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 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(data_hints.get_hint(self.data, TAX_ID))
self.useAttr = data_hints.get_hint(self.data,
GENE_NAME,
default=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 self.__runstate == OWKEGGPathwayBrowser.Initializing:
self.__initialize_finish()
self.closeContext()
self.data = data
self.warning(0)
self.error(0)
self.information(0)
if data is not None:
vars = data.domain.variables + data.domain.metas
vars = [
var for var in vars
if isinstance(var, Orange.data.StringVariable)
]
self.geneAttrCandidates[:] = vars
# Try to guess the gene name variable
if vars:
names_lower = [v.name.lower() for v in vars]
scores = [(name == "gene", "gene" in name)
for name in names_lower]
imax, _ = max(enumerate(scores), key=itemgetter(1))
else:
imax = -1
self.geneAttrIndex = imax
taxid = data_hints.get_hint(data, "taxid", None)
if taxid:
try:
code = kegg.from_taxid(taxid)
self.organismIndex = self.organismCodes.index(code)
except Exception as ex:
print(ex, taxid)
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
if len(self.geneAttrCandidates) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
else:
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.geneAttrCandidates) - 1)
else:
self.Clear()
self.__invalidated = True
def SetData(self, data=None):
if self.__runstate == OWKEGGPathwayBrowser.Initializing:
self.__initialize_finish()
self.closeContext()
self.data = data
self.warning(0)
self.error(0)
self.information(0)
if data is not None:
vars = data.domain.variables + data.domain.metas
vars = [var for var in vars
if isinstance(var, Orange.data.StringVariable)]
self.geneAttrCandidates[:] = vars
# Try to guess the gene name variable
if vars:
names_lower = [v.name.lower() for v in vars]
scores = [(name == "gene", "gene" in name)
for name in names_lower]
imax, _ = max(enumerate(scores), key=itemgetter(1))
else:
imax = -1
self.geneAttrIndex = imax
taxid = data_hints.get_hint(data, "taxid", None)
if taxid:
try:
code = kegg.from_taxid(taxid)
self.organismIndex = self.organismCodes.index(code)
except Exception as ex:
print(ex, taxid)
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
if len(self.geneAttrCandidates) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
else:
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.geneAttrCandidates) - 1)
else:
self.Clear()
self.__invalidated = True
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 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):
self.closeContext()
self.clear()
self.error([0, 1])
self.data = data
if self.data is not None:
self.initialize(data)
if self.data is not None and not self.targets:
# If both attr. labels and classes are missing, show an error
self.error(
1,
"Cannot compute gene scores! Differential expression "
"widget requires a data-set with a discrete class "
"variable(s) or column labels!",
)
self.data = None
if self.data is not None:
# Initialize the selected groups/labels.
# Default selected group key
index = 0
rowshint = data_hints.get_hint(data, GENE_AS_ATTRIBUTE_NAME, False)
if not rowshint:
# Select the first row group split candidate (if available)
indices = [
i for i, grp in enumerate(self.targets)
if isinstance(grp, guiutils.RowGroup)
]
if indices:
index = indices[0]
self.current_group_index = index
# Restore target label selection from context settings
items = {(grp.name, val)
for grp in self.targets for val in grp.values}
self.openContext(items)
# Restore current group / selection
model = self.label_selection_widget.model()
selection = [
model.index(i, 0, model.index(keyind, 0))
for keyind, selection in enumerate(self.stored_selections)
for i in selection
]
selection = guiutils.itemselection(selection)
self.label_selection_widget.setSelection(selection)
self.label_selection_widget.setCurrentGroupIndex(
self.current_group_index)
self.commit()
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(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 set_data(self, data):
self.closeContext()
self.data = data
if data is not None:
self.varmodel[:] = string_variables(data.domain)
taxid = data_hints.get_hint(data, "taxid", default=self.taxid)
if taxid in self.taxids:
self.set_organism(self.taxids.index(taxid))
self.use_attr_names = data_hints.get_hint(
data, "genesinrows", default=self.use_attr_names)
if not (0 <= self.gene_var_index < len(self.varmodel)):
self.gene_var_index = len(self.varmodel) - 1
self.openContext(data)
self.invalidate()
self.commit()
else:
self.varmodel[:] = []
self.send("Network", None)
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):
"""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 set_data(self, data=None):
self.closeContext()
self.clear()
self.data = data
self.error(0)
self.warning([0, 1])
if data is not None:
self.init_from_data()
if not self.targets:
self.error(0, "Data has no suitable defined groups/labels")
genesinrows = data_hints.get_hint(data, "genesinrows", True)
# Select the first RowGroup if genesinrows hint is False
if not genesinrows:
ind = [
i for i, grp in enumerate(self.targets)
if isinstance(grp, grouputils.RowGroup)
]
if ind:
self.current_group_index = ind[0]
else:
self.current_group_index = 0 if self.targets else -1
else:
self.current_group_index = 0
# TODO: Why does the current_group_index not get restored
self.openContext([(grp.name, v) for grp in self.targets
for v in grp.values])
model = self.target_widget.model()
# FIX: This assumes fixed target key/values order.
indices = [
model.index(i, 0, model.index(
keyind,
0,
)) for keyind, selected in enumerate(self.stored_selections)
for i in selected
]
selection = guiutils.itemselection(indices)
self.target_widget.setCurrentGroupIndex(self.current_group_index)
self.target_widget.setSelection(selection)
self.plot()
else:
self.infoLabel.setText("No data on input.")
self.unconditional_commit()
def set_data(self, data):
self.closeContext()
self.data = data
if data is not None:
self.varmodel[:] = string_variables(data.domain)
taxid = data_hints.get_hint(data, "taxid", default=self.taxid)
if taxid in self.taxids:
self.set_organism(self.taxids.index(taxid))
self.use_attr_names = data_hints.get_hint(
data, "genesinrows", default=self.use_attr_names
)
if not (0 <= self.gene_var_index < len(self.varmodel)):
self.gene_var_index = len(self.varmodel) - 1
self.openContext(data)
self.invalidate()
self.commit()
else:
self.varmodel[:] = []
self.send("Network", None)
def set_data(self, data):
self.closeContext()
self.clear()
self.error([0, 1])
self.data = data
if self.data is not None:
self.initialize(data)
if self.data is not None and not self.targets:
# If both attr. labels and classes are missing, show an error
self.error(
1, "Cannot compute gene scores! Differential expression "
"widget requires a data-set with a discrete class "
"variable(s) or attribute labels!"
)
self.data = None
if self.data is not None:
# Initialize the selected groups/labels.
# Default selected group key
index = 0
rowshint = data_hints.get_hint(data, "genesinrows", False)
if not rowshint:
# Select the first row group split candidate (if available)
indices = [i for i, grp in enumerate(self.targets)
if isinstance(grp, grouputils.RowGroup)]
if indices:
index = indices[0]
self.current_group_index = index
# Restore target label selection from context settings
items = {(grp.name, val)
for grp in self.targets for val in grp.values}
self.openContext(items)
# Restore current group / selection
model = self.label_selection_widget.model()
selection = [model.index(i, 0, model.index(keyind, 0))
for keyind, selection in enumerate(self.stored_selections)
for i in selection]
selection = guiutils.itemselection(selection)
self.label_selection_widget.setSelection(selection)
self.label_selection_widget.setCurrentGroupIndex(
self.current_group_index)
self.commit()
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 set_data(self, data=None):
self.closeContext()
self.clear()
self.data = data
self.error(0)
self.warning([0, 1])
if data is not None:
self.init_from_data()
if not self.targets:
self.error(0, "Data has no suitable defined groups/labels")
genesinrows = data_hints.get_hint(data, "genesinrows", True)
# Select the first RowGroup if genesinrows hint is False
if not genesinrows:
ind = [i for i, grp in enumerate(self.targets)
if isinstance(grp, grouputils.RowGroup)]
if ind:
self.current_group_index = ind[0]
else:
self.current_group_index = 0 if self.targets else -1
else:
self.current_group_index = 0
# TODO: Why does the current_group_index not get restored
self.openContext([(grp.name, v)
for grp in self.targets for v in grp.values])
model = self.target_widget.model()
# FIX: This assumes fixed target key/values order.
indices = [model.index(i, 0, model.index(keyind, 0,))
for keyind, selected in enumerate(self.stored_selections)
for i in selected]
selection = guiutils.itemselection(indices)
self.target_widget.setCurrentGroupIndex(self.current_group_index)
self.target_widget.setSelection(selection)
self.plot()
else:
self.infoLabel.setText("No data on input.")
self.unconditional_commit()
