def __init__(self,
parent=None,
signalManager=None,
title="Molecule visualizer"):
super(OWMoleculeVisualizer, self).__init__(parent, signalManager,
title)
self.colorFragments = 1
self.showFragments = 0
self.selectedFragment = ""
self.moleculeSmiles = []
self.fragmentSmiles = []
self.defFragmentSmiles = []
self.smiles_var = 0
self.moleculeTitleAttr = 0
self.moleculeTitleAttributeList = []
self.selectedMoleculeTitleAttrs = []
self.fragmentSmilesAttr = 0
self.imageSize = 200
self.numColumns = 4
self.commitOnChange = 0
## GUI
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoLabel = OWGUI.label(box, self, "Chemicals:")
box = OWGUI.radioButtonsInBox(self.controlArea,
self,
"showFragments",
["Show molecules", "Show fragments"],
"Show",
callback=self.updateitems)
self.showFragmentsRadioButton = box.buttons[-1]
self.markFragmentsCheckBox = OWGUI.checkBox(box,
self,
"colorFragments",
"Mark fragments",
callback=self._update)
box.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Maximum))
OWGUI.separator(self.controlArea)
self.moleculeSmilesCombo = OWGUI.comboBox(self.controlArea,
self,
"smiles_var",
"Molecule SMILES Attribute",
callback=self.updateitems)
self.moleculeSmilesCombo.box.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum))
self.smiles_var_model = VariableListModel(parent=self)
self.moleculeSmilesCombo.setModel(self.smiles_var_model)
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea,
"Molecule Title Attributes",
addSpace=True)
self.title_var_view = QListView(
selectionMode=QListView.ExtendedSelection)
self.title_var_model = VariableListModel(parent=self)
self.title_var_view.setModel(self.title_var_model)
self.title_var_view.selectionModel().selectionChanged.connect(
self._title_selection_changed)
box.layout().addWidget(self.title_var_view)
OWGUI.separator(self.controlArea)
self.fragmentSmilesCombo = OWGUI.comboBox(
self.controlArea,
self,
"fragmentSmilesAttr",
"Fragment SMILES Attribute",
callback=self.updateFragmentsListBox)
self.fragmentSmilesCombo.setModel(VariableListModel(parent=self))
self.fragmentSmilesCombo.box.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum))
OWGUI.separator(self.controlArea)
box = OWGUI.spin(self.controlArea,
self,
"imageSize",
50,
500,
10,
box="Image Size",
callback=self._image_size_changed)
box.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Maximum))
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Selection", addSpace=True)
OWGUI.checkBox(box, self, "commitOnChange", "Commit on change")
self.selectMarkedMoleculesButton = OWGUI.button(
box, self, "Select &matched molecules", self.select_marked)
OWGUI.button(box, self, "&Commit", callback=self.commit, default=True)
OWGUI.separator(self.controlArea)
OWGUI.rubber(self.controlArea)
spliter = QSplitter(Qt.Vertical)
self.scrollArea = ScrollArea(spliter)
self.grid = GridWidget()
self.grid.selectionChanged.connect(self._on_selection_changed)
self.scrollArea.setWidget(self.grid)
self.scrollArea.setWidgetResizable(True)
self.mainArea.layout().addWidget(spliter)
if pybel:
self.listBox = QListWidget(spliter)
else:
self.listBox = QListWidget(None)
self.listBox.setHidden(True)
self.listBox.itemClicked.connect(self.fragmentSelection)
self.fragmentSmilesCombo.box.setDisabled(not pybel)
self.data = None
self.data_subset = []
self.fragment_data = None
self.resize(800, 600)
self.listBox.setMaximumHeight(150)
self.fragmentSmilesCombo.setDisabled(True)
self.selectMarkedMoleculesButton.setDisabled(True)
self.markFragmentsCheckBox.setDisabled(True)
self.showFragmentsRadioButton.setDisabled(True)
self.loadSettings()
if not pybel:
self.showFragments = 0
self.warning(
10, "Pybel module not installed. To view molecule fragments\n"
"please install openbabel python extension.")
