def __init__(self,parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, "&Display Motifs", 0)
# set default settings
self.colorBy = None
self.pvalThresholdIndex = None
self.pvalThreshold = None
#load settings
self.loadSettings()
# GUI
self.graph = OWGraph(self.mainArea)
self.graph.setYRlabels(None)
self.graph.enableGridXB(0)
self.graph.enableGridYL(1)
self.graph.setAxisMaxMinor(QwtPlot.xBottom, 10)
self.graph.setAxisMaxMajor(QwtPlot.xBottom, 10)
self.graph.setAxisAutoScale(QwtPlot.xBottom)
self.graph.setAxisScale(QwtPlot.xBottom, -1020, 0, 0)
self.mainArea.layout().addWidget(self.graph)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.cdata, Default), ("Genes", list, self.newGeneList, Default), ("Motifs", list, self.newMotifList, Default)]
self.data = None
self.motifLines = []
self.visibleValues = []
self.valueToCurve = {}
self.allGenes = [] ## genes displayed always in same order
self.geneList = [] ## selected genes
self.motifList = [] ## selected motifs
self.valuesPresentInData = []
self.clusterPostProbThreshold = 0
# GUI
self.selValues = OWGUI.widgetBox(self.controlArea, "Values")
self.selcolorBy = OWGUI.widgetBox(self.controlArea, "Color By")
self.colorByCombo = OWGUI.comboBox(self.selcolorBy, self, "colorBy",
items=[],
callback=self.colorByChanged)
self.pvalThresholdCombo = OWGUI.comboBox(self.selValues, self, "pvalThresholdIndex",
items=[],
callback=self.pvalThresholdChanged)
self.valuesQLB = QListWidget(self.selValues)
self.valuesQLB.setSelectionMode(QListWidget.MultiSelection)
self.connect(self.valuesQLB, SIGNAL("itemSelectionChanged()"), self.valuesSelectionChange)
self.selValues.layout().addWidget(self.valuesQLB)
self.unselectAllQLB = OWGUI.button(self.selValues, self, "Unselect all",
callback = self.unselAll)
def __init__(self, parent=None, signalManager=None,
title="Databases Pack"):
super(OWDatabasesPack, self).__init__(
parent, signalManager, title, wantMainArea=False)
self.fileslist = [("Taxonomy", "ncbi_taxonomy.tar.gz")]
self.downloadurl = "https://dl.dropboxusercontent.com/u/100248799/sf_pack.tar.gz"
self.downloadmessage = (
"Downloading a subset of available databases for a smoother " +
"ride through the workshop"
)
self.loadSettings()
self._tmpfile = None
self.reply = None
# Locks held on server files
self.locks = []
self.net_manager = QNetworkAccessManager()
# Lock all files in files list so any other (in process) atempt to
# download the files waits)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, self.downloadmessage)
self.info.setWordWrap(True)
box = OWGUI.widgetBox(self.controlArea, "Status")
self.statusinfo = OWGUI.widgetLabel(box, "Please wait")
self.statusinfo.setWordWrap(True)
self.progressbar = QProgressBar()
box.layout().addWidget(self.progressbar)
self.setMinimumWidth(250)
already_available = [(domain, filename)
for domain in serverfiles.listdomains()
for filename in serverfiles.listfiles(domain)]
if set(self.fileslist) <= set(already_available):
# All files are already downloaded
self.statusinfo.setText("All files already available")
self.setStatusMessage("Done")
else:
for domain, filename in self.fileslist + [("_tmp_cache_", "pack")]:
manager = serverfiles._lock_file(domain, filename)
try:
manager.__enter__()
except Exception:
warnings.warn("Could not acquire lock for {0} {0}"
.format(domain, filename))
self.warning(0, "...")
