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="Vulcano Plot"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Examples", ExampleTable, self.setData)]
self.outputs = [("Examples with selected attributes", ExampleTable)]
self.genes_in_columns = False
self.showXTitle = True
self.showYTitle = True
self.auto_commit = False
self.selection_changed_flag = False
self.target_group = None, []
self.label_selections = []
self.graph = VulcanoGraph(self)
self.connect(self.graph, SIGNAL("selectionChanged()"),
self.on_selection_changed)
self.mainArea.layout().addWidget(self.graph)
self.loadSettings()
## GUI
box = OWGUI.widgetBox(self.controlArea, "Info")
self.infoLabel = OWGUI.label(box, self, "")
self.infoLabel.setText("No data on input")
self.infoLabel2 = OWGUI.label(box, self, "")
self.infoLabel2.setText("0 selected genes")
box = OWGUI.widgetBox(self.controlArea, "Target Labels")
self.target_widget = LabelSelectionWidget(self)
self.connect(self.target_widget,
SIGNAL("selection_changed(PyQt_PyObject, PyQt_PyObject)"),
self.on_target_changed)
self.connect(self.target_widget,
SIGNAL("label_activated(int)"),
self.on_label_activated)
box.layout().addWidget(self.target_widget)
self.genesInColumnsCheck = OWGUI.checkBox(box, self, "genes_in_columns",
"Genes in columns",
callback=[self.init_from_data, self.plot])
box = OWGUI.widgetBox(self.controlArea, "Settings")
OWGUI.hSlider(box, self, "graph.symbolSize", label="Symbol size: ", minValue=2, maxValue=20, step=1, callback = self.graph.updateSymbolSize)
OWGUI.checkBox(box, self, "showXTitle", "X axis title", callback=self.setAxesTitles)
OWGUI.checkBox(box, self, "showYTitle", "Y axis title", callback=self.setAxesTitles)
toolbar = ZoomSelectToolbar(self, self.controlArea, self.graph, buttons=[ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan])
top_layout = toolbar.layout()
top_layout.setDirection(QBoxLayout.TopToBottom)
button_layotu = QHBoxLayout()
top_layout.insertLayout(0, button_layotu)
for i in range(1, top_layout.count()):
item = top_layout.itemAt(1)
top_layout.removeItem(item)
button_layotu.addItem(item)
OWGUI.checkBox(toolbar, self, "graph.symetricSelections", "Symetric selection", callback=self.graph.reselect)
box = OWGUI.widgetBox(self.controlArea, "Commit")
b = OWGUI.button(box, self, "Commit", callback=self.commit, default=True)
cb = OWGUI.checkBox(box, self, "auto_commit", "Commit automatically")
OWGUI.setStopper(self, b, cb, "selection_changed_flag", self.commit_if)
self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile)
OWGUI.rubber(self.controlArea)
self.data = None
self.target_group = None, []
self.current_selection = []
self.graph.reselect(True)
self.resize(800, 600)
def __init__(self, parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, 'ANOVA')
# input / output data: [("name1", [orange.ExampleTable1a,...]), ("name2", [orange.ExampleTable2a,...])]
self.inputs = [("Structured Data", DataFiles, self.onDataInput)]
self.outputs = [("Example Selection", ExampleSelection, Default), ("Selected Structured Data", DataFiles, Default), ("Other Structured Data", DataFiles)]
# data, p-values, selected examples
self.dataStructure = None # input data
self.numExamples = 0
self.numVariables = 0
self.ps = None # p-values: 2D Numeric.array of shape (3, numExamples)
self.selectorName = "" # for Example Selection output: (self.selectorName, [0,1,0,...])
# Settings
self.anovaType = 0 # 0: single-sample t-test, 1: one-way (A), 2: one-way (B), 3: two-way (A,B), 4: ful factorial (A, B, A*B)
self.compareToValue = 0 # single sample t-test, value to compare to
self._interaction = 0 # 0: no interaction, 1: test for interaction effect (set this value manually !!!)
self.selectorA = True
self.selectorB = False
self.selectorI = False
self.alphaA = "0.05"
self.alphaB = "0.05"
self.alphaI = "0.05"
self.autoUpdateSelName = 1
self.sendNotSelectedData = 1
self.sendProbabilities = 0
self.commitOnChange = 0
self.loadSettings()
# GUI
self.mainArea.setFixedWidth(0)
ca = self.controlArea
# info
box = OWGUI.widgetBox(ca, "Info")
#gl.addWidget(box,0,0)
self.infoa = OWGUI.label(box, self, 'No data on input.')