self.__loop = None
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, name="Gene selection"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True, showSaveGraph=True)
self.inputs = [("Examples", ExampleTable, self.set_data)]
self.outputs = [("Example table with selected genes", ExampleTable), ("Example table with remaining genes", ExampleTable), ("Selected genes", ExampleTable)]
self.method_index = 0
self.genes_in_columns = False
self.compute_null = False
self.permutations_count = 10
self.auto_commit = False
self.selectNBest = 20
self.selectPValue = 0.01
self.data_changed_flag = False
self.add_scores_to_output = True
self.thresholds = {
"fold change": (0.5, 2.),
"log2 fold change": (-1, 1),
"t-test": (-2, 2),
"t-test p-value": (0.01, 0.01),
}
self.oneTailTestHi = oneTailTestHi = lambda array, low, hi: array >= hi
self.oneTailTestLow = oneTailTestLow = lambda array, low, hi: array <= low
self.twoTailTest = twoTailTest = lambda array, low, hi: (array >= hi) | (array <= low)
self.middleTest = middleTest = lambda array, low, hi: (array <= hi) | (array >= low)
self.histType = {oneTailTestHi:"hiTail", oneTailTestLow:"lowTail", twoTailTest:"twoTail", middleTest:"middle"}
# [(name, func, tail test, two sample test), ...]
self.score_methods = [("fold change", ExpressionSignificance_FoldChange, twoTailTest, True),
("log2 fold change", ExpressionSignificance_Log2FoldChange, twoTailTest, True),
("t-test", ExpressionSignificance_TTest_T, twoTailTest, True),
("t-test p-value", ExpressionSignificance_TTest_PValue, oneTailTestLow, True),
("anova", ExpressionSignificance_ANOVA_F, oneTailTestHi, False),
("anova p-value", ExpressionSignificance_ANOVA_PValue, oneTailTestLow, False),
("signal to noise ratio", ExpressionSignificance_SignalToNoise, twoTailTest, True),
("info gain", ExpressionSignificance_Info, oneTailTestHi, True),
("chi-square", ExpressionSignificance_ChiSquare, oneTailTestHi, True),
("mann-whitney", ExpressionSignigicance_MannWhitneyu_U, oneTailTestLow, True)]
boxHistogram = OWGUI.widgetBox(self.mainArea)
self.histogram = ScoreHist(self, boxHistogram)
boxHistogram.layout().addWidget(self.histogram)
self.histogram.show()
box = OWGUI.widgetBox(self.controlArea, "Info")
self.dataInfoLabel = OWGUI.widgetLabel(box, "\n\n")
self.dataInfoLabel.setWordWrap(True)
self.selectedInfoLabel = OWGUI.widgetLabel(box, "")
box1 = OWGUI.widgetBox(self.controlArea, "Scoring Method")
self.testRadioBox = OWGUI.comboBox(box1, self, "method_index",
items=[sm[0] for sm in self.score_methods],
callback=[self.on_scoring_method_changed, self.update_scores])
box = OWGUI.widgetBox(self.controlArea, "Target Labels")
self.label_selection_widget = LabelSelectionWidget(self)
self.label_selection_widget.setMaximumHeight(150)
box.layout().addWidget(self.label_selection_widget)
self.connect(self.label_selection_widget,
SIGNAL("selection_changed()"),
self.on_target_changed)
self.connect(self.label_selection_widget,
SIGNAL("label_activated(int)"),
self.on_label_activated)
self.genes_in_columns_check = OWGUI.checkBox(box, self, "genes_in_columns",
"Genes in columns",
callback=self.on_genes_in_columns_change)
box = OWGUI.widgetBox(self.controlArea, "Selection")
box.layout().setSpacing(0)
self.upperBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.upperBoundary",
min=-1e6, max=1e6, step= 1e-6,
label="Upper threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
self.lowerBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.lowerBoundary",
min=-1e6, max=1e6, step= 1e-6,
label="Lower threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
check = OWGUI.checkBox(box, self, "compute_null", "Compute null distribution",
callback=self.update_scores)
check.disables.append(OWGUI.spin(box, self, "permutations_count", min=1, max=10,
label="Permutations:", callback=self.update_scores,
callbackOnReturn=True))
box1 = OWGUI.widgetBox(box, orientation='horizontal')
check.disables.append(OWGUI.doubleSpin(box1, self, "selectPValue",
min=2e-7, max=1.0, step=1e-7,
label="P-value:"))
check.disables.append(OWGUI.button(box1, self, "Select", callback=self.select_p_best))
check.makeConsistent()
box1 = OWGUI.widgetBox(box, orientation='horizontal')
OWGUI.spin(box1, self, "selectNBest", 0, 10000, step=1, label="Best Ranked:")
OWGUI.button(box1, self, "Select", callback=self.select_n_best)
box = OWGUI.widgetBox(self.controlArea, "Output")
b = OWGUI.button(box, self, "&Commit", callback=self.commit)
cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change")
OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit)
OWGUI.checkBox(box, self, "add_scores_to_output", "Add gene scores to output",
callback=self.commit_if)
OWGUI.rubber(self.controlArea)
self.connect(self.graphButton, SIGNAL("clicked()"), self.histogram.saveToFile)
self.loadSettings()
self.data = None
self.discData = None
self.scoreCache = {}
self.nullDistCache = {}
self.cuts = {}
self.null_dist = []
self.targets = []
self.scores = {}
self.genes_in_columns = True
self.target_selections = None
self.on_scoring_method_changed()
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Gene selection"):
OWWidget.__init__(self,
parent,
signalManager,
name,
wantGraph=True,
showSaveGraph=True)
self.inputs = [("Examples", ExampleTable, self.set_data)]
self.outputs = [("Example table with selected genes", ExampleTable),
("Example table with remaining genes", ExampleTable),
("Selected genes", ExampleTable)]
self.method_index = 0
self.genes_in_columns = False
self.compute_null = False
self.permutations_count = 10
self.auto_commit = False
self.selectNBest = 20
self.selectPValue = 0.01
self.data_changed_flag = False
self.add_scores_to_output = True
self.thresholds = {
"fold change": (0.5, 2.),
"log2 fold change": (-1, 1),
"t-test": (-2, 2),
"t-test p-value": (0.01, 0.01),
}
self.oneTailTestHi = oneTailTestHi = lambda array, low, hi: array >= hi
self.oneTailTestLow = oneTailTestLow = lambda array, low, hi: array <= low
self.twoTailTest = twoTailTest = lambda array, low, hi: (
array >= hi) | (array <= low)
self.middleTest = middleTest = lambda array, low, hi: (array <= hi) | (
array >= low)
self.histType = {
oneTailTestHi: "hiTail",
oneTailTestLow: "lowTail",
twoTailTest: "twoTail",
middleTest: "middle"
