def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.selectionChanged = False
self.filterString = ""
self.datasetName = ""
## GUI
box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoBox = gui.widgetLabel(box, "Initializing\n\n")
box = gui.widgetBox(self.controlArea, "Output", addSpace=True)
gui.radioButtonsInBox(box,
self,
"outputRows",
["Genes in rows", "Samples in rows"],
"Rows",
callback=self.commitIf)
gui.checkBox(box,
self,
"mergeSpots",
"Merge spots of same gene",
callback=self.commitIf)
gui.separator(box)
self.nameEdit = gui.lineEdit(
box,
self,
"datasetName",
"Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited)
self.nameEdit.setPlaceholderText("")
if sys.version_info < (3, ):
box = gui.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = gui.button(box,
self,
"Commit",
callback=self.commit)
cb = gui.checkBox(box, self, "autoCommit", "Commit on any change")
gui.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
else:
gui.auto_commit(self.controlArea,
self,
"autoCommit",
"Commit",
box="Commit")
self.commitIf = self.commit
gui.rubber(self.controlArea)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(textChanged=self.filter)
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.completer)
self.mainArea.layout().addWidget(self.filterLineEdit)
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QTreeView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = gui.widgetBox(splitterH, "Description")
self.infoGDS = gui.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
gui.rubber(box)
box = gui.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"])
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = [
"dataset_id", "title", "platform_organism", "description"
]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float, )))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.selectionChanged = False
self.filterString = ""
self.datasetName = ""
## GUI
box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoBox = gui.widgetLabel(box, "Initializing\n\n")
box = gui.widgetBox(self.controlArea, "Output", addSpace=True)
gui.radioButtonsInBox(box, self, "outputRows",
["Genes in rows", "Samples in rows"], "Rows",
callback=self.commitIf)
gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene",
callback=self.commitIf)
gui.separator(box)
self.nameEdit = gui.lineEdit(
box, self, "datasetName", "Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited
)
self.nameEdit.setPlaceholderText("")
if sys.version_info < (3, ):
box = gui.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = gui.button(
box, self, "Commit", callback=self.commit)
cb = gui.checkBox(box, self, "autoCommit", "Commit on any change")
gui.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
else:
gui.auto_commit(self.controlArea, self, "autoCommit", "Commit",
box="Commit")
self.commitIf = self.commit
gui.rubber(self.controlArea)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive
)
self.filterLineEdit.setCompleter(self.completer)
self.mainArea.layout().addWidget(self.filterLineEdit)
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QTreeView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self.treeWidget,
role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection
)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = gui.widgetBox(splitterH, "Description")
self.infoGDS = gui.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
gui.rubber(box)
box = gui.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"]
)
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged
)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = ["dataset_id", "title", "platform_organism",
"description"]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float,)))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.outputs = [("Expression Data", ExampleTable)]
## Settings
self.selectedAnnotation = 0
self.includeIf = False
self.minSamples = 3
self.autoCommit = False
self.outputRows = 0
self.mergeSpots = True
self.filterString = ""
self.currentGds = None
self.selectionChanged = False
self.autoCommit = False
self.gdsSelectionStates = {}
self.splitterSettings = [
'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02',
'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01'
]
self.datasetNames = {}
self.loadSettings()
self.datasetName = ""
## GUI
self.infoBox = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n\n"
)
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True)
OWGUI.radioButtonsInBox(box, self, "outputRows",
["Genes or spots", "Samples"], "Rows",
callback=self.commitIf)
OWGUI.checkBox(box, self, "mergeSpots", "Merge spots of same gene",
callback=self.commitIf)
OWGUI.separator(box)
self.nameEdit = OWGUI.lineEdit(
box, self, "datasetName", "Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited
)
self.nameEdit.setPlaceholderText("")
box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = OWGUI.button(box, self, "Commit",
callback=self.commit)
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on any change")
OWGUI.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
OWGUI.rubber(self.controlArea)
self.filterLineEdit = OWGUIEx.lineEditHint(
self.mainArea, self, "filterString", "Filter",
caseSensitive=False, matchAnywhere=True,
callback=self.filter, delimiters=" ")
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QAbstractItemView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, OWGUI.IndicatorItemDelegate(self.treeWidget,
role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection
)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = OWGUI.widgetBox(splitterH, "Description")
self.infoGDS = OWGUI.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
OWGUI.rubber(box)
box = OWGUI.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"]
)
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged
)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = ["dataset_id", "title", "platform_organism",
"description"]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float,)))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
def __init__(self, parent=None, signalManager=None, title="Expression Profile Distances"):
OWWidget.__init__(self, parent, signalManager, title)
self.inputs = [("Example Table", ExampleTable, self.set_data)]
self.outputs = [("Distances", Orange.core.SymMatrix), ("Sorted Example Table", ExampleTable)]
self.distance_measure = 0
self.auto_commit = False
self.changed_flag = False
self.loadSettings()
########
# GUI
########
self.info_box = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Input", addSpace=True), "No data on input\n"
)
box = OWGUI.widgetBox(self.controlArea, "Separate By", addSpace=True)
self.separate_view = QListView()
self.separate_view.setSelectionMode(QListView.MultiSelection)
box.layout().addWidget(self.separate_view)
box = OWGUI.widgetBox(self.controlArea, "Sort By", addSpace=True)
self.relevant_view = QListView()
self.relevant_view.setSelectionMode(QListView.MultiSelection)
box.layout().addWidget(self.relevant_view)
self.distance_view = OWGUI.comboBox(
self.controlArea,
self,
"distance_measure",
box="Distance Measure",
items=[d[0] for d in self.DISTANCE_FUNCTIONS],
)
OWGUI.rubber(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Commit")
cb = OWGUI.checkBox(
box,
self,
"auto_commit",
"Commit on any change",
tooltip="Compute and send the distances on any change.",
callback=self.commit_if,
)
b = OWGUI.button(
box,
self,
"Commit",
tooltip="Compute the distances and send the output signals.",
callback=self.commit,
default=True,
)
OWGUI.setStopper(self, b, cb, "changed_flag", callback=self.commit)
self.groups_box = OWGUI.widgetBox(self.mainArea, "Groups")
self.groups_scroll_area = QScrollArea()
self.groups_box.layout().addWidget(self.groups_scroll_area)
self.data = None
self.partitions = []
self.matrix = None
self.split_groups = []
self._disable_updates = False
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.outputs = [("Expression Data", ExampleTable)]
## Settings
self.selectedAnnotation = 0
self.includeIf = False
self.minSamples = 3
self.autoCommit = False
self.outputRows = 1
self.mergeSpots = True
self.filterString = ""
self.currentGds = None
self.selectionChanged = False
self.autoCommit = False
self.gdsSelectionStates = {}
self.splitterSettings = [
'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02',
'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01'
]
self.datasetNames = {}
self.loadSettings()
self.datasetName = ""
## GUI
self.infoBox = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n\n"
)
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True)
OWGUI.radioButtonsInBox(box, self, "outputRows",
["Genes in rows", "Samples in rows"], "Rows",
callback=self.commitIf)
OWGUI.checkBox(box, self, "mergeSpots", "Merge spots of same gene",
callback=self.commitIf)
OWGUI.separator(box)
self.nameEdit = OWGUI.lineEdit(
box, self, "datasetName", "Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited
)
self.nameEdit.setPlaceholderText("")
box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = OWGUI.button(box, self, "Commit",
callback=self.commit)
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on any change")
OWGUI.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
OWGUI.rubber(self.controlArea)
self.filterLineEdit = OWGUIEx.lineEditHint(
self.mainArea, self, "filterString", "Filter",
caseSensitive=False, matchAnywhere=True,
callback=self.filter, delimiters=" ")
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QAbstractItemView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, OWGUI.IndicatorItemDelegate(self.treeWidget,
role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection
)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = OWGUI.widgetBox(splitterH, "Description")
self.infoGDS = OWGUI.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
OWGUI.rubber(box)
box = OWGUI.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"]
)
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged
)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = ["dataset_id", "title", "platform_organism",
"description"]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float,)))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
def __init__(self, parent=None, signalManager = None):
# self.callbackDeposit = [] # deposit for OWGUI callback functions
OWWidget.__init__(self, parent, signalManager, 'Expression Profiles', 1)
#set default settings
self.ShowAverageProfile = 1
self.ShowSingleProfiles = 0
self.PointWidth = 2
self.CurveWidth = 1
self.AverageCurveWidth = 4
self.BoxPlotWidth = 2
self.SelectedClasses = []
self.Classes = []
self.autoSendSelected = 0
self.selectionChangedFlag = False
self.CutLow = 0; self.CutHigh = 0; self.CutEnabled = 0
self.profileLabel = None
#load settings
self.loadSettings()
# GUI
self.graph = profilesGraph(self, self.mainArea, "")
self.mainArea.layout().addWidget(self.graph)
self.graph.hide()
self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile)
# GUI definition
self.tabs = OWGUI.tabWidget(self.space)
# GRAPH TAB
GraphTab = OWGUI.createTabPage(self.tabs, "Graph")
## display options
self.infoLabel = OWGUI.widgetLabel(OWGUI.widgetBox(GraphTab, "Info"), "No data on input.")
displayOptBox = OWGUI.widgetBox(GraphTab, "Display") #QVButtonGroup("Display", GraphTab)
displayOptButtons = ['Majority Class', 'Majority Class Probability', 'Target Class Probability', 'Number of Instances']
OWGUI.checkBox(displayOptBox, self, 'ShowSingleProfiles', 'Expression Profiles', tooltip='', callback=self.updateShowSingleProfiles)
OWGUI.checkBox(displayOptBox, self, 'ShowAverageProfile', 'Box Plot', tooltip='', callback=self.updateShowAverageProfile)
## class selection (classQLB)
self.classQVGB = OWGUI.widgetBox(GraphTab, "Classes") #QVGroupBox(GraphTab)
## self.classQVGB.setTitle("Classes")
self.classQLB = OWGUI.listBox(self.classQVGB, self, "SelectedClasses", "Classes", selectionMode=QListWidget.MultiSelection, callback=self.classSelectionChange) #QListBox(self.classQVGB)
## self.classQLB.setSelectionMode(QListBox.Multi)
self.unselectAllClassedQLB = OWGUI.button(self.classQVGB, self, "Unselect all", callback=self.SUAclassQLB) #QPushButton("(Un)Select All", self.classQVGB)
## self.connect(self.unselectAllClassedQLB, SIGNAL("clicked()"), self.SUAclassQLB)
## self.connect(self.classQLB, SIGNAL("selectionChanged()"), self.classSelectionChange)
## show single/average profile
## self.showAverageQLB = QPushButton("Box Plot", self.classQVGB)
## self.showAverageQLB.setToggleButton(1)
## self.showAverageQLB.setOn(self.ShowAverageProfile)
## self.showSingleQLB = QPushButton("Single Profiles", self.classQVGB)
## self.showSingleQLB.setToggleButton(1)
## self.showSingleQLB.setOn(self.ShowSingleProfiles)
## self.connect(self.showAverageQLB, SIGNAL("toggled(bool)"), self.updateShowAverageProfile)
## self.connect(self.showSingleQLB, SIGNAL("toggled(bool)"), self.updateShowSingleProfiles)
## self.tabs.insertTab(GraphTab, "Graph")
# SETTINGS TAB
SettingsTab = OWGUI.createTabPage(self.tabs, "Settings") #QVGroupBox(self)
self.profileLabelComboBox = OWGUI.comboBox(SettingsTab, self, 'profileLabel', 'Profile Labels', sendSelectedValue=True, valueType=str)
OWGUI.hSlider(SettingsTab, self, 'PointWidth', box='Point Width', minValue=0, maxValue=9, step=1, callback=self.updatePointWidth, ticks=1)
OWGUI.hSlider(SettingsTab, self, 'CurveWidth', box='Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateCurveWidth, ticks=1)
OWGUI.hSlider(SettingsTab, self, 'AverageCurveWidth', box='Average Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateAverageCurveWidth, ticks=1)
OWGUI.hSlider(SettingsTab, self, 'BoxPlotWidth', box='Box Plot Width', minValue=0, maxValue=9, step=1, callback=self.updateBoxPlotWidth, ticks=1)
OWGUI.checkBox(SettingsTab, self, 'graph.renderAntialiased', "Render antialiased", callback=self.graph.setCurveRenderHints)
## graph y scale
box = OWGUI.widgetBox(SettingsTab, "Threshold/ Values") #QVButtonGroup("Threshol/ Values", SettingsTab)
OWGUI.checkBox(box, self, 'CutEnabled', "Enabled", callback=self.setCutEnabled)
self.sliderCutLow = OWGUI.qwtHSlider(box, self, 'CutLow', label='Low:', labelWidth=33, minValue=-20, maxValue=0, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis)
self.sliderCutHigh = OWGUI.qwtHSlider(box, self, 'CutHigh', label='High:', labelWidth=33, minValue=0, maxValue=20, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis)
if not self.CutEnabled:
self.sliderCutLow.box.setDisabled(1)
self.sliderCutHigh.box.setDisabled(1)
## self.tabs.insertTab(SettingsTab, "Settings")
self.toolbarSelection = ZoomSelectToolbar(self, self.controlArea, self.graph, self.autoSendSelected, buttons=(ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan, ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconSpace,
ZoomSelectToolbar.IconRemoveLast, ZoomSelectToolbar.IconRemoveAll, ZoomSelectToolbar.IconSendSelection))
cb = OWGUI.checkBox(self.controlArea, self, "autoSendSelected", "Auto send on selection change")
OWGUI.setStopper(self, self.toolbarSelection.buttonSendSelections, cb, "selectionChangedFlag", self.commit)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.data, Default + Multiple)]
self.outputs = [("Examples", ExampleTable, Default)]
# temp variables
self.MAdata = []
self.classColor = None
self.classBrighterColor = None
self.numberOfClasses = 0
self.classValues = []
self.ctrlPressed = False
self.attrIcons = self.createAttributeIconDict()
self.graph.canvas().setMouseTracking(1)
# self.zoomStack = []
## self.connect(self.graph,
## SIGNAL('plotMousePressed(const QMouseEvent&)'),
## self.onMousePressed)
## self.connect(self.graph,
## SIGNAL('plotMouseReleased(const QMouseEvent&)'),
## self.onMouseReleased)
self.resize(800,600)
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, 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,
name="Normalize Expression Array"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Expression array", ExampleTable, self.setData)]
self.outputs = [("Normalized expression array", ExampleTable, Default),
("Filtered expression array", ExampleTable)]
self.selectedGroup = 0
self.selectedCenterMethod = 0
self.selectedMergeMethod = 0
self.zCutoff = 1.96
self.appendZScore = False
self.appendRIValues = False
self.autoCommit = False
self.loadSettings()
## GUI
self.infoBox = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"No data on input.")
box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True)
self.groupCombo = OWGUI.comboBox(box,
self,
"selectedGroup",
callback=self.onGroupSelection)
self.centerCombo = OWGUI.comboBox(
self.controlArea,
self,
"selectedCenterMethod",
box="Center Fold-change Using",
items=[name for name, _ in self.CENTER_METHODS],
callback=self.onCenterMethodChange,
addSpace=True)
self.mergeCombo = OWGUI.comboBox(
self.controlArea,
self,
"selectedMergeMethod",
box="Merge Replicates",
items=[name for name, _ in self.MERGE_METHODS],
tooltip="Select the method for replicate merging",
callback=self.onMergeMethodChange,
addSpace=True)
box = OWGUI.doubleSpin(self.controlArea,
self,
"zCutoff",
0.0,
3.0,
0.01,
box="Z-Score Cutoff",
callback=[self.replotMA, self.commitIf])
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Ouput")
OWGUI.checkBox(box,
self,
"appendZScore",
"Append Z-Scores",
tooltip="Append calculated Z-Scores to output",
callback=self.commitIf)
OWGUI.checkBox(
box,
self,
"appendRIValues",
"Append Log Ratio and Intensity values",
tooltip=
"Append calculated Log Ratio and Intensity values to output data",
callback=self.commitIf)
cb = OWGUI.checkBox(box,
self,
"autoCommit",
"Commit on change",
tooltip="Commit data on any change",
callback=self.commitIf)
b = OWGUI.button(box, self, "Commit", callback=self.commit)
OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit)
self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph)
OWGUI.rubber(self.controlArea)
self.graph = OWGraph(self.mainArea)
self.graph.setAxisTitle(QwtPlot.xBottom,
"Intensity: log<sub>10</sub>(R*G)")
self.graph.setAxisTitle(QwtPlot.yLeft,
"Log ratio: log<sub>2</sub>(R/G)")
self.graph.showFilledSymbols = True
self.mainArea.layout().addWidget(self.graph)
self.groups = []
self.split_data = None, None
self.merged_splits = None, None
self.centered = None, None
self.changedFlag = False
self.data = None
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Gene Info"):
OWWidget.__init__(self, parent, signalManager, name)
self.inputs = [("Examples", Orange.data.Table, self.setData)]
self.outputs = [("Selected Examples", Orange.data.Table)]
self.organismIndex = 0
self.taxid = None
self.geneAttr = 0
self.useAttr = False
self.autoCommit = False
self.searchString = ""
self.selectionChangedFlag = False
self.useAltSource = 0
self.loadSettings()
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.infoLabel = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n"
)
self.organisms = None
self.organismBox = OWGUI.widgetBox(
self.controlArea, "Organism", addSpace=True)
self.organismComboBox = OWGUI.comboBox(
self.organismBox, self, "organismIndex",
callback=self._onSelectedOrganismChanged,
debuggingEnabled=0)
# For now only support one alt source, with a checkbox
# In the future this can be extended to multiple selections
self.altSourceCheck = OWGUI.checkBox(self.organismBox, self,
"useAltSource", "Show information from dictyBase",
callback=self.onAltSourceChange,
# debuggingEnabled=0,
)
self.altSourceCheck.hide()
box = OWGUI.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = OWGUI.comboBox(
box, self, "geneAttr",
"Gene atttibute", callback=self.updateInfoItems
)
OWGUI.checkBox(box, self, "useAttr", "Use attribute names",
callback=self.updateInfoItems,
disables=[(-1, self.geneAttrComboBox)])
self.geneAttrComboBox.setDisabled(bool(self.useAttr))
box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True)
b = OWGUI.button(box, self, "Commit", callback=self.commit)
c = OWGUI.checkBox(box, self, "autoCommit", "Commit on change")
OWGUI.setStopper(self, b, c, "selectionChangedFlag",
callback=self.commit)
# A label for dictyExpress link
self.dictyExpressBox = OWGUI.widgetBox(
self.controlArea, "Dicty Express")
self.linkLabel = OWGUI.widgetLabel(self.dictyExpressBox, "")
self.linkLabel.setOpenExternalLinks(False)
self.connect(self.linkLabel, SIGNAL("linkActivated(QString)"),
self.onDictyExpressLink)
self.dictyExpressBox.hide()
OWGUI.rubber(self.controlArea)
OWGUI.lineEdit(self.mainArea, self, "searchString", "Filter",
callbackOnType=True, callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSelectionMode(
QAbstractItemView.ExtendedSelection)
self.treeWidget.setItemDelegate(
LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.viewport().setMouseTracking(True)
self.treeWidget.setSortingEnabled(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = OWGUI.widgetBox(self.mainArea, "",
orientation="horizontal")
OWGUI.button(box, self, "Select Filtered",
callback=self.selectFiltered)
OWGUI.button(box, self, "Clear Selection",
callback=self.treeWidget.clearSelection)
self.resize(1000, 700)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
self.selectionUpdateInProgress = False
self.setBlocking(True)
self.executor = ThreadExecutor(self)
self.progressBarInit()
task = Task(
function=partial(
taxonomy.ensure_downloaded,
callback=methodinvoke(self, "advance", ())
)
)
task.resultReady.connect(self.initialize)
task.exceptionReady.connect(self._onInitializeError)
self.initfuture = self.executor.submit(task)
def __init__(self, parent=None, signalManager=None, name="KEGG Pathways"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Examples", Orange.data.Table, self.SetData),
("Reference", Orange.data.Table, self.SetRefData)]
self.outputs = [("Selected Examples", Orange.data.Table),
("Unselected Examples", Orange.data.Table)]
self.organismIndex = 0
self.geneAttrIndex = 0
self.autoCommit = False
self.autoResize = True
self.useReference = False
self.useAttrNames = 0
self.showOrthology = True
self.loadSettings()
self.organismCodes = []
self._changedFlag = False
self.controlArea.setMaximumWidth(250)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.infoLabel = OWGUI.widgetLabel(box, "No data on input\n")
# Organism selection.
box = OWGUI.widgetBox(self.controlArea, "Organism")
self.organismComboBox = OWGUI.comboBox(
box, self, "organismIndex",
items=[],
callback=self.Update,
addSpace=True,
debuggingEnabled=0,
tooltip="Select the organism of the input genes")
# Selection of genes attribute
box = OWGUI.widgetBox(self.controlArea, "Gene attribute")
self.geneAttrCandidates = VariableListModel(parent=self)
self.geneAttrCombo = OWGUI.comboBox(
box, self, "geneAttrIndex", callback=self.Update)
self.geneAttrCombo.setModel(self.geneAttrCandidates)
OWGUI.checkBox(box, self, "useAttrNames",
"Use variable names",
disables=[(-1, self.geneAttrCombo)],
callback=self.Update)
self.geneAttrCombo.setDisabled(bool(self.useAttrNames))
OWGUI.separator(self.controlArea)
OWGUI.checkBox(self.controlArea, self, "useReference",
"From signal",
box="Reference",
callback=self.Update)
OWGUI.separator(self.controlArea)
OWGUI.checkBox(self.controlArea, self, "showOrthology",
"Show pathways in full orthology",
box="Orthology",
callback=self.UpdateListView)
OWGUI.checkBox(self.controlArea, self, "autoResize",
"Resize to fit",
box="Image",
callback=self.UpdatePathwayViewTransform)
box = OWGUI.widgetBox(self.controlArea, "Cache Control")
OWGUI.button(box, self, "Clear cache",
callback=self.ClearCache,
tooltip="Clear all locally cached KEGG data.")
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Selection")
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on update")
button = OWGUI.button(box, self, "Commit", callback=self.Commit,
default=True)
OWGUI.setStopper(self, button, cb, "_changedFlag", self.Commit)
OWGUI.rubber(self.controlArea)
spliter = QSplitter(Qt.Vertical, self.mainArea)
self.pathwayView = PathwayView(self, spliter)
self.pathwayView.scene().selectionChanged.connect(
self._onSelectionChanged
)
self.mainArea.layout().addWidget(spliter)
self.listView = QTreeWidget(spliter)
spliter.addWidget(self.listView)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(4)
self.listView.setHeaderLabels(["Pathway", "P value",
"Genes", "Reference"])
self.listView.setSelectionMode(QTreeWidget.SingleSelection)
self.listView.setSortingEnabled(True)
self.listView.setMaximumHeight(200)
self.connect(self.listView,
SIGNAL("itemSelectionChanged()"),
self.UpdatePathwayView)
self.connect(self.graphButton,
SIGNAL("clicked()"),
self.saveGraph)
select = QAction(
"Select All", self,
shortcut=QKeySequence.SelectAll
)
select.triggered.connect(self.selectAll)
self.addAction(select)
self.data = None
self.refData = None
self.resize(800, 600)
self.connect(self,
SIGNAL("widgetStateChanged(QString, int, QString)"),
self.onStateChange)
self.has_new_data = False
self.has_new_reference_set = False
self._executor = ThreadExecutor()
self.setEnabled(False)
self.setBlocking(True)
QTimer.singleShot(0, self._initialize)
self.infoLabel.setText("Fetching organism definitions\n")
def __init__(self, parent=None, signalManager=None):
# self.callbackDeposit = [] # deposit for OWGUI callback functions
OWWidget.__init__(self, parent, signalManager, 'Expression Profiles',
1)
#set default settings
self.ShowAverageProfile = 1
self.ShowSingleProfiles = 0
self.PointWidth = 2
self.CurveWidth = 1
self.AverageCurveWidth = 4
self.BoxPlotWidth = 2
self.SelectedClasses = []
self.Classes = []
self.autoSendSelected = 0
self.selectionChangedFlag = False
self.CutLow = 0
self.CutHigh = 0
self.CutEnabled = 0
self.profileLabel = None
#load settings
self.loadSettings()
# GUI
self.graph = profilesGraph(self, self.mainArea, "")
self.mainArea.layout().addWidget(self.graph)
self.graph.hide()
self.connect(self.graphButton, SIGNAL("clicked()"),
self.graph.saveToFile)
# GUI definition
self.tabs = OWGUI.tabWidget(self.space)
# GRAPH TAB
GraphTab = OWGUI.createTabPage(self.tabs, "Graph")
## display options
self.infoLabel = OWGUI.widgetLabel(OWGUI.widgetBox(GraphTab, "Info"),
"No data on input.")
displayOptBox = OWGUI.widgetBox(
GraphTab, "Display") #QVButtonGroup("Display", GraphTab)
displayOptButtons = [
'Majority Class', 'Majority Class Probability',
'Target Class Probability', 'Number of Instances'
]
OWGUI.checkBox(displayOptBox,
self,
'ShowSingleProfiles',
'Expression Profiles',
tooltip='',
callback=self.updateShowSingleProfiles)
OWGUI.checkBox(displayOptBox,
self,
'ShowAverageProfile',
'Box Plot',
tooltip='',
callback=self.updateShowAverageProfile)
## class selection (classQLB)
self.classQVGB = OWGUI.widgetBox(GraphTab,
"Classes") #QVGroupBox(GraphTab)
## self.classQVGB.setTitle("Classes")
self.classQLB = OWGUI.listBox(
self.classQVGB,
self,
"SelectedClasses",
"Classes",
selectionMode=QListWidget.MultiSelection,
callback=self.classSelectionChange) #QListBox(self.classQVGB)
## self.classQLB.setSelectionMode(QListBox.Multi)
self.unselectAllClassedQLB = OWGUI.button(
self.classQVGB, self, "Unselect all", callback=self.SUAclassQLB
) #QPushButton("(Un)Select All", self.classQVGB)
## self.connect(self.unselectAllClassedQLB, SIGNAL("clicked()"), self.SUAclassQLB)
## self.connect(self.classQLB, SIGNAL("selectionChanged()"), self.classSelectionChange)
## show single/average profile
## self.showAverageQLB = QPushButton("Box Plot", self.classQVGB)
## self.showAverageQLB.setToggleButton(1)
## self.showAverageQLB.setOn(self.ShowAverageProfile)
## self.showSingleQLB = QPushButton("Single Profiles", self.classQVGB)
## self.showSingleQLB.setToggleButton(1)
## self.showSingleQLB.setOn(self.ShowSingleProfiles)
## self.connect(self.showAverageQLB, SIGNAL("toggled(bool)"), self.updateShowAverageProfile)
## self.connect(self.showSingleQLB, SIGNAL("toggled(bool)"), self.updateShowSingleProfiles)
## self.tabs.insertTab(GraphTab, "Graph")
# SETTINGS TAB
SettingsTab = OWGUI.createTabPage(self.tabs,
"Settings") #QVGroupBox(self)
self.profileLabelComboBox = OWGUI.comboBox(SettingsTab,
self,
'profileLabel',
'Profile Labels',
sendSelectedValue=True,
valueType=str)
OWGUI.hSlider(SettingsTab,
self,
'PointWidth',
box='Point Width',
minValue=0,
maxValue=9,
step=1,
callback=self.updatePointWidth,
ticks=1)
OWGUI.hSlider(SettingsTab,
self,
'CurveWidth',
box='Profile Width',
minValue=1,
maxValue=9,
step=1,
callback=self.updateCurveWidth,
ticks=1)
OWGUI.hSlider(SettingsTab,
self,
'AverageCurveWidth',
box='Average Profile Width',
minValue=1,
maxValue=9,
step=1,
callback=self.updateAverageCurveWidth,
ticks=1)
OWGUI.hSlider(SettingsTab,
self,
'BoxPlotWidth',
box='Box Plot Width',
minValue=0,
maxValue=9,
step=1,
callback=self.updateBoxPlotWidth,
ticks=1)
OWGUI.checkBox(SettingsTab,
self,
'graph.renderAntialiased',
"Render antialiased",
callback=self.graph.setCurveRenderHints)
## graph y scale
box = OWGUI.widgetBox(
SettingsTab, "Threshold/ Values"
) #QVButtonGroup("Threshol/ Values", SettingsTab)
OWGUI.checkBox(box,
self,
'CutEnabled',
"Enabled",
callback=self.setCutEnabled)
self.sliderCutLow = OWGUI.qwtHSlider(box,
self,
'CutLow',
label='Low:',
labelWidth=33,
minValue=-20,
maxValue=0,
step=0.1,
precision=1,
ticks=0,
maxWidth=80,
callback=self.updateYaxis)
self.sliderCutHigh = OWGUI.qwtHSlider(box,
self,
'CutHigh',
label='High:',
labelWidth=33,
minValue=0,
maxValue=20,
step=0.1,
precision=1,
ticks=0,
maxWidth=80,
callback=self.updateYaxis)
if not self.CutEnabled:
self.sliderCutLow.box.setDisabled(1)
self.sliderCutHigh.box.setDisabled(1)
## self.tabs.insertTab(SettingsTab, "Settings")
self.toolbarSelection = ZoomSelectToolbar(
self,
self.controlArea,
self.graph,
self.autoSendSelected,
buttons=(ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan,
ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconSpace,
ZoomSelectToolbar.IconRemoveLast,
ZoomSelectToolbar.IconRemoveAll,
ZoomSelectToolbar.IconSendSelection))
cb = OWGUI.checkBox(self.controlArea, self, "autoSendSelected",
"Auto send on selection change")
OWGUI.setStopper(self, self.toolbarSelection.buttonSendSelections, cb,
"selectionChangedFlag", self.commit)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.data,
Default + Multiple)]
self.outputs = [("Examples", ExampleTable, Default)]
# temp variables
self.MAdata = []
self.classColor = None
self.classBrighterColor = None
self.numberOfClasses = 0
self.classValues = []
self.ctrlPressed = False
self.attrIcons = self.createAttributeIconDict()
self.graph.canvas().setMouseTracking(1)
# self.zoomStack = []
## self.connect(self.graph,
## SIGNAL('plotMousePressed(const QMouseEvent&)'),
## self.onMousePressed)
## self.connect(self.graph,
## SIGNAL('plotMouseReleased(const QMouseEvent&)'),
## self.onMouseReleased)
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None,
title="Venn Diagram"):
super(OWVennDiagram, self).__init__(parent, signalManager, title,
wantGraph=True)
self.autocommit = False
# Selected disjoint subset indices
self.selection = []
# Stored input set hints
# {(index, inputname, attributes): (selectedattrname, itemsettitle)}
# The 'selectedattrname' can be None
self.inputhints = {}
# Use identifier columns for instance matching
self.useidentifiers = 1
self.loadSettings()
# Output changed flag
self._changed = False
# Diagram update is in progress
self._updating = False
# Input update is in progress
self._inputUpdate = False
# All input tables have the same domain.
self.samedomain = True
# Input datasets in the order they were 'connected'.
self.data = OrderedDict()
# Extracted input item sets in the order they were 'connected'
self.itemsets = OrderedDict()
# GUI
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, "No data on input\n")
self.identifiersBox = OWGUI.radioButtonsInBox(
self.controlArea, self, "useidentifiers", [],
box="Data Instance Identifiers",
callback=self._on_useidentifiersChanged
)
self.useequalityButton = OWGUI.appendRadioButton(
self.identifiersBox, self, "useidentifiers",
"Use instance equality"
)
rb = OWGUI.appendRadioButton(
self.identifiersBox, self, "useidentifiers",
"Use identifiers"
)
self.inputsBox = OWGUI.indentedBox(
self.identifiersBox, sep=OWGUI.checkButtonOffsetHint(rb)
)
self.inputsBox.setEnabled(self.useidentifiers == 1)
for i in range(5):
box = OWGUI.widgetBox(self.inputsBox, "Data set #%i" % (i + 1),
flat=True)
model = OWItemModels.VariableListModel(parent=self)
cb = QComboBox()
cb.setModel(model)
cb.activated[int].connect(self._on_inputAttrActivated)
box.setEnabled(False)
# Store the combo in the box for later use.
box.combo_box = cb
box.layout().addWidget(cb)
OWGUI.rubber(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Output")
cb = OWGUI.checkBox(box, self, "autocommit", "Commit on any change")
b = OWGUI.button(box, self, "Commit", callback=self.commit,
default=True)
OWGUI.setStopper(self, b, cb, "_changed", callback=self.commit)
# Main area view
self.scene = QGraphicsScene()
self.view = QGraphicsView(self.scene)
self.view.setRenderHint(QPainter.Antialiasing)
self.view.setBackgroundRole(QPalette.Window)
self.view.setFrameStyle(QGraphicsView.StyledPanel)
self.mainArea.layout().addWidget(self.view)
self.vennwidget = VennDiagram()
self.vennwidget.resize(400, 400)
self.vennwidget.itemTextEdited.connect(self._on_itemTextEdited)
self.scene.selectionChanged.connect(self._on_selectionChanged)
self.scene.addItem(self.vennwidget)
self.resize(self.controlArea.sizeHint().width() + 550,
max(self.controlArea.sizeHint().height(), 550))
self._queue = []
self.graphButton.clicked.connect(self.saveImage)
def __init__(self, parent=None, signalManager=None, name="Normalize Expression Array"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Expression array", ExampleTable, self.setData)]
self.outputs = [("Normalized expression array", ExampleTable, Default), ("Filtered expression array", ExampleTable)]
self.selectedGroup = 0
self.selectedCenterMethod = 0
self.selectedMergeMethod = 0
self.zCutoff = 1.96
self.appendZScore = False
self.appendRIValues = False
self.autoCommit = False
self.loadSettings()
## GUI
self.infoBox = OWGUI.widgetLabel(OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"No data on input.")
box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True)
self.groupCombo = OWGUI.comboBox(box, self, "selectedGroup",
callback=self.onGroupSelection
)
self.centerCombo = OWGUI.comboBox(self.controlArea, self, "selectedCenterMethod",
box="Center Fold-change Using",
items=[name for name, _ in self.CENTER_METHODS],
callback=self.onCenterMethodChange,
addSpace=True
)
self.mergeCombo = OWGUI.comboBox(self.controlArea, self, "selectedMergeMethod",
box="Merge Replicates",
items=[name for name, _ in self.MERGE_METHODS],
tooltip="Select the method for replicate merging",
callback=self.onMergeMethodChange,
addSpace=True
)
box = OWGUI.doubleSpin(self.controlArea, self, "zCutoff", 0.0, 3.0, 0.01,
box="Z-Score Cutoff",
callback=[self.replotMA, self.commitIf])
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Ouput")
OWGUI.checkBox(box, self, "appendZScore", "Append Z-Scores",
tooltip="Append calculated Z-Scores to output",
callback=self.commitIf
)
OWGUI.checkBox(box, self, "appendRIValues", "Append Log Ratio and Intensity values",
tooltip="Append calculated Log Ratio and Intensity values to output data",
callback=self.commitIf
)
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on change",
tooltip="Commit data on any change",
callback=self.commitIf
)
b = OWGUI.button(box, self, "Commit", callback=self.commit)
OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit)
self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph)
OWGUI.rubber(self.controlArea)
self.graph = OWGraph(self.mainArea)
self.graph.setAxisTitle(QwtPlot.xBottom, "Intensity: log<sub>10</sub>(R*G)")
self.graph.setAxisTitle(QwtPlot.yLeft, "Log ratio: log<sub>2</sub>(R/G)")
self.graph.showFilledSymbols = True
self.mainArea.layout().addWidget(self.graph)
self.groups = []
self.split_data = None, None
self.merged_splits = None, None
self.centered = None, None
self.changedFlag = False
self.data = None
self.resize(800, 600)
def __init__(self,
parent=None,
signalManager=None,
title="Expression Profile Distances"):
OWWidget.__init__(self, parent, signalManager, title)
self.inputs = [("Example Table", ExampleTable, self.set_data)]
self.outputs = [("Distances", Orange.core.SymMatrix),
("Sorted Example Table", ExampleTable)]
self.distance_measure = 0
self.auto_commit = False
self.changed_flag = False
self.loadSettings()
########
# GUI
########
self.info_box = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Input", addSpace=True),
"No data on input\n")
box = OWGUI.widgetBox(self.controlArea, "Separate By", addSpace=True)
self.separate_view = QListView()
self.separate_view.setSelectionMode(QListView.MultiSelection)
box.layout().addWidget(self.separate_view)
box = OWGUI.widgetBox(self.controlArea, "Sort By", addSpace=True)
self.relevant_view = QListView()
self.relevant_view.setSelectionMode(QListView.MultiSelection)
box.layout().addWidget(self.relevant_view)
self.distance_view = OWGUI.comboBox(
self.controlArea,
self,
"distance_measure",
box="Distance Measure",
items=[d[0] for d in self.DISTANCE_FUNCTIONS])
OWGUI.rubber(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Commit")
cb = OWGUI.checkBox(
box,
self,
"auto_commit",
"Commit on any change",
tooltip="Compute and send the distances on any change.",
callback=self.commit_if)
b = OWGUI.button(
box,
self,
"Commit",
tooltip="Compute the distances and send the output signals.",
callback=self.commit,
default=True)
OWGUI.setStopper(self, b, cb, "changed_flag", callback=self.commit)
self.groups_box = OWGUI.widgetBox(self.mainArea, "Groups")
self.groups_scroll_area = QScrollArea()
self.groups_box.layout().addWidget(self.groups_scroll_area)
self.data = None
self.partitions = []
self.matrix = None
self.split_groups = []
self._disable_updates = False
self.resize(800, 600)