self.infob = OWGUI.label(box, self, "")
self.infoc = OWGUI.label(box, self, "")
# ANOVA type
# group selection
anovaTypes = ["Single sample t-test",
"Single-factor (A, variables)",
"Single-factor (B, data sets)",
"Two-factor",
"Two-factor with interaction effect"]
self.boxAnovaType = OWGUI.widgetBox(ca, "Anova Type")
self.anovaTypeS = OWGUI.radioButtonsInBox(self.boxAnovaType, self, "anovaType", btnLabels=anovaTypes)
self.boxAnovaType.setDisabled(1)
self.boxCompareTo = OWGUI.widgetBox(self.boxAnovaType)
OWGUI.lineEdit(self.boxCompareTo, self, "compareToValue", callback=self.onCompareToChange, label="compare to")
# selection of examples
self.boxSelection = OWGUI.widgetBox(ca, "Example Selection")
self.lblNumGenes = [] # list of labels
# selector A
self.boxSelectorA = OWGUI.widgetBox(self.boxSelection)
self.cbSelectorA = OWGUI.checkBox(self.boxSelectorA, self, "selectorA", "Factor A (variables)", callback=self.onSelectionChange,
tooltip='H0: The mean does not depend on factor A (represented by variables).')
frmA = OWGUI.widgetBox(self.boxSelectorA)
leA = OWGUI.lineEdit(frmA, self, "alphaA", orientation="horizontal", callback=lambda x=0: self.onAlphaChange(x), label= "p <= ")
self.lblNumGenes.append(OWGUI.label(frmA, self, ""))
# selector B
self.boxSelectorB = OWGUI.widgetBox(self.boxSelection)
self.cbSelectorB = OWGUI.checkBox(self.boxSelectorB, self, "selectorB", "Factor B (data sets)", callback=self.onSelectionChange,
tooltip='H0: The mean does not depend on factor B (represented by data sets).')
frmB = OWGUI.widgetBox(self.boxSelectorB)
leB = OWGUI.lineEdit(frmB, self, "alphaB", orientation="horizontal", callback=lambda x=1: self.onAlphaChange(x), label= "p <= ")
self.lblNumGenes.append(OWGUI.label(frmB, self, ""))
# selector I
self.boxSelectorI = OWGUI.widgetBox(self.boxSelection)
self.cbSelectorI = OWGUI.checkBox(self.boxSelectorI, self, "selectorI", "Interaction (variables * data sets)", callback=self.onSelectionChange,
tooltip='H0: There is no interaction between factor A and factor B.')
frmI = OWGUI.widgetBox(self.boxSelectorI)
leI = OWGUI.lineEdit(frmI, self, "alphaI", orientation="horizontal", callback=lambda x=2: self.onAlphaChange(x), label= "p <= ")
self.lblNumGenes.append(OWGUI.label(frmI, self, ""))
# output
box = OWGUI.widgetBox(ca, "Output")
self.leSelectorName = OWGUI.lineEdit(box, self, 'selectorName', label='Selector Name: ')
self.leSelectorName.setReadOnly(self.autoUpdateSelName)
OWGUI.checkBox(box, self, 'autoUpdateSelName', 'Automatically update selector name', callback=self.onAutoUpdateSelNameChange)
OWGUI.checkBox(box, self, 'sendNotSelectedData', 'Send not selected data', callback=self.onSendNotSelectedChange)
OWGUI.checkBox(box, self, 'sendProbabilities', 'Show p-values', callback=self.onSendProbabilitiesChange)
OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change', callback=lambda: self.onCommit(self.commitOnChange))
self.btnCommit = OWGUI.button(box, self, "Commit", callback=self.onCommit)
# enable/disable anova type box, example selection box, commit button, update the number of examples for individual selectors
self.updateAnovaTypeBox()
self.updateSelectorBox()
self.updateSelectorInfos()
self.updateSelectorName()
self.resize(283, self.sizeHint().height())
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "MeshBrowser")
self.inputs = [("Reference data", ExampleTable, self.getReferenceData),
("Cluster data", ExampleTable, self.getClusterData)]
self.outputs = [("Selected examples", ExampleTable)]
# widget variables
self.loadedRef = 0
self.loadedClu = 0
self.maxPValue = 0.05
self.minExamplesInTerm = 5
self.multi = 1
self.reference = None
self.cluster = None
self.loadSettings()
self.mesh = obiMeSH() # main object is created
self.dataLoaded = self.mesh.dataLoaded
# left pane
box = OWGUI.widgetBox(self.controlArea, "Info")
#box = QGroupBox("Info", self.controlArea)
self.infoa = OWGUI.label(box, self, "No reference data.")
self.infob = OWGUI.label(box, self, "No cluster data.")
self.ratio = OWGUI.label(box, self, "")
self.ref_att = OWGUI.label(box, self, "")
self.clu_att = OWGUI.label(box, self, "")
self.resize(960, 600)
OWGUI.separator(self.controlArea)
self.optionsBox = OWGUI.widgetBox(self.controlArea, "Options")
self.maxp = OWGUI.lineEdit(self.optionsBox,
self,
"maxPValue",
label="threshold:",
orientation="horizontal",
labelWidth=120,
valueType=float)
self.minf = OWGUI.lineEdit(self.optionsBox,
self,
"minExamplesInTerm",
label="min. frequency:",
orientation="horizontal",
labelWidth=120,
valueType=int)
#OWGUI.checkBox(self.optionsBox, self, 'multi', 'Multiple selection', callback= self.checkClicked)
OWGUI.button(self.optionsBox, self, "Refresh", callback=self.refresh)
# right pane
self.col_size = [280, 84, 84, 100, 110]
self.sort_col = 0
self.sort_dir = True
self.columns = [
'MeSH term', '# reference', '# cluster', 'p value',
'fold enrichment'
] # both datasets
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.meshLV = QTreeWidget(self.splitter)
#self.meshLV.setSelectionMode(QAbstractItemView.MultiSelection)
self.meshLV.setAllColumnsShowFocus(1)
self.meshLV.setColumnCount(len(self.columns))
self.meshLV.setHeaderLabels(self.columns)
self.meshLV.header().setClickable(True)
#self.meshLV.header().setSortIndicatorShown(True)
#self.meshLV.setSortingEnabled(True)
self.meshLV.setRootIsDecorated(True)
self.connect(self.meshLV, SIGNAL("itemSelectionChanged()"),
self.viewSelectionChanged)
#self.meshLV.setItemDelegateForColumn(3, EnrichmentColumnItemDelegate(self))
#self.tooltips = ListViewToolTip(self.meshLV,0, self.mesh.toDesc)
# table of significant mesh terms
self.sigTermsTable = QTableWidget(self.splitter)
self.sigTermsTable.setColumnCount(len(self.columns))
self.sigTermsTable.setRowCount(4)
## hide the vertical header
self.sigTermsTable.verticalHeader().hide()
#self.sigTermsTable.setLeftMargin(0)
#self.sigTermsTable.setSelectionMode(QAbstractItemView.MultiSelection)
for i in range(0, len(self.columns)):
self.sigTermsTable.horizontalHeader().resizeSection(
i, self.col_size[i])
self.meshLV.header().resizeSection(i, self.col_size[i])
self.sigTermsTable.setHorizontalHeaderLabels(self.columns)
self.connect(self.sigTermsTable, SIGNAL("itemSelectionChanged()"),
self.tableSelectionChanged)
self.connect(self.sigTermsTable,
SIGNAL("clicked(int,int,int,const QPoint&)"),
self.tableClicked)
self.splitter.show()
self.optionsBox.setDisabled(1)
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "Parallel Coordinates",
True)
#add a graph widget
self.graph = OWParallelGraph(self, self.mainArea)
self.mainArea.layout().addWidget(self.graph)
self.showAllAttributes = 0
self.inputs = [("Data", ExampleTable, self.setData, Default),
("Data Subset", ExampleTable, self.setSubsetData),
("Features", AttributeList, self.setShownAttributes)]
self.outputs = [("Selected Data", ExampleTable),
("Other Data", ExampleTable),
("Features", AttributeList)]
#set default settings
self.data = None
self.subsetData = None
self.autoSendSelection = 1
self.attrDiscOrder = "Unordered"
self.attrContOrder = "Unordered"
self.projections = None
self.correlationDict = {}
self.middleLabels = "Correlations"
self.attributeSelectionList = None
self.toolbarSelection = 0
self.colorSettings = None
self.selectedSchemaIndex = 0
self.graph.jitterSize = 10
self.graph.showDistributions = 1
self.graph.showStatistics = 0
self.graph.showAttrValues = 1
self.graph.useSplines = 0
self.graph.enabledLegend = 1
#load settings
self.loadSettings()
#GUI
self.tabs = OWGUI.tabWidget(self.controlArea)
self.GeneralTab = OWGUI.createTabPage(self.tabs, "Main")
self.SettingsTab = OWGUI.createTabPage(self.tabs, "Settings")
self.createShowHiddenLists(self.GeneralTab, callback=self.updateGraph)
self.connect(self.shownAttribsLB,
SIGNAL('itemDoubleClicked(QListWidgetItem*)'),
self.flipAttribute)
self.optimizationDlg = ParallelOptimization(
self, signalManager=self.signalManager)
self.optimizationDlgButton = OWGUI.button(
self.GeneralTab,
self,
"Optimization Dialog",
callback=self.optimizationDlg.reshow,
debuggingEnabled=0)
self.zoomSelectToolbar = OWToolbars.ZoomSelectToolbar(
self,
self.GeneralTab,
self.graph,
self.autoSendSelection,
buttons=(1, 2, 0, 7, 8))
self.connect(self.zoomSelectToolbar.buttonSendSelections,
SIGNAL("clicked()"), self.sendSelections)
#connect controls to appropriate functions
self.connect(self.graphButton, SIGNAL("clicked()"),
self.graph.saveToFile)
# ####################################
# SETTINGS functionality
box = OWGUI.widgetBox(self.SettingsTab, "Transparency")
OWGUI.hSlider(box,
self,
'graph.alphaValue',
label="Examples: ",
minValue=0,
maxValue=255,
step=10,
callback=self.updateGraph,
tooltip="Alpha value used for drawing example lines")
OWGUI.hSlider(
box,
self,
'graph.alphaValue2',
label="Rest: ",
minValue=0,
maxValue=255,
step=10,
callback=self.updateGraph,
tooltip="Alpha value used to draw statistics, example subsets, ..."
)
box = OWGUI.widgetBox(self.SettingsTab, "Jittering Options")
OWGUI.comboBox(box,
self,
"graph.jitterSize",
label='Jittering size (% of size): ',
orientation='horizontal',
callback=self.setJitteringSize,
items=self.jitterSizeNums,
sendSelectedValue=1,
valueType=float)
# visual settings
box = OWGUI.widgetBox(self.SettingsTab, "Visual Settings")
OWGUI.checkBox(box,
self,
'graph.showAttrValues',
'Show attribute values',
callback=self.updateGraph)
OWGUI.checkBox(box,
self,
'graph.useAntialiasing',
'Use antialiasing',
callback=self.updateGraph)
OWGUI.checkBox(box,
self,
'graph.useSplines',
'Show splines',
callback=self.updateGraph,
tooltip="Show lines using splines")
OWGUI.checkBox(box,
self,
'graph.enabledLegend',
'Show legend',
callback=self.updateGraph)
box = OWGUI.widgetBox(self.SettingsTab, "Axis Distance")
resizeColsBox = OWGUI.widgetBox(box, 0, "horizontal", 0)
OWGUI.label(resizeColsBox, self, "Increase/decrease distance: ")
OWGUI.toolButton(resizeColsBox,
self,
"+",
callback=self.increaseAxesDistance,
tooltip="Increase the distance between the axes",
width=30,
height=20)
OWGUI.toolButton(resizeColsBox,
self,
"-",
callback=self.decreaseAxesDistance,
tooltip="Decrease the distance between the axes",
width=30,
height=20)
OWGUI.rubber(resizeColsBox)
OWGUI.checkBox(
box,
self,
"graph.autoUpdateAxes",
"Auto scale X axis",
tooltip="Auto scale X axis to show all visualized attributes",
callback=self.updateGraph)
box = OWGUI.widgetBox(self.SettingsTab, "Statistical Information")
OWGUI.comboBox(
box,
self,
"graph.showStatistics",
label="Statistics: ",
orientation="horizontal",
labelWidth=90,
items=["No statistics", "Means, deviations", "Median, quartiles"],
callback=self.updateGraph,
sendSelectedValue=0,
valueType=int)
OWGUI.comboBox(
box,
self,
"middleLabels",
label="Middle labels: ",
orientation="horizontal",
labelWidth=90,
items=["No labels", "Correlations", "VizRank"],
callback=self.updateGraph,
tooltip=
"The information do you wish to view on top in the middle of coordinate axes",
sendSelectedValue=1,
valueType=str)
OWGUI.checkBox(
box,
self,
'graph.showDistributions',
'Show distributions',
callback=self.updateGraph,
tooltip=
"Show bars with distribution of class values (only for discrete attributes)"
)
box = OWGUI.widgetBox(self.SettingsTab,
"Colors",
orientation="horizontal")
OWGUI.button(
box,
self,
"Set colors",
self.setColors,
tooltip=
"Set the canvas background color and color palette for coloring continuous variables",
debuggingEnabled=0)
box = OWGUI.widgetBox(self.SettingsTab,
"Auto Send Selected Data When...")
OWGUI.checkBox(
box,
self,
'autoSendSelection',
'Adding/Removing selection areas',
callback=self.selectionChanged,
tooltip=
"Send selected data whenever a selection area is added or removed")
OWGUI.checkBox(
box,
self,
'graph.sendSelectionOnUpdate',
'Moving/Resizing selection areas',
tooltip=
"Send selected data when a user moves or resizes an existing selection area"
)
self.graph.autoSendSelectionCallback = self.selectionChanged
self.SettingsTab.layout().addStretch(100)
self.icons = self.createAttributeIconDict()
dlg = self.createColorDialog()
self.graph.contPalette = dlg.getContinuousPalette("contPalette")
self.graph.discPalette = dlg.getDiscretePalette("discPalette")
self.graph.setCanvasBackground(dlg.getColor("Canvas"))
apply([
self.zoomSelectToolbar.actionZooming,
self.zoomSelectToolbar.actionRectangleSelection,
self.zoomSelectToolbar.actionPolygonSelection
][self.toolbarSelection], [])
self.cbShowAllAttributes()
self.resize(900, 700)
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "MeshBrowser")
self.inputs = [("Reference data", ExampleTable, self.getReferenceData), ("Cluster data", ExampleTable, self.getClusterData)]
self.outputs = [("Selected examples", ExampleTable)]
# widget variables
self.loadedRef = 0
self.loadedClu = 0
self.maxPValue = 0.05
self.minExamplesInTerm = 5
self.multi = 1
self.reference = None
self.cluster = None
self.loadSettings()
self.mesh = obiMeSH() # main object is created
self.dataLoaded = self.mesh.dataLoaded
# left pane
box = OWGUI.widgetBox(self.controlArea, "Info")
#box = QGroupBox("Info", self.controlArea)
self.infoa = OWGUI.label(box, self, "No reference data.")
self.infob = OWGUI.label(box, self, "No cluster data.")
self.ratio = OWGUI.label(box, self, "")
self.ref_att = OWGUI.label(box, self, "")
self.clu_att = OWGUI.label(box, self, "")
self.resize(960, 600)
OWGUI.separator(self.controlArea)
self.optionsBox = OWGUI.widgetBox(self.controlArea, "Options")
self.maxp = OWGUI.lineEdit(self.optionsBox, self, "maxPValue", label="threshold:", orientation="horizontal", labelWidth=120, valueType=float)
self.minf = OWGUI.lineEdit(self.optionsBox, self, "minExamplesInTerm", label="min. frequency:", orientation="horizontal", labelWidth=120, valueType=int)
#OWGUI.checkBox(self.optionsBox, self, 'multi', 'Multiple selection', callback= self.checkClicked)
OWGUI.button(self.optionsBox, self, "Refresh", callback=self.refresh)
# right pane
self.col_size = [280, 84, 84, 100, 110]
self.sort_col = 0
self.sort_dir = True
self.columns = ['MeSH term', '# reference', '# cluster', 'p value', 'fold enrichment'] # both datasets
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.meshLV = QTreeWidget(self.splitter)
#self.meshLV.setSelectionMode(QAbstractItemView.MultiSelection)
self.meshLV.setAllColumnsShowFocus(1)
self.meshLV.setColumnCount(len(self.columns))
self.meshLV.setHeaderLabels(self.columns)
self.meshLV.header().setClickable(True)
#self.meshLV.header().setSortIndicatorShown(True)
#self.meshLV.setSortingEnabled(True)
self.meshLV.setRootIsDecorated(True)
self.connect(self.meshLV, SIGNAL("itemSelectionChanged()"), self.viewSelectionChanged)
#self.meshLV.setItemDelegateForColumn(3, EnrichmentColumnItemDelegate(self))
#self.tooltips = ListViewToolTip(self.meshLV,0, self.mesh.toDesc)
# table of significant mesh terms
self.sigTermsTable = QTableWidget(self.splitter)
self.sigTermsTable.setColumnCount(len(self.columns))
self.sigTermsTable.setRowCount(4)
## hide the vertical header
self.sigTermsTable.verticalHeader().hide()
#self.sigTermsTable.setLeftMargin(0)
#self.sigTermsTable.setSelectionMode(QAbstractItemView.MultiSelection)
for i in range(0, len(self.columns)):
self.sigTermsTable.horizontalHeader().resizeSection(i, self.col_size[i])
self.meshLV.header().resizeSection(i, self.col_size[i])
self.sigTermsTable.setHorizontalHeaderLabels(self.columns)
self.connect(self.sigTermsTable, SIGNAL("itemSelectionChanged()"), self.tableSelectionChanged)
self.connect(self.sigTermsTable, SIGNAL("clicked(int,int,int,const QPoint&)"), self.tableClicked)
self.splitter.show()
self.optionsBox.setDisabled(1)
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):
OWWidget.__init__(self, parent, signalManager, "Parallel Coordinates", True)
#add a graph widget
self.graph = OWParallelGraph(self, self.mainArea)
self.mainArea.layout().addWidget(self.graph)
self.showAllAttributes = 0
self.inputs = [("Data", ExampleTable, self.setData, Default),
("Data Subset", ExampleTable, self.setSubsetData),
("Features", AttributeList, self.setShownAttributes)]
self.outputs = [("Selected Data", ExampleTable),
("Other Data", ExampleTable),
("Features", AttributeList)]
#set default settings
self.data = None
self.subsetData = None
self.autoSendSelection = 1
self.attrDiscOrder = "Unordered"
self.attrContOrder = "Unordered"
self.projections = None
self.correlationDict = {}
self.middleLabels = "Correlations"
self.attributeSelectionList = None
self.toolbarSelection = 0
self.colorSettings = None
self.selectedSchemaIndex = 0
self.graph.jitterSize = 10
self.graph.showDistributions = 1
self.graph.showStatistics = 0
self.graph.showAttrValues = 1
self.graph.useSplines = 0
self.graph.enabledLegend = 1
#load settings
self.loadSettings()
#GUI
self.tabs = OWGUI.tabWidget(self.controlArea)
self.GeneralTab = OWGUI.createTabPage(self.tabs, "Main")
self.SettingsTab = OWGUI.createTabPage(self.tabs, "Settings")
self.createShowHiddenLists(self.GeneralTab, callback=self.updateGraph)
self.connect(self.shownAttribsLB, SIGNAL('itemDoubleClicked(QListWidgetItem*)'), self.flipAttribute)
self.optimizationDlg = ParallelOptimization(self, signalManager=self.signalManager)
self.optimizationDlgButton = OWGUI.button(self.GeneralTab, self, "Optimization Dialog",
callback=self.optimizationDlg.reshow, debuggingEnabled=0)
self.zoomSelectToolbar = OWToolbars.ZoomSelectToolbar(self, self.GeneralTab, self.graph, self.autoSendSelection,
buttons=(1, 2, 0, 7, 8))
self.connect(self.zoomSelectToolbar.buttonSendSelections, SIGNAL("clicked()"), self.sendSelections)
#connect controls to appropriate functions
self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile)
# ####################################
# SETTINGS functionality
box = OWGUI.widgetBox(self.SettingsTab, "Transparency")
OWGUI.hSlider(box, self, 'graph.alphaValue', label="Examples: ", minValue=0, maxValue=255, step=10,
callback=self.updateGraph, tooltip="Alpha value used for drawing example lines")
OWGUI.hSlider(box, self, 'graph.alphaValue2', label="Rest: ", minValue=0, maxValue=255, step=10,
callback=self.updateGraph, tooltip="Alpha value used to draw statistics, example subsets, ...")
box = OWGUI.widgetBox(self.SettingsTab, "Jittering Options")
OWGUI.comboBox(box, self, "graph.jitterSize", label='Jittering size (% of size): ', orientation='horizontal',
callback=self.setJitteringSize, items=self.jitterSizeNums, sendSelectedValue=1, valueType=float)
# visual settings
box = OWGUI.widgetBox(self.SettingsTab, "Visual Settings")
OWGUI.checkBox(box, self, 'graph.showAttrValues', 'Show attribute values', callback=self.updateGraph)
OWGUI.checkBox(box, self, 'graph.useAntialiasing', 'Use antialiasing', callback=self.updateGraph)
OWGUI.checkBox(box, self, 'graph.useSplines', 'Show splines', callback=self.updateGraph,
tooltip="Show lines using splines")
OWGUI.checkBox(box, self, 'graph.enabledLegend', 'Show legend', callback=self.updateGraph)
box = OWGUI.widgetBox(self.SettingsTab, "Axis Distance")
resizeColsBox = OWGUI.widgetBox(box, 0, "horizontal", 0)
OWGUI.label(resizeColsBox, self, "Increase/decrease distance: ")
OWGUI.toolButton(resizeColsBox, self, "+", callback=self.increaseAxesDistance,
tooltip="Increase the distance between the axes", width=30, height=20)
OWGUI.toolButton(resizeColsBox, self, "-", callback=self.decreaseAxesDistance,
tooltip="Decrease the distance between the axes", width=30, height=20)
OWGUI.rubber(resizeColsBox)
OWGUI.checkBox(box, self, "graph.autoUpdateAxes", "Auto scale X axis",
tooltip="Auto scale X axis to show all visualized attributes", callback=self.updateGraph)
box = OWGUI.widgetBox(self.SettingsTab, "Statistical Information")
OWGUI.comboBox(box, self, "graph.showStatistics", label="Statistics: ", orientation="horizontal", labelWidth=90,
items=["No statistics", "Means, deviations", "Median, quartiles"], callback=self.updateGraph,
sendSelectedValue=0, valueType=int)
OWGUI.comboBox(box, self, "middleLabels", label="Middle labels: ", orientation="horizontal", labelWidth=90,
items=["No labels", "Correlations", "VizRank"], callback=self.updateGraph,
tooltip="The information do you wish to view on top in the middle of coordinate axes",
sendSelectedValue=1, valueType=str)
OWGUI.checkBox(box, self, 'graph.showDistributions', 'Show distributions', callback=self.updateGraph,
tooltip="Show bars with distribution of class values (only for discrete attributes)")
box = OWGUI.widgetBox(self.SettingsTab, "Colors", orientation="horizontal")
OWGUI.button(box, self, "Set colors", self.setColors,
tooltip="Set the canvas background color and color palette for coloring continuous variables",
debuggingEnabled=0)
box = OWGUI.widgetBox(self.SettingsTab, "Auto Send Selected Data When...")
OWGUI.checkBox(box, self, 'autoSendSelection', 'Adding/Removing selection areas',
callback=self.selectionChanged,
tooltip="Send selected data whenever a selection area is added or removed")
OWGUI.checkBox(box, self, 'graph.sendSelectionOnUpdate', 'Moving/Resizing selection areas',
tooltip="Send selected data when a user moves or resizes an existing selection area")
self.graph.autoSendSelectionCallback = self.selectionChanged
self.SettingsTab.layout().addStretch(100)
self.icons = self.createAttributeIconDict()
dlg = self.createColorDialog()
self.graph.contPalette = dlg.getContinuousPalette("contPalette")
self.graph.discPalette = dlg.getDiscretePalette("discPalette")
self.graph.setCanvasBackground(dlg.getColor("Canvas"))
apply([self.zoomSelectToolbar.actionZooming, self.zoomSelectToolbar.actionRectangleSelection,
self.zoomSelectToolbar.actionPolygonSelection][self.toolbarSelection], [])
self.cbShowAllAttributes()
self.resize(900, 700)