}
# [(name, func, tail test, two sample test), ...]
self.score_methods = [
("fold change", ExpressionSignificance_FoldChange, twoTailTest,
True),
("log2 fold change", ExpressionSignificance_Log2FoldChange,
twoTailTest, True),
("t-test", ExpressionSignificance_TTest_T, twoTailTest, True),
("t-test p-value", ExpressionSignificance_TTest_PValue,
oneTailTestLow, True),
("anova", ExpressionSignificance_ANOVA_F, oneTailTestHi, False),
("anova p-value", ExpressionSignificance_ANOVA_PValue,
oneTailTestLow, False),
("signal to noise ratio", ExpressionSignificance_SignalToNoise,
twoTailTest, True),
("info gain", ExpressionSignificance_Info, oneTailTestHi, True),
("chi-square", ExpressionSignificance_ChiSquare, oneTailTestHi,
True),
("mann-whitney", ExpressionSignigicance_MannWhitneyu_U,
oneTailTestLow, True)
]
boxHistogram = OWGUI.widgetBox(self.mainArea)
self.histogram = ScoreHist(self, boxHistogram)
boxHistogram.layout().addWidget(self.histogram)
self.histogram.show()
box = OWGUI.widgetBox(self.controlArea, "Info")
self.dataInfoLabel = OWGUI.widgetLabel(box, "\n\n")
self.dataInfoLabel.setWordWrap(True)
self.selectedInfoLabel = OWGUI.widgetLabel(box, "")
box1 = OWGUI.widgetBox(self.controlArea, "Scoring Method")
self.testRadioBox = OWGUI.comboBox(
box1,
self,
"method_index",
items=[sm[0] for sm in self.score_methods],
callback=[self.on_scoring_method_changed, self.update_scores])
box = OWGUI.widgetBox(self.controlArea, "Target Labels")
self.label_selection_widget = LabelSelectionWidget(self)
self.label_selection_widget.setMaximumHeight(150)
box.layout().addWidget(self.label_selection_widget)
self.connect(self.label_selection_widget,
SIGNAL("selection_changed()"), self.on_target_changed)
self.connect(self.label_selection_widget,
SIGNAL("label_activated(int)"), self.on_label_activated)
self.genes_in_columns_check = OWGUI.checkBox(
box,
self,
"genes_in_columns",
"Genes in columns",
callback=self.on_genes_in_columns_change)
box = OWGUI.widgetBox(self.controlArea, "Selection")
box.layout().setSpacing(0)
self.upperBoundarySpin = OWGUI.doubleSpin(
box,
self,
"histogram.upperBoundary",
min=-1e6,
max=1e6,
step=1e-6,
label="Upper threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
self.lowerBoundarySpin = OWGUI.doubleSpin(
box,
self,
"histogram.lowerBoundary",
min=-1e6,
max=1e6,
step=1e-6,
label="Lower threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
check = OWGUI.checkBox(box,
self,
"compute_null",
"Compute null distribution",
callback=self.update_scores)
check.disables.append(
OWGUI.spin(box,
self,
"permutations_count",
min=1,
max=10,
label="Permutations:",
callback=self.update_scores,
callbackOnReturn=True))
box1 = OWGUI.widgetBox(box, orientation='horizontal')
check.disables.append(
OWGUI.doubleSpin(box1,
self,
"selectPValue",
min=2e-7,
max=1.0,
step=1e-7,
label="P-value:"))
check.disables.append(
OWGUI.button(box1, self, "Select", callback=self.select_p_best))
check.makeConsistent()
box1 = OWGUI.widgetBox(box, orientation='horizontal')
OWGUI.spin(box1,
self,
"selectNBest",
0,
10000,
step=1,
label="Best Ranked:")
OWGUI.button(box1, self, "Select", callback=self.select_n_best)
box = OWGUI.widgetBox(self.controlArea, "Output")
b = OWGUI.button(box, self, "&Commit", callback=self.commit)
cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change")
OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit)
OWGUI.checkBox(box,
self,
"add_scores_to_output",
"Add gene scores to output",
callback=self.commit_if)
OWGUI.rubber(self.controlArea)
self.connect(self.graphButton, SIGNAL("clicked()"),
self.histogram.saveToFile)
self.loadSettings()
self.data = None
self.discData = None
self.scoreCache = {}
self.nullDistCache = {}
self.cuts = {}
self.null_dist = []
self.targets = []
self.scores = {}
self.genes_in_columns = True
self.target_selections = None
self.on_scoring_method_changed()
