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 _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]
import Orange
from orangecontrib.bio import dicty, geneset, gsea, gene
dbc = dicty.DictyExpress()
data = dbc.get_data(sample='pkaC-', time="8")
#select the first chip (the first attribute)
data = data.translate([data.domain.attributes[0]], True)
matcher = gene.matcher([[gene.GMKEGG("dicty"), gene.GMDicty()]])
genesets = geneset.collections((("KEGG",), "dicty"))
res = gsea.direct(data, matcher=matcher, min_part=0.05,
gene_sets=genesets)
print "%-40s %6s %6s %6s %7s" % ("LABEL", "NES", "P-VAL", "SIZE", "MATCHED")
for name,resu in sorted(res.items()[:10], key=lambda x: x[1]["p"]):
print "%-40s %6.3f %6.3f %6d %7d" % (name.name[:35], resu["nes"],
resu["p"], resu["size"], resu["matched_size"])
def create():
return gene.matcher([m(taxid) for m in matchers])
def _invalidateGeneMatcher(self):
_, f = self.__genematcher
f.cancel()
self.__genematcher = (None, fulfill(gene.matcher([])))
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 = QtGui.QTreeWidget(self)
self.groupsWidget.setHeaderLabels(["Category"])
box.layout().addWidget(self.groupsWidget)
hLayout = QtGui.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 = QtGui.QLineEdit(
self, placeholderText="Filter ...")
self.filterCompleter = QtGui.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 = QtGui.QTreeView(
alternatingRowColors=True,
sortingEnabled=True,
selectionMode=QtGui.QTreeView.ExtendedSelection,
rootIsDecorated=False,
editTriggers=QtGui.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", "ncbi_taxonomy.tar.gz"),
(geneset.sfdomain, "index.pck")]
)
task.finished.connect(self.__initialize_finish)
self.setStatusMessage("Initializing")
self._executor = ThreadExecutor(
parent=self, threadPool=QtCore.QThreadPool(self))
self._executor.submit(task)
def create():
return gene.matcher([m(taxid) for m in matchers])
def _invalidateGeneMatcher(self):
_, f = self.__genematcher
f.cancel()
self.__genematcher = (None, fulfill(gene.matcher([])))
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)
import Orange
from orangecontrib.bio import dicty, geneset, gsea, gene, geo
gds = geo.GDS("GDS10")
data = gds.getdata(transpose=True)
matcher = gene.matcher([gene.GMKEGG("H**o sapiens")])
genesets = geneset.collections((("KEGG", ), "H**o sapiens"))
#the number of permutations (n) should be much higher
res = gsea.run(data,
gene_sets=genesets,
matcher=matcher,
min_part=0.05,
permutation="phenotype",
n=10,
phen_desc=data.domain["tissue"],
gene_desc=True)
print
print "GSEA results (descriptor: tissue)"
print "%-40s %6s %6s %6s %7s" % ("LABEL", "NES", "FDR", "SIZE", "MATCHED")
for gs, resu in sorted(res.items(), key=lambda x: x[1]["fdr"])[:10]:
print "%-40s %6.3f %6.3f %6d %7d" % (gs.name[:30], resu["nes"],
resu["fdr"], resu["size"],
resu["matched_size"])
import Orange
from orangecontrib.bio import dicty, geneset, gsea, gene, geo
gds = geo.GDS("GDS10")
data = gds.getdata()
matcher = gene.matcher([gene.GMKEGG("H**o sapiens")])
genesets = geneset.collections((("KEGG",), "H**o sapiens"))
#the number of permutations (n) should be much higher
res = gsea.run(data, gene_sets=genesets, matcher=matcher,
min_part=0.05, permutation="phenotype", n=10,
phen_desc="tissue", gene_desc="gene")
print
print "GSEA results (descriptor: tissue)"
print "%-40s %6s %6s %6s %7s" % ("LABEL", "NES", "FDR", "SIZE", "MATCHED")
for gs, resu in sorted(res.items(), key=lambda x: x[1]["fdr"])[:10]:
print "%-40s %6.3f %6.3f %6d %7d" % (gs.name[:30],
resu["nes"], resu["fdr"], resu["size"], resu["matched_size"])
