def set_data(self, data):
"""
Set the input profile dataset.
"""
self.closeContext()
self.clear()
self.data = data
if data is not None:
if is_discrete(data.domain.class_var):
class_vals = data.domain.class_var.values
else:
class_vals = []
self.classes = list(class_vals)
self.class_colors = colorpalette.ColorPaletteGenerator(len(class_vals))
self.selected_classes = list(range(len(class_vals)))
for i in range(len(class_vals)):
item = self.group_listbox.item(i)
item.setIcon(colorpalette.ColorPixmap(self.class_colors[i]))
variables = data.domain.variables + data.domain.metas
annotvars = [var for var in variables if is_discrete(var) or is_string(var)]
for var in annotvars:
self.annot_cb.addItem(*gui.attributeItem(var))
if data.domain.class_var in annotvars:
self.annot_index = annotvars.index(data.domain.class_var)
self.annotation_variables = annotvars
self.openContext(data)
self._setup_plot()
self.commit()
def set_data(self, data):
"""
Set the input profile dataset.
"""
self.closeContext()
self.clear()
self.data = data
if data is not None:
n_instances = len(data)
n_attrs = len(data.domain.attributes)
self.infoLabel.setText("%i instances on input\n%i attributes" % (n_instances, n_attrs))
annotvars = [var for var in data.domain.variables + data.domain.metas if is_discrete(var) or is_string(var)]
for var in annotvars:
self.annot_cb.addItem(*gui.attributeItem(var))
if data.domain.class_var in annotvars:
self.annot_index = annotvars.index(data.domain.class_var)
self.annotation_variables = annotvars
self.graph_variables = [var for var in data.domain.attributes if var.is_continuous]
groupvars = [var for var in data.domain.variables + data.domain.metas if is_discrete(var)]
if len(groupvars) > 0:
self.cb_attr.addItems([str(var) for var in groupvars])
self.group_var = str(groupvars[0])
self.group_variables = groupvars
self.update_group_var()
self.openContext(data)
self.commit()
def setData(self, data=None):
if not self.__initialized:
self.initfuture.result()
self.initialize()
if self.itemsfuture is not None:
raise Exception("Already processing")
self.data = data
if data is not None:
self.geneAttrComboBox.clear()
self.attributes = [
attr for attr in data.domain.variables + data.domain.metas
if isinstance(attr, (Orange.data.StringVariable,
Orange.data.DiscreteVariable))
]
for var in self.attributes:
self.geneAttrComboBox.addItem(*gui.attributeItem(var))
self.taxid = str(self.data.attributes.get(TAX_ID, ''))
self.useAttr = self.data.attributes.get(GENE_AS_ATTRIBUTE_NAME,
self.useAttr)
self.gene_attr = min(self.gene_attr, len(self.attributes) - 1)
if self.taxid in self.organisms:
self.organism_index = self.organisms.index(self.taxid)
self.updateInfoItems()
else:
self.clear()
def setData(self, data=None):
if not self.__initialized:
self.initfuture.result()
self.initialize()
if self.itemsfuture is not None:
raise Exception("Already processing")
self.closeContext()
self.data = data
if data is not None:
self.geneAttrComboBox.clear()
self.attributes = \
[attr for attr in data.domain.variables + data.domain.metas
if isinstance(attr, (Orange.data.StringVariable,
Orange.data.DiscreteVariable))]
for var in self.attributes:
self.geneAttrComboBox.addItem(*gui.attributeItem(var))
self.taxid = data_hints.get_hint(self.data, "taxid", self.taxid)
self.useAttr = data_hints.get_hint(
self.data, "genesinrows", self.useAttr)
self.openContext(data)
self.gene_attr = min(self.gene_attr, len(self.attributes) - 1)
if self.taxid in self.organisms:
self.organism_index = self.organisms.index(self.taxid)
self.updateInfoItems()
else:
self.clear()
def add_row(self, attr=None, condition_type=None, condition_value=None):
model = self.cond_list.model()
row = model.rowCount()
model.insertRow(row)
attr_combo = gui.OrangeComboBox(
minimumContentsLength=12,
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon)
attr_combo.row = row
for var in self._visible_variables(self.data.domain):
attr_combo.addItem(*gui.attributeItem(var))
attr_combo.setCurrentIndex(attr or 0)
self.cond_list.setCellWidget(row, 0, attr_combo)
index = QPersistentModelIndex(model.index(row, 3))