self.resize(800, 600)
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
def __init__(self, parent=None, signalManager=None,
title="Molecule visualizer"):
super(OWMoleculeVisualizer, self).__init__(parent, signalManager, title)
self.colorFragments = 1
self.showFragments = 0
self.selectedFragment = ""
self.moleculeSmiles = []
self.fragmentSmiles = []
self.defFragmentSmiles = []
self.smiles_var = 0
self.moleculeTitleAttr = 0
self.moleculeTitleAttributeList = []
self.selectedMoleculeTitleAttrs = []
self.fragmentSmilesAttr = 0
self.imageSize = 200
self.numColumns = 4
self.commitOnChange = 0
## GUI
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoLabel = OWGUI.label(box, self, "Chemicals:")
box = OWGUI.radioButtonsInBox(
self.controlArea, self, "showFragments",
["Show molecules", "Show fragments"], "Show",
callback=self.updateitems
)
self.showFragmentsRadioButton = box.buttons[-1]
self.markFragmentsCheckBox = OWGUI.checkBox(
box, self, "colorFragments", "Mark fragments",
callback=self._update
)
box.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum))
OWGUI.separator(self.controlArea)
self.moleculeSmilesCombo = OWGUI.comboBox(
self.controlArea, self, "smiles_var",
"Molecule SMILES Attribute",
callback=self.updateitems
)
self.moleculeSmilesCombo.box.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum)
)
self.smiles_var_model = VariableListModel(parent=self)
self.moleculeSmilesCombo.setModel(self.smiles_var_model)
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Molecule Title Attributes",
addSpace=True)
self.title_var_view = QListView(
selectionMode=QListView.ExtendedSelection
)
self.title_var_model = VariableListModel(parent=self)
self.title_var_view.setModel(self.title_var_model)
self.title_var_view.selectionModel().selectionChanged.connect(
self._title_selection_changed
)
box.layout().addWidget(self.title_var_view)
OWGUI.separator(self.controlArea)
self.fragmentSmilesCombo = OWGUI.comboBox(
self.controlArea, self, "fragmentSmilesAttr",
"Fragment SMILES Attribute",
callback=self.updateFragmentsListBox
)
self.fragmentSmilesCombo.setModel(VariableListModel(parent=self))
self.fragmentSmilesCombo.box.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum)
)
OWGUI.separator(self.controlArea)
box = OWGUI.spin(self.controlArea, self, "imageSize", 50, 500, 10,
box="Image Size", callback=self._image_size_changed)
box.setSizePolicy(
QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum))
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Selection", addSpace=True)
OWGUI.checkBox(box, self, "commitOnChange", "Commit on change")
self.selectMarkedMoleculesButton = OWGUI.button(
box, self, "Select &matched molecules", self.select_marked
)
OWGUI.button(box, self, "&Commit", callback=self.commit, default=True)
OWGUI.separator(self.controlArea)
OWGUI.rubber(self.controlArea)
spliter = QSplitter(Qt.Vertical)
self.scrollArea = ScrollArea(spliter)
self.grid = GridWidget()
self.grid.selectionChanged.connect(self._on_selection_changed)
self.scrollArea.setWidget(self.grid)
self.scrollArea.setWidgetResizable(True)
self.mainArea.layout().addWidget(spliter)
if pybel:
self.listBox = QListWidget(spliter)
else:
self.listBox = QListWidget(None)
self.listBox.setHidden(True)
self.listBox.itemClicked.connect(self.fragmentSelection)
self.fragmentSmilesCombo.box.setDisabled(not pybel)
self.data = None
self.data_subset = []
self.fragment_data = None
self.resize(800, 600)
self.listBox.setMaximumHeight(150)
self.fragmentSmilesCombo.setDisabled(True)
self.selectMarkedMoleculesButton.setDisabled(True)
self.markFragmentsCheckBox.setDisabled(True)
self.showFragmentsRadioButton.setDisabled(True)
self.loadSettings()
if not pybel:
self.showFragments = 0
self.warning(10,
"Pybel module not installed. To view molecule fragments\n"
"please install openbabel python extension.")
self.__loop = None
