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
def __init__(self,parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, "Nomogram", 1)
#self.setWFlags(Qt.WResizeNoErase | Qt.WRepaintNoErase) #this works like magic.. no flicker during repaint!
self.parent = parent
# self.setWFlags(self.getWFlags()+Qt.WStyle_Maximize)
self.callbackDeposit = [] # deposit for OWGUI callback functions
self.alignType = 0
self.contType = 0
self.yAxis = 0
self.probability = 0
self.verticalSpacing = 60
self.verticalSpacingContinuous = 100
self.diff_between_ordinal = 30
self.fontSize = 9
self.lineWidth = 1
self.histogram = 0
self.histogram_size = 10
self.data = None
self.cl = None
self.confidence_check = 0
self.confidence_percent = 95
self.sort_type = 0
self.loadSettings()
self.pointsName = ["Total", "Total"]
self.totalPointsName = ["Probability", "Probability"]
self.bnomogram = None
self.inputs=[("Classifier", orange.Classifier, self.classifier), ("Data", Orange.data.Table, self.data)]
self.TargetClassIndex = 0
self.targetCombo = OWGUI.comboBox(self.controlArea, self, "TargetClassIndex", " Target Class ", addSpace=True, tooltip='Select target (prediction) class in the model.', callback = self.setTarget)
self.alignRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'alignType', ['Align left', 'Align by zero influence'], box='Attribute placement',
tooltips=['Attributes in nomogram are left aligned', 'Attributes are not aligned, top scale represents true (normalized) regression coefficient value'],
addSpace=True,
callback=self.showNomogram)
self.verticalSpacingLabel = OWGUI.spin(self.alignRadio, self, 'verticalSpacing', 15, 200, label = 'Vertical spacing:', orientation = 0, tooltip='Define space (pixels) between adjacent attributes.', callback = self.showNomogram)
self.ContRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'contType', ['1D projection', '2D curve'], 'Continuous attributes',
tooltips=['Continuous attribute are presented on a single scale', 'Two dimensional space is used to present continuous attributes in nomogram.'],
addSpace=True,
callback=[lambda:self.verticalSpacingContLabel.setDisabled(not self.contType), self.showNomogram])
self.verticalSpacingContLabel = OWGUI.spin(OWGUI.indentedBox(self.ContRadio, sep=OWGUI.checkButtonOffsetHint(self.ContRadio.buttons[-1])), self, 'verticalSpacingContinuous', 15, 200, label = "Height", orientation=0, tooltip='Define space (pixels) between adjacent 2d presentation of attributes.', callback = self.showNomogram)
self.verticalSpacingContLabel.setDisabled(not self.contType)
self.yAxisRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'yAxis', ['Point scale', 'Log odds ratios'], 'Scale',
tooltips=['values are normalized on a 0-100 point scale','values on top axis show log-linear contribution of attribute to full model'],
addSpace=True,
callback=self.showNomogram)
layoutBox = OWGUI.widgetBox(self.controlArea, "Display", orientation=1, addSpace=True)
self.probabilityCheck = OWGUI.checkBox(layoutBox, self, 'probability', 'Show prediction', tooltip='', callback = self.setProbability)
self.CICheck, self.CILabel = OWGUI.checkWithSpin(layoutBox, self, 'Confidence intervals (%):', min=1, max=99, step = 1, checked='confidence_check', value='confidence_percent', checkCallback=self.showNomogram, spinCallback = self.showNomogram)
self.histogramCheck, self.histogramLabel = OWGUI.checkWithSpin(layoutBox, self, 'Show histogram, size', min=1, max=30, checked='histogram', value='histogram_size', step = 1, tooltip='-(TODO)-', checkCallback=self.showNomogram, spinCallback = self.showNomogram)
OWGUI.separator(layoutBox)
self.sortOptions = ["No sorting", "Absolute importance", "Positive influence", "Negative influence"]
self.sortBox = OWGUI.comboBox(layoutBox, self, "sort_type", label="Sort by ", items=self.sortOptions, callback = self.sortNomogram, orientation="horizontal")
OWGUI.rubber(self.controlArea)
self.connect(self.graphButton, SIGNAL("clicked()"), self.menuItemPrinter)
#add a graph widget
self.header = OWNomogramHeader(None, self.mainArea)
self.header.setFixedHeight(60)
self.header.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.header.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.graph = OWNomogramGraph(self.bnomogram, self.mainArea)
self.graph.setMinimumWidth(200)
self.graph.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.footer = OWNomogramHeader(None, self.mainArea)
self.footer.setFixedHeight(60*2+10)
self.footer.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.footer.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.mainArea.layout().addWidget(self.header)
self.mainArea.layout().addWidget(self.graph)
self.mainArea.layout().addWidget(self.footer)
self.resize(700,500)
#self.repaint()
#self.update()
# mouse pressed flag
self.mousepr = False