else:
self.locks.append(manager)
QTimer.singleShot(0, self.show)
QTimer.singleShot(0, self.run)
def __init__(self, parent=None, signalManager=None, title="Databases Pack"):
super(OWDatabasesPack, self).__init__(parent, signalManager, title, wantMainArea=False)
self.fileslist = [("Taxonomy", "ncbi_taxonomy.tar.gz")]
self.downloadurl = "https://dl.dropboxusercontent.com/u/100248799/sf_pack.tar.gz"
self.downloadmessage = (
"Downloading a subset of available databases for a smoother " + "ride through the workshop"
)
self.loadSettings()
self._tmpfile = None
self.reply = None
# Locks held on server files
self.locks = []
self.net_manager = QNetworkAccessManager()
# Lock all files in files list so any other (in process) atempt to
# download the files waits)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, self.downloadmessage)
self.info.setWordWrap(True)
box = OWGUI.widgetBox(self.controlArea, "Status")
self.statusinfo = OWGUI.widgetLabel(box, "Please wait")
self.statusinfo.setWordWrap(True)
self.progressbar = QProgressBar()
box.layout().addWidget(self.progressbar)
self.setMinimumWidth(250)
already_available = [
(domain, filename) for domain in serverfiles.listdomains() for filename in serverfiles.listfiles(domain)
]
if set(self.fileslist) <= set(already_available):
# All files are already downloaded
self.statusinfo.setText("All files already available")
self.setStatusMessage("Done")
else:
for domain, filename in self.fileslist + [("_tmp_cache_", "pack")]:
manager = serverfiles._lock_file(domain, filename)
try:
manager.__enter__()
except Exception:
warnings.warn("Could not acquire lock for {0} {0}".format(domain, filename))
self.warning(0, "...")
else:
self.locks.append(manager)
QTimer.singleShot(0, self.show)
QTimer.singleShot(0, self.run)
def Commit(self):
if not self.dbc:
self.Connect()
allTables = []
import time
start = time.time()
pb = OWGUI.ProgressBar(self, iterations=1000)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
ids += str(item.text(5)).split(",")
table = self.dbc.get_single_data(
ids=ids,
callback=pb.advance,
exclude_constant_labels=self.excludeconstant)
end = int(time.time() - start)
pb.finish()
#self.send("Example table", None)
# table.taxid = "352472"
# table.genesinrows = False
from Orange.orng.orngDataCaching import data_hints
data_hints.set_hint(table, "taxid", "352472", 10.0)
data_hints.set_hint(table, "genesinrows", False, 10.0)
self.send("Example table", table)
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self,
parent,
signalManager,
'Data Files Selector',
wantMainArea=0,
resizingEnabled=1)
self.callbackDeposit = []
self.inputs = [("Structured Data", DataFiles, self.onDataInput)]
self.outputs = [("Examples", ExampleTable),
("Structured Data", DataFiles)]
self.dataStructure = None
self.datasets = None
self.lastSentIds = []
# Settings
self.applyOnChange = 0
self.loadSettings()
# GUI
# info
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoa = OWGUI.widgetLabel(box, 'No data loaded.')
self.infob = OWGUI.widgetLabel(box, '')
self.infoc = OWGUI.widgetLabel(box, '')
# LIST VIEW
frmListView = OWGUI.widgetBox(self.controlArea, None, addSpace=True)
self.tree = QTreeWidget(frmListView)
self.tree.setSelectionMode(QAbstractItemView.MultiSelection)
self.tree.setHeaderLabel("Directory/Data File")
frmListView.layout().addWidget(self.tree)
self.connect(self.tree, SIGNAL('itemSelectionChanged()'),
self.selectionChanged)
# Output
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True)
OWGUI.checkBox(box, self, 'applyOnChange',
'Commit data on selection change')
self.commitBtn = OWGUI.button(box,
self,
"Commit",
callback=self.sendData,
disabled=1)
self.resize(300, 600)
def __init__(self, parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, "Save Data Files", wantMainArea = 0, resizingEnabled = 1)
self.inputs = [("Structured Data", DataFiles, self.structuredData, Default)]
self.outputs = []
self.dataStructure = None
# Settings
self.recentDirs=[]
self.selectedDirName = "(none)"
self.loadSettings()
# GUI
rfbox = OWGUI.widgetBox(self.controlArea, "Directory", orientation="horizontal", addSpace = True)
self.dircombo = QComboBox(rfbox)
rfbox.layout().addWidget(self.dircombo)
browse = OWGUI.button(rfbox, self, '&...', callback = self.browseDirectory, disabled=0)
browse.setMaximumWidth(25)
# info
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace = True)
self.infoa = OWGUI.widgetLabel(box, 'No data on input.')
