def __init__(self, parent=None, signalManager = None, name='GSEA'):
OWWidget.__init__(self, parent, signalManager, name)
self.inputs = [("Examples", ExampleTable, self.setData)]
self.outputs = [("Examples with selected genes only", ExampleTable), ("Results", ExampleTable), ("Distance Matrix", orange.SymMatrix) ]
self.res = None
self.dm = None
self.name = 'GSEA'
self.minSubsetSize = 3
self.minSubsetSizeC = True
self.maxSubsetSize = 1000
self.maxSubsetSizeC = True
self.minSubsetPart = 10
self.minSubsetPartC = True
self.perms = 100
self.csgm = False
self.gsgo = False
self.gskegg = False
self.buildDistances = False
self.selectedPhenVar = 0
self.organismIndex = 0
self.atLeast = 3
self.permutationTypes = [("Phenotype", "p"),("Gene", "g") ]
self.ptype = 0
self.correlationTypes = [ ("Signal2Noise", "s2n") ]
self.ctype = 0
self.data = None
self.geneSets = {}
self.tabs = OWGUI.tabWidget(self.controlArea)
ca = OWGUI.createTabPage(self.tabs, "Basic")
box = OWGUI.widgetBox(ca, 'Organism')
#FROM KEGG WIDGET - organism selection
self.organismTaxids = []
self.organismComboBox = cb = OWGUI.comboBox(box, self, "organismIndex", items=[], debuggingEnabled=0) #changed
cb.setMaximumWidth(200)
#OWGUI.checkBox(box, self, "csgm", "Case sensitive gene matching")
box2 = OWGUI.widgetBox(ca, "Descriptors")
self.phenCombo = OWGUI.comboBox(box2, self, "selectedPhenVar", items=[], callback=self.phenComboChange, label="Phenotype:")
self.geneCombo = OWGUI.comboBox(box2, self, "selectedGeneVar", items=[], label = "Gene:")
self.allowComboChangeCallback = False
ma = self.mainArea
self.listView = QTreeWidget(ma)
ma.layout().addWidget(self.listView)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(9)
self.listView.setHeaderLabels(["Collection", "Geneset", "NES", "ES", "P-value", "FDR", "Size", "Matched Size", "Genes"])
self.listView.header().setStretchLastSection(True)
self.listView.header().setClickable(True)
self.listView.header().setSortIndicatorShown(True)
self.listView.setSortingEnabled(True)
#self.listView.header().setResizeMode(0, QHeaderView.Stretch)
self.listView.setSelectionMode(QAbstractItemView.NoSelection)
self.connect(self.listView, SIGNAL("itemSelectionChanged()"), self.newPathwaySelected)
OWGUI.separator(ca)
OWGUI.widgetLabel(ca, "Phenotype selection:")
self.psel = PhenotypesSelection(ca)
self.resize(600,50)
OWGUI.separator(ca)
OWGUI.checkBox(ca, self, "buildDistances", "Compute geneset distances")
self.btnApply = OWGUI.button(ca, self, "&Compute", callback = self.compute, disabled=0)
fileBox = OWGUI.widgetBox(ca, orientation='horizontal')
OWGUI.button(fileBox, self, "Load", callback = self.loadData, disabled=0, debuggingEnabled=0)
OWGUI.button(fileBox, self, "Save", callback = self.saveData, disabled=0, debuggingEnabled=0)
#ca.layout().addStretch(1)
ca = OWGUI.createTabPage(self.tabs, "Gene sets")
box = OWGUI.widgetBox(ca)
self.gridSel = []
self.geneSel = [] #FIXME temporary disabled - use the same as in new "David" widget
self.lbgs = OWGUI.listBox(box, self, "gridSel", "geneSel", selectionMode = QListWidget.MultiSelection)
OWGUI.button(box, self, "From &File", callback = self.addCollection, disabled=0, debuggingEnabled=0)
box = OWGUI.widgetBox(box, "Additional sources:")
OWGUI.checkBox(box, self, "gskegg", "KEGG pathways")
OWGUI.checkBox(box, self, "gsgo", "GO terms")
#ca.layout().addStretch(1)
ca = OWGUI.createTabPage(self.tabs, "Settings")
box = OWGUI.widgetBox(ca, 'Properties')
self.permTypeF = OWGUI.comboBoxWithCaption(box, self, "ptype", items=nth(self.permutationTypes, 0), \
tooltip="Permutation type.", label="Permute")
_ = OWGUI.spin(box, self, "perms", 50, 1000, orientation="horizontal", label="Times")
self.corTypeF = OWGUI.comboBoxWithCaption(box, self, "ctype", items=nth(self.correlationTypes, 0), \
tooltip="Correlation type.", label="Correlation")
box = OWGUI.widgetBox(ca, 'Subset Filtering')
_,_ = OWGUI.checkWithSpin(box, self, "Min. Subset Size", 1, 10000, "minSubsetSizeC", "minSubsetSize", "") #TODO check sizes
_,_ = OWGUI.checkWithSpin(box, self, "Max. Subset Size", 1, 10000, "maxSubsetSizeC", "maxSubsetSize", "")
_,_ = OWGUI.checkWithSpin(box, self, "Min. Subset Part (%)", 1, 100, "minSubsetPartC", "minSubsetPart", "")
box = OWGUI.widgetBox(ca, 'Gene Filtering')
_ = OWGUI.spin(box, self, "atLeast", 2, 10, label="Min. Values in Group")
ca.layout().addStretch(1)
self.addComment("Computation was not started.")
if sys.platform == "darwin":
self.loadFileName = os.path.expanduser("~/")
else:
self.loadFileName = "."
self.gridSels = []
self.loadSettings()
self.setBlocking(True)
QTimer.singleShot(0, self.UpdateOrganismComboBox)
def cleanInvalid(maxn):
"""
Removes invalid gene set selection
"""
notAllOk = True
while notAllOk:
self.gridSels = getattr(self, "gridSels")
notAllOk = False
for i,a in enumerate(self.gridSels):
if a >= maxn:
self.gridSels.pop(i)
notAllOk = True
break
cleanInvalid(len(self.geneSel))
self.gridSel = self.gridSels
self.gridSels = self.gridSel