temp_button = QPushButton(
'×',
self,
flat=True,
styleSheet='* {font-size: 16pt; color: silver}'
'*:hover {color: black}')
temp_button.clicked.connect(lambda: self.remove_one(index.row()))
self.cond_list.setCellWidget(row, 3, temp_button)
self.remove_all_button.setDisabled(False)
self.set_new_operators(attr_combo, attr is not None, condition_type,
condition_value)
attr_combo.currentIndexChanged.connect(
lambda _: self.set_new_operators(attr_combo, False))
self.cond_list.resizeRowToContents(row)
def add_row(self, attr=None, condition_type=None, condition_value=None):
model = self.cond_list.model()
row = model.rowCount()
model.insertRow(row)
attr_combo = gui.OrangeComboBox(
minimumContentsLength=12,
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon)
attr_combo.row = row
for var in self._visible_variables(self.data.domain):
attr_combo.addItem(*gui.attributeItem(var))
attr_combo.setCurrentIndex(attr or 0)
self.cond_list.setCellWidget(row, 0, attr_combo)
index = QPersistentModelIndex(model.index(row, 3))
temp_button = QPushButton('×', self, flat=True,
styleSheet='* {font-size: 16pt; color: silver}'
'*:hover {color: black}')
temp_button.clicked.connect(lambda: self.remove_one(index.row()))
self.cond_list.setCellWidget(row, 3, temp_button)
self.remove_all_button.setDisabled(False)
self.set_new_operators(attr_combo, attr is not None,
condition_type, condition_value)
attr_combo.currentIndexChanged.connect(
lambda _: self.set_new_operators(attr_combo, False))
self.cond_list.resizeRowToContents(row)
def standarditem_from_rowgroup(rowgroup):
item = QtGui.QStandardItem(rowgroup.name)
icon, _ = gui.attributeItem(rowgroup.var)
item.setIcon(icon)
item.setToolTip(guiutils.variable_tooltip(rowgroup.var))
item.setData(rowgroup, Qt.UserRole)
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
children = [guiutils.standarditem_from(val) for val in rowgroup.values]
item.appendRows(children)
return item
def standarditem_from_rowgroup(rowgroup):
item = QStandardItem(rowgroup.name)
icon, _ = gui.attributeItem(rowgroup.var)
item.setIcon(icon)
item.setToolTip(variable_tooltip(rowgroup.var))
item.setData(rowgroup, Qt.UserRole)
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
children = [standarditem_from(val) for val in rowgroup.values]
item.appendRows(children)
return item
def add_row(self, attr=None):
model = self.cond_list.model()
row = model.rowCount()
model.insertRow(row)
attr_combo = QtGui.QComboBox()
attr_combo.row = row
attr_combo.setStyleSheet("border: none")
for var in chain(self.data.domain.variables, self.data.domain.metas):
attr_combo.addItem(*gui.attributeItem(var))
attr_combo.setCurrentIndex(attr or 0)
self.cond_list.setCellWidget(row, 0, attr_combo)
self.remove_all_button.setDisabled(False)
self.set_new_operators(attr_combo, attr is not None)
attr_combo.currentIndexChanged.connect(
lambda _: self.set_new_operators(attr_combo, False))
def setDataset(self, data=None):
if self.__state == OWGOEnrichmentAnalysis.Initializing:
self.__initialize_finish()
self.closeContext()
self.clear()
self.clusterDataset = data
if data is not None:
domain = data.domain
allvars = domain.variables + domain.metas
self.candidateGeneAttrs = [var for var in allvars if isstring(var)]
self.geneAttrIndexCombo.clear()
for var in self.candidateGeneAttrs:
self.geneAttrIndexCombo.addItem(*gui.attributeItem(var))
taxid = data_hints.get_hint(data, "taxid", "")
code = None
try:
code = go.from_taxid(taxid)
except KeyError:
pass
except Exception as ex:
print(ex)
if code is not None:
filename = "gene_association.%s.tar.gz" % code
if filename in self.annotationFiles.values():
self.annotationIndex = \
[i for i, name in enumerate(self.annotationCodes) \
if self.annotationFiles[name] == filename].pop()
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.candidateGeneAttrs) - 1)
if len(self.candidateGeneAttrs) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
elif self.geneAttrIndex < len(self.candidateGeneAttrs):
self.geneAttrIndex = len(self.candidateGeneAttrs) - 1
self._updateEnrichment()
def set_data(self, data):
"""
Set the input profile dataset.