# Output
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace = True)
self.save = OWGUI.button(box, self, '&Save', callback = self.saveData, disabled=1)
self.adjustSize()
# initial settings
self.recentDirs=filter(os.path.exists, self.recentDirs)
self.setDirlist()
self.dircombo.setCurrentIndex(0)
self.resize(300,self.height())
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, 'Data Distance')
self.inputs = [("Structured Data", DataFiles, self.chipdata)]
self.outputs = [("Distance Matrix", orange.SymMatrix)]
self.Metrics = 0
self.loadSettings()
self.data = []
## self.metrics = [("Euclidean", orange.ExamplesDistanceConstructor_Euclidean),
## ("Manhattan", orange.ExamplesDistanceConstructor_Manhattan),
## ("Hamming", orange.ExamplesDistanceConstructor_Hamming)]
self.metrics = [("Manhattan", distManhattan),
("Euclidean", distEuclidean),
("1 - (Pearson correlation coefficient)", distPearson),
("1 - (Spearman rank correlation coefficient)",
distSpearman)]
# GUI
self.mainArea.setFixedWidth(0)
# Info box
box = QVGroupBox("Info", self.controlArea)
self.infoa = QLabel('No data on input.', box)
self.infob = QLabel('', box)
OWGUI.separator(self.controlArea)
# Distance metrics selection
items = [x[0] for x in self.metrics]
OWGUI.comboBox(
self.controlArea,
self,
"Metrics",
box="Distance Metrics",
items=items,
tooltip="Metrics to measure distance between data sets.",
callback=self.onMetricsChange)
self.resize(384, 138)
def __init__(self, parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, 'Example Selector')
self.callbackDeposit = []
self.inputs = [("Example Selection", ExampleSelection, self.loadselection, Multiple + Default), ("Structured Data", DataFiles, self.chipdata)]
self.outputs = [("Example Selection", ExampleSelection), ("Selected Structured Data", DataFiles, Default), ("Other Structured Data", DataFiles)]
# Settings
self.negate = 0
self.commitOnChange = 1
self.sendNotSelectedData = 1
self.loadSettings()
self.selectors = {}
self.data = None
# GUI
# info
box = QVGroupBox("Info", self.controlArea)
self.infoa = QLabel('No data on input.', box)
self.infob = QLabel('', box)
OWGUI.separator(self.controlArea)
box.setMinimumWidth(170)
# gene selection
self.layout=QVBoxLayout(self.mainArea)
box = QVGroupBox("Gene Selection", self.mainArea)
self.table=QTable(box)
self.table.setSelectionMode(QTable.NoSelection)
self.layout.add(box)
self.table.hide()
self.drawtable()
OWGUI.checkBox(box, self, 'negate', 'Negate', callback = self.selectionChange)
# output
box = QVGroupBox("Output", self.controlArea)
OWGUI.checkBox(box, self, 'sendNotSelectedData', 'Send not selected data', callback=self.selectionChange)
OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on change')
self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.senddata, disabled=1)
self.resize(700,100)
def chipdata(self, data):
self.data = []
if data:
self.infob.setText("")
numFiles = reduce(lambda a, b: a + len(b[1]), data, 0)
lenSD = len(data)
self.infoa.setText("%d set%s, total of %d data file%s." %
(lenSD, ["", "s"][lenSD != 1], numFiles,
["", "s"][numFiles != 1]))
numExamplesList = []
# construct a list of ExampleTable lengths and a list of attribute names
for (name, etList) in data:
for et in etList:
setattr(et, "dirname", name)
setattr(et, "strain", name)
self.data.append(et)
numExamplesList.append(len(et))
if len(self.data) > 1:
# test that files contain the same attributes and equal number of examples
attrSorted = self.data[0].domain.attributes
attrSorted.sort()
numEx = len(self.data[0])
for et in self.data[1:]:
attrSorted2 = et.domain.attributes
attrSorted2.sort()
if map(lambda x: x.name, attrSorted) != map(
lambda x: x.name, attrSorted2):
self.data = []
self.infob.setText(
"Error: data files contain different attributes, aborting distance computation."
