1)
nspaces = int(math.ceil(math.log10(maxcount or 1)))
refspaces = int(math.ceil(math.log(maxrefcount or 1)))
query_fmt = "%" + str(nspaces) + "s (%.2f%%)"
ref_fmt = "%" + str(refspaces) + "s (%.2f%%)"
def fmt_count(fmt, count, total):
return fmt % (count, 100.0 * count / (total or 1))
fmt_query_count = partial(fmt_count, query_fmt)
fmt_ref_count = partial(fmt_count, ref_fmt)
linkFont = QFont(self.annotationsChartView.viewOptions().font)
linkFont.setUnderline(True)
def item(value=None, tooltip=None, user=None):
si = QStandardItem()
if value is not None:
si.setData(value, Qt.DisplayRole)
if tooltip is not None:
si.setData(tooltip, Qt.ToolTipRole)
if user is not None:
si.setData(user, Qt.UserRole)
else:
si.setData(value, Qt.UserRole)
return si
model = QStandardItemModel()
model.setSortRole(Qt.UserRole)
model.setHorizontalHeaderLabels([
"Category", "Term", "Count", "Reference count", "p-value", "FDR",
"Enrichment"
])
for i, (gset, enrich) in enumerate(results):
if len(enrich.query_mapped) == 0:
continue
nquery_mapped = len(enrich.query_mapped)
nref_mapped = len(enrich.reference_mapped)
row = [
item(", ".join(gset.hierarchy)),
item(gsname(gset), tooltip=gset.link),
item(fmt_query_count(nquery_mapped, nquery),
tooltip=nquery_mapped,
user=nquery_mapped),
item(fmt_ref_count(nref_mapped, nref),
tooltip=nref_mapped,
user=nref_mapped),
item(fmtp(enrich.p_value), user=enrich.p_value),
item(
), # column 5, FDR, is computed in filterAnnotationsChartView
item(enrich.enrichment_score,
tooltip="%.3f" % enrich.enrichment_score,
user=enrich.enrichment_score)
]
row[0].geneset = gset
row[0].enrichment = enrich
row[1].setData(gset.link, gui.LinkRole)
row[1].setFont(linkFont)
row[1].setForeground(QColor(Qt.blue))
model.appendRow(row)
self.annotationsChartView.setModel(model)
self.annotationsChartView.selectionModel().selectionChanged.connect(
self.commit)
if not model.rowCount():
self.warning(0, "No enriched sets found.")
else:
self.warning(0)
allnames = set(
gsname(geneset) for geneset, (count, _, _, _) in results if count)
allnames |= reduce(operator.ior,
(set(word_split(name)) for name in allnames), set())
self.filterCompleter.setModel(None)
self.completerModel = QStringListModel(sorted(allnames))
self.filterCompleter.setModel(self.completerModel)
if results:
max_score = max(
(e.enrichment_score
for _, e in results if np.isfinite(e.enrichment_score)),
default=1)
self.annotationsChartView.setItemDelegateForColumn(
6, BarItemDelegate(self, scale=(0.0, max_score)))
self.annotationsChartView.setItemDelegateForColumn(
1, gui.LinkStyledItemDelegate(self.annotationsChartView))
header = self.annotationsChartView.header()
for i in range(model.columnCount()):
sh = self.annotationsChartView.sizeHintForColumn(i)
sh = max(sh, header.sectionSizeHint(i))
self.annotationsChartView.setColumnWidth(i, max(min(sh, 300), 30))
# self.annotationsChartView.resizeColumnToContents(i)
self.filterAnnotationsChartView()
self.progressBarFinished()
self.setStatusMessage("")
def _updatesummary(self):
state = self.state
if state is None:
self.error(0, )
self.warning(0)
self.infoBox.setText("No data on input.\n")
return
text = "{.query_count} unique names on input\n".format(state)
if state.results.done() and not state.results.exception():
mapped, _, _ = state.results.result()
ratio_mapped = (len(mapped) /
state.query_count if state.query_count else 0)
text += ("%i (%.1f%%) gene names matched" %
(len(mapped), 100.0 * ratio_mapped))
elif not state.results.done():
text += "..."
else:
text += "<Error {}>".format(str(state.results.exception()))
self.infoBox.setText(text)
# TODO: warn on no enriched sets found (i.e no query genes
# mapped to any set)
def filterAnnotationsChartView(self, filterString=""):
if self.__state & OWSetEnrichment.RunningEnrichment:
return
# TODO: Move filtering to a filter proxy model
# TODO: Re-enable string search
categories = set(", ".join(cat)
for cat, _ in self.selectedCategories())
# filterString = str(self.filterLineEdit.text()).lower()
model = self.annotationsChartView.model()
def ishidden(index):
# Is item at index (row) hidden
item = model.item(index)
item_cat = item.data(Qt.DisplayRole)
return item_cat not in categories
hidemask = [ishidden(i) for i in range(model.rowCount())]
# compute FDR according the selected categories
pvals = [
model.item(i, 4).data(Qt.UserRole)
for i, hidden in enumerate(hidemask) if not hidden
]
fdrs = utils.stats.FDR(pvals)
# update FDR for the selected collections and apply filtering rules
itemsHidden = []
fdriter = iter(fdrs)
for index, hidden in enumerate(hidemask):
if not hidden:
fdr = next(fdriter)
pval = model.index(index, 4).data(Qt.UserRole)
count = model.index(index, 2).data(Qt.ToolTipRole)
hidden = (self.useMinCountFilter and count < self.minClusterCount) or \
(self.useMaxPValFilter and pval > self.maxPValue) or \
(self.useMaxFDRFilter and fdr > self.maxFDR)
if not hidden:
fdr_item = model.item(index, 5)
fdr_item.setData(fmtpdet(fdr), Qt.ToolTipRole)
fdr_item.setData(fmtp(fdr), Qt.DisplayRole)
fdr_item.setData(fdr, Qt.UserRole)
self.annotationsChartView.setRowHidden(index, QModelIndex(),
hidden)
itemsHidden.append(hidden)
if model.rowCount() and all(itemsHidden):
self.information(0, "All sets were filtered out.")
else:
self.information(0)
self._updatesummary()
@Slot(float)
def _setProgress(self, value):
assert QThread.currentThread() is self.thread()
self.progressBarSet(value, processEvents=None)
@Slot(str)
def _setRunInfo(self, text):
self.setStatusMessage(text)
def commit(self):
if self.data is None or \
self.__state & OWSetEnrichment.RunningEnrichment:
return
model = self.annotationsChartView.model()
rows = self.annotationsChartView.selectionModel().selectedRows(0)
selected = [model.item(index.row(), 0) for index in rows]
mapped = reduce(operator.ior, (set(item.enrichment.query_mapped)
for item in selected), set())
assert self.state.namematcher.done()
matcher = self.state.namematcher.result()
axis = 1 if self.genesinrows else 0
if axis == 1:
mapped = [
attr for attr in self.data.domain.attributes
if matcher.umatch(attr.name) in mapped
]
newdomain = Orange.data.Domain(mapped, self.data.domain.class_vars,
self.data.domain.metas)
data = self.data.from_table(newdomain, self.data)
else:
geneattr = self.geneAttrs[self.geneattr]
selected = [
i for i, ex in enumerate(self.data)
if matcher.umatch(str(ex[geneattr])) in mapped
]
data = self.data[selected]
self.send("Data subset", data)
def onDeleteWidget(self):
if self.state is not None:
self._cancelPending()
self.state = None
self._executor.shutdown(wait=False)
def __init__(self):
super().__init__()
#: widget's runtime state
self.__state = State.NoState
self.corpus = None
self.n_text_categories = 0
self.n_text_data = 0
self.skipped_documents = []
self.__invalidated = False
self.__pendingTask = None
layout = QGridLayout()
layout.setSpacing(4)
gui.widgetBox(self.controlArea, orientation=layout, box='Source')
source_box = gui.radioButtons(None, self, "source", box=True,
callback=self.start, addToLayout=False)
rb_button = gui.appendRadioButton(source_box, "Folder:",
addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Fixed)
self.recent_cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=16,
acceptDrops=True
)
self.recent_cb.installEventFilter(self)
self.recent_cb.activated[int].connect(self.__onRecentActivated)
browseaction = QAction(
"Open/Load Documents", self,
iconText="\N{HORIZONTAL ELLIPSIS}",
icon=self.style().standardIcon(QStyle.SP_DirOpenIcon),
toolTip="Select a folder from which to load the documents"
)
browseaction.triggered.connect(self.__runOpenDialog)
reloadaction = QAction(
"Reload", self,
icon=self.style().standardIcon(QStyle.SP_BrowserReload),
toolTip="Reload current document set"
)
reloadaction.triggered.connect(self.reload)
self.__actions = namespace(
browse=browseaction,
reload=reloadaction,
)
browsebutton = QPushButton(
browseaction.iconText(),
icon=browseaction.icon(),
toolTip=browseaction.toolTip(),
clicked=browseaction.trigger,
default=False,
autoDefault=False,
)
reloadbutton = QPushButton(
reloadaction.iconText(),
icon=reloadaction.icon(),
clicked=reloadaction.trigger,
default=False,
autoDefault=False,
)
box.layout().addWidget(self.recent_cb)
layout.addWidget(box, 0, 1)
layout.addWidget(browsebutton, 0, 2)
layout.addWidget(reloadbutton, 0, 3)
rb_button = gui.appendRadioButton(source_box, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = PyListModel()
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Fixed)
url_combo.setEditable(True)
url_combo.setInsertPolicy(url_combo.InsertAtTop)
url_edit = url_combo.lineEdit()
l, t, r, b = url_edit.getTextMargins()
url_edit.setTextMargins(l + 5, t, r, b)
layout.addWidget(url_combo, 3, 1, 1, 3)
url_combo.activated.connect(self._url_set)
# whit completer we set that combo box is case sensitive when
# matching the history
completer = QCompleter()
completer.setCaseSensitivity(Qt.CaseSensitive)
url_combo.setCompleter(completer)
self.addActions([browseaction, reloadaction])
reloadaction.changed.connect(
lambda: reloadbutton.setEnabled(reloadaction.isEnabled())
)
box = gui.vBox(self.controlArea, "Info")
self.infostack = QStackedWidget()
self.info_area = QLabel(
text="No document set selected",
wordWrap=True
)
self.progress_widget = QProgressBar(
minimum=0, maximum=100
)
self.cancel_button = QPushButton(
"Cancel",
icon=self.style().standardIcon(QStyle.SP_DialogCancelButton),
default=False,
autoDefault=False,
)
self.cancel_button.clicked.connect(self.cancel)
w = QWidget()
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.addWidget(self.progress_widget)
hlayout.addWidget(self.cancel_button)
vlayout.addLayout(hlayout)
self.pathlabel = TextLabel()
self.pathlabel.setTextElideMode(Qt.ElideMiddle)
self.pathlabel.setAttribute(Qt.WA_MacSmallSize)
vlayout.addWidget(self.pathlabel)
w.setLayout(vlayout)
self.infostack.addWidget(self.info_area)
self.infostack.addWidget(w)
box.layout().addWidget(self.infostack)
self.__initRecentItemsModel()
self.__invalidated = True
self.__executor = ThreadExecutor(self)
QApplication.postEvent(self, QEvent(RuntimeEvent.Init))