"""
self.closeContext()
self.clear()
self.clear_legend()
self.data = data
if data is not None:
n_instances = len(data)
n_attrs = len(data.domain.attributes)
self.infoLabel.setText("%i genes on input\n%i attributes" %
(n_instances, n_attrs))
if is_discrete(data.domain.class_var):
class_vals = data.domain.class_var.values
else:
class_vals = []
self.classes = list(class_vals)
self.class_colors = \
colorpalette.ColorPaletteGenerator(len(class_vals))
self.selected_classes = list(range(len(class_vals)))
for i in range(len(class_vals)):
item = self.group_listbox.item(i)
item.setIcon(colorpalette.ColorPixmap(self.class_colors[i]))
variables = data.domain.variables + data.domain.metas
annotvars = [
var for var in variables if is_discrete(var) or is_string(var)
]
for var in annotvars:
self.annot_cb.addItem(*gui.attributeItem(var))
if data.domain.class_var in annotvars:
self.annot_index = annotvars.index(data.domain.class_var)
self.annotation_variables = annotvars
self.openContext(data)
if n_attrs:
self._setup_plot()
self.commit()
def setDataset(self, data=None):
if self.__state == OWGOEnrichmentAnalysis.Initializing:
self.__initialize_finish()
self.closeContext()
self.clear()
self.clusterDataset = data
if data is not None:
domain = data.domain
allvars = domain.variables + domain.metas
self.candidateGeneAttrs = [var for var in allvars if isstring(var)]
self.geneAttrIndexCombo.clear()
for var in self.candidateGeneAttrs:
self.geneAttrIndexCombo.addItem(*gui.attributeItem(var))
taxid = data_hints.get_hint(data, "taxid", "")
code = None
try:
code = go.from_taxid(taxid)
except KeyError:
pass
except Exception as ex:
print(ex)
if code is not None:
filename = "gene_association.%s.tar.gz" % code
if filename in self.annotationFiles.values():
self.annotationIndex = \
[i for i, name in enumerate(self.annotationCodes) \
if self.annotationFiles[name] == filename].pop()
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.candidateGeneAttrs) - 1)
if len(self.candidateGeneAttrs) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
elif self.geneAttrIndex < len(self.candidateGeneAttrs):
self.geneAttrIndex = len(self.candidateGeneAttrs) - 1
self._updateEnrichment()
def add_row(self, attr=None, condition_type=None, condition_value=None):
model = self.cond_list.model()
row = model.rowCount()
model.insertRow(row)
attr_combo = QtGui.QComboBox()
attr_combo.row = row
for var in chain(self.data.domain.variables, self.data.domain.metas):
attr_combo.addItem(*gui.attributeItem(var))
attr_combo.setCurrentIndex(attr or 0)
self.cond_list.setCellWidget(row, 0, attr_combo)
self.remove_all_button.setDisabled(False)
self.set_new_operators(attr_combo, attr is not None, condition_type,
condition_value)
attr_combo.currentIndexChanged.connect(
lambda _: self.set_new_operators(attr_combo, False))
self.cond_list.resizeRowToContents(row)
def setDataset(self, data=None):
self.closeContext()
self.clear()
self.clusterDataset = data
if data is not None:
domain = data.domain
allvars = domain.variables + domain.metas
self.candidateGeneAttrs = [var for var in allvars if isstring(var)]
self.geneAttrIndexCombo.clear()
for var in self.candidateGeneAttrs:
self.geneAttrIndexCombo.addItem(*gui.attributeItem(var))
taxid = data_hints.get_hint(data, "taxid", "")
try:
code = go.from_taxid(taxid)
except KeyError:
pass
else:
_c2i = {
a.orgcode: i
for i, a in enumerate(self.availableAnnotations)
}
try:
self.annotationIndex = _c2i[code]
except KeyError:
pass
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.candidateGeneAttrs) - 1)
if len(self.candidateGeneAttrs) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
elif self.geneAttrIndex < len(self.candidateGeneAttrs):
self.geneAttrIndex = len(self.candidateGeneAttrs) - 1
self.__invalidate()
def add_row(self, attr=None, condition_type=None, condition_value=None):
model = self.cond_list.model()
row = model.rowCount()
model.insertRow(row)
attr_combo = QtGui.QComboBox(
minimumContentsLength=12,
sizeAdjustPolicy=QtGui.QComboBox.AdjustToMinimumContentsLengthWithIcon)
attr_combo.row = row
for var in chain(self.data.domain.variables, self.data.domain.metas):
attr_combo.addItem(*gui.attributeItem(var))
attr_combo.setCurrentIndex(attr or 0)
self.cond_list.setCellWidget(row, 0, attr_combo)
self.remove_all_button.setDisabled(False)
self.set_new_operators(attr_combo, attr is not None,
condition_type, condition_value)
attr_combo.currentIndexChanged.connect(
lambda _: self.set_new_operators(attr_combo, False))
self.cond_list.resizeRowToContents(row)
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 setDataset(self, data=None):
self.closeContext()
self.clear()
self.clusterDataset = data
if data is not None:
domain = data.domain
allvars = domain.variables + domain.metas
self.candidateGeneAttrs = [var for var in allvars if isstring(var)]
self.geneAttrIndexCombo.clear()
for var in self.candidateGeneAttrs:
self.geneAttrIndexCombo.addItem(*gui.attributeItem(var))
taxid = data_hints.get_hint(data, "taxid", "")
try:
code = go.from_taxid(taxid)
except KeyError:
pass
else:
_c2i = {a.orgcode: i
for i, a in enumerate(self.availableAnnotations)}
try:
self.annotationIndex = _c2i[code]
except KeyError:
pass
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.candidateGeneAttrs) - 1)
if len(self.candidateGeneAttrs) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
elif self.geneAttrIndex < len(self.candidateGeneAttrs):
self.geneAttrIndex = len(self.candidateGeneAttrs) - 1
self.__invalidate()
def setData(self, data=None):
"""Set the input dataset with query gene names"""
if self.__state & OWSetEnrichment.Initializing:
self.__initialize_finish()
self.Error.clear()
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 setDataset(self, data=None):
self.closeContext()
self.clear()
self.clusterDataset = data
if data is not None:
domain = data.domain
allvars = domain.variables + domain.metas
self.candidateGeneAttrs = [var for var in allvars if isstring(var)]
self.geneAttrIndexCombo.clear()
for var in self.candidateGeneAttrs:
self.geneAttrIndexCombo.addItem(*gui.attributeItem(var))
tax_id = data_hints.get_hint(data, TAX_ID, '')
if tax_id is not None:
_c2i = {
a.taxid: i
for i, a in enumerate(self.availableAnnotations)
}
try:
self.annotationIndex = _c2i[tax_id]
except KeyError:
pass
self.useAttrNames = data_hints.get_hint(data,
GENE_NAME,
default=self.useAttrNames)
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.candidateGeneAttrs) - 1)
if len(self.candidateGeneAttrs) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
elif self.geneAttrIndex < len(self.candidateGeneAttrs):
self.geneAttrIndex = len(self.candidateGeneAttrs) - 1
self.__invalidate()
def setData(self, data=None):
if not self.__initialized:
self.initfuture.result()
self.initialize()
if self.itemsfuture is not None:
raise Exception("Already processing")
self.closeContext()
self.data = data
if data is not None:
self.geneAttrComboBox.clear()
self.attributes = \
[attr for attr in data.domain.variables + data.domain.metas
if isinstance(attr, (Orange.data.StringVariable,
Orange.data.DiscreteVariable))]
for var in self.attributes:
self.geneAttrComboBox.addItem(*gui.attributeItem(var))
self.taxid = data_hints.get_hint(self.data, "taxid", self.taxid)
self.useAttr = data_hints.get_hint(self.data, "genesinrows",
self.useAttr)
self.openContext(data)
self.gene_attr = min(self.gene_attr, len(self.attributes) - 1)
if self.taxid in self.organisms:
self.organism_index = self.organisms.index(self.taxid)
else:
self.organism_index = 0
self.taxid = self.organisms[self.organism_index]
self.updateInfoItems()
else:
self.clear()
def handle_input(self, data):
if data:
self.input_data = data
self.gene_matcher = gene.GeneMatcher(self._get_selected_organism())
self.gene_column_combobox.clear()
self.column_candidates = [
attr for attr in data.domain.variables + data.domain.metas
if isinstance(attr, (StringVariable, DiscreteVariable))
]
for var in self.column_candidates:
self.gene_column_combobox.addItem(*attributeItem(var))
self.tax_id = str(data_hints.get_hint(self.input_data, TAX_ID))
self.use_attr_names = data_hints.get_hint(
self.input_data, GENE_NAME, default=self.use_attr_names)
self.gene_col_index = min(self.gene_col_index,
len(self.column_candidates) - 1)
if self.tax_id in self.organisms:
self.selected_organism = self.organisms.index(self.tax_id)
self.on_input_option_change()
def handle_input(self, data):
if data:
self.input_data = data
self.gene_column_combobox.clear()
self.column_candidates = [
attr for attr in data.domain.variables + data.domain.metas
if isinstance(attr, (StringVariable, DiscreteVariable))
]
for var in self.column_candidates:
self.gene_column_combobox.addItem(*attributeItem(var))
self.tax_id = str(self.input_data.attributes.get(TAX_ID, ''))
self.use_attr_names = self.input_data.attributes.get(
GENE_AS_ATTRIBUTE_NAME, self.use_attr_names)
self.gene_col_index = min(self.gene_col_index,
len(self.column_candidates) - 1)
if self.tax_id in self.organisms:
self.selected_organism = self.organisms.index(self.tax_id)
self.on_input_option_change()
def standarditem_from_var(var):
item = QtGui.QStandardItem(var.name)
_, icon = _gui.attributeItem(var)
item.setIcon(icon)
item.setToolTip(itemmodels.Variable)
def standarditem_from_var(var):
item = QtGui.QStandardItem(var.name)
_, icon = _gui.attributeItem(var)
item.setIcon(icon)
item.setToolTip(itemmodels.Variable)