)
return
if len(et) != numEx:
self.data = []
self.infob.setText(
"Error: data files contain unequal number of examples, aborting distance computation."
)
return
# compute distances
pb = OWGUI.ProgressBar(self, iterations=len(self.data))
self.computeMatrix()
pb.finish()
else:
self.data = []
self.infob.setText(
'Error: not enough data, aborting distance computation.')
else:
self.infoa.setText('No data on input.')
def __init__(self, parent):
QObject.__init__(self)
grid = OWGUI.widgetBox(parent, "", orientation = "horizontal")
grid.setMinimumWidth(250)
grid.setMinimumHeight(100)
self.boxes = [ OWGUI.listBox(grid, self) for a in range(2) ]
for box in self.boxes:
#box.setSelectionMode(QListWidget.SingleSelection)
box.setSelectionMode(QListWidget.MultiSelection)
self.connect(self.boxes[0], SIGNAL("itemSelectionChanged ()"), self.highlighted1)
self.connect(self.boxes[1], SIGNAL("itemSelectionChanged ()"), self.highlighted2)
self.classes = []
def createSquarePixmap(color = Qt.black):
return OWGUI.createAttributePixmap("", color)
self.whiteSq = createSquarePixmap(Qt.white)
self.marked = [ createSquarePixmap(Qt.red), createSquarePixmap(Qt.blue) ]
self.classVals = []
def update_distances(self, base_indices=()):
"""Recompute the experiment distances.
"""
distance = self.selected_distance()
if base_indices == ():
base_group_index = self.selected_base_group_index()
base_indices = [ind[base_group_index] \
for _, ind in self.groups]
assert (len(base_indices) == len(self.groups))
base_distances = []
attributes = self.data.domain.attributes
pb = OWGUI.ProgressBar(self, len(self.groups) * \
len(attributes))
cached_distances, filled_set = self.get_cached_distances(distance)
for (group, indices), base_index in zip(self.groups, base_indices):
# Base column of the group
if base_index is not None:
base_vec = exp.linearize(self.data, [base_index])
distances = []
# Compute the distances between base column
# and all the rest data columns.
for i in range(len(attributes)):
if i == base_index:
distances.append(0.0)
elif self.get_cached_distance(distance, i,
base_index) is not None:
distances.append(
self.get_cached_distance(distance, i, base_index))
else:
vec_i = exp.linearize(self.data, [i])
dist = distance(base_vec, vec_i)
self.store_distance(distance, i, base_index, dist)
distances.append(dist)
pb.advance()
base_distances.append(distances)
else:
base_distances.append(None)
pb.finish()
self.distances = base_distances
def __init__(self, parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, 'Data Files Selector', wantMainArea = 0, resizingEnabled = 1)
self.callbackDeposit = []
self.inputs = [("Structured Data", DataFiles, self.onDataInput)]
self.outputs = [("Examples", ExampleTable), ("Structured Data", DataFiles)]
self.dataStructure = None
self.datasets = None
self.lastSentIds = []
# Settings
self.applyOnChange = 0
self.loadSettings()
# GUI
# info
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace = True)
self.infoa = OWGUI.widgetLabel(box, 'No data loaded.')
self.infob = OWGUI.widgetLabel(box, '')
self.infoc = OWGUI.widgetLabel(box, '')
# LIST VIEW
frmListView = OWGUI.widgetBox(self.controlArea, None, addSpace = True)
self.tree = QTreeWidget(frmListView)
self.tree.setSelectionMode(QAbstractItemