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:
self.geneAttrComboBox.clear()
self.attributes = \
[attr for attr in (data.domain.variables +
data.domain.getmetas().values())
if isinstance(attr, (Orange.feature.String,
Orange.feature.Discrete))]
self.geneAttrComboBox.addItems(
[attr.name for attr in self.attributes])
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.geneAttr = min(self.geneAttr, len(self.attributes) - 1)
if self.taxid in self.organisms:
self.organismIndex = self.organisms.index(self.taxid)
self.updateInfoItems()
else:
self.clear()
def set_data(self, data):
self.closeContext("Data")
self.closeContext("TargetSelection")
self.error([0, 1])
self.warning(0)
self.clear()
self.genes_in_columns_check.setEnabled(True)
self.data = data
self.init_from_data(data)
if self.data:
self.genes_in_columns = not data_hints.get_hint(
data, "genesinrows", False)
self.openContext("Data", data)
# If only attr. labels or only class values then disable
# the 'Genes in columns' control
if not self.attribute_targets or not self.class_targets:
self.genes_in_columns_check.setEnabled(False)
self.genes_in_columns = bool(self.attribute_targets)
self.update_targets_widget()
if self.data is not None and \
not (self.attribute_targets or self.class_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 "
"or attribute labels!")
self.data = None
if self.data:
# Load context selection
items = [(label, v) for label, values in self.data_labels
for v in values]
self.target_selections = [
values[:1] for _, values in self.data_labels
]
label, values = self.data_labels[0]
self.current_target_selection = label, values[:
1] # Default selections
self.openContext("TargetSelection",
set(items)) # Load selections from context
self.label_selection_widget.set_selection(
*self.current_target_selection)
if not self.data:
self.send("Example table with selected genes", None)
self.send("Example table with remaining genes", None)
self.send("Selected genes", None)
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.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 SetData(self, data=None):
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.getmetas().values()
vars = [var for var in vars
if isinstance(var, (Orange.feature.String,
Orange.feature.Discrete))]
self.geneAttrCandidates[:] = vars
# Try to guess the gene name variable
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))
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)
else:
self.Clear()
self.has_new_data = True
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:
self.geneAttrComboBox.clear()
self.attributes = \
[attr for attr in (data.domain.variables +
data.domain.getmetas().values())
if isinstance(attr, (Orange.feature.String,
Orange.feature.Discrete))]
self.geneAttrComboBox.addItems(
[attr.name for attr in self.attributes]
)
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.geneAttr = min(self.geneAttr, len(self.attributes) - 1)
if self.taxid in self.organisms:
self.organismIndex = self.organisms.index(self.taxid)
self.updateInfoItems()
else:
self.clear()
def setData(self, data=None):
# self.closeContext("")
self.closeContext("targets")
self.clear()
self.data = data
self.error(0)
self.warning([0, 1])
if data:
self.genes_in_columns = not bool(data.domain.classVar)
self.genesInColumnsCheck.setDisabled(not bool(data.domain.classVar))
if self.genes_in_columns:
self.genes_in_columns = not data_hints.get_hint(data, "genesinrows", not self.genes_in_columns)
# self.openContext("", data)
else:
self.infoLabel.setText("No data on input.")
self.init_from_data()
def set_data(self, data):
self.closeContext("Data")
self.closeContext("TargetSelection")
self.error([0, 1])
self.warning(0)
self.clear()
self.genes_in_columns_check.setEnabled(True)
self.data = data
self.init_from_data(data)
if self.data:
self.genes_in_columns = not data_hints.get_hint(data, "genesinrows", False)
self.openContext("Data", data)
# If only attr. labels or only class values then disable
# the 'Genes in columns' control
if not self.attribute_targets or not self.class_targets:
self.genes_in_columns_check.setEnabled(False)
self.genes_in_columns = bool(self.attribute_targets)
self.update_targets_widget()
if self.data is not None and \
not (self.attribute_targets or self.class_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 "
"or attribute labels!")
self.data = None
if self.data:
# Load context selection
items = [(label, v) for label, values in self.data_labels for v in values]
self.target_selections = [values[:1] for _, values in self.data_labels]
label, values = self.data_labels[0]
self.current_target_selection = label, values[:1] # Default selections
self.openContext("TargetSelection", set(items)) # Load selections from context
self.label_selection_widget.set_selection(*self.current_target_selection)
if not self.data:
self.send("Example table with selected genes", None)
self.send("Example table with remaining genes", None)
self.send("Selected genes", None)
def setData(self, data):
self.allowComboChangeCallback = False
self.data = data
if data:
taxid = data_hints.get_hint(data, "taxid", None)
try:
self.organismIndex = self.organismTaxids.index(taxid)
except Exception, ex:
pass
if obiGsea.already_have_correlations(data):
#disable correlation type
comboboxItems(self.corTypeF, [])
self.corTypeF.setDisabled(True)
#set permutation type to fixed
self.ptype = 1
self.permTypeF.setDisabled(True)
else:
#enable correlation type
comboboxItems(self.corTypeF, nth(self.correlationTypes, 0))
self.corTypeF.setDisabled(False)
#allow change of permutation type
self.permTypeF.setDisabled(False)
#print "set classes"
self.phenCombo.clear()
self.phenCands = obiGsea.phenotype_cands(data)
self.phenCombo.addItems(map(lambda x: str(x[0]), self.phenCands))
self.phenCombo.setDisabled(len(self.phenCands) <= 1)
self.selectedPhenVar = 0
self.allowComboChangeCallback = True
self.phenComboChange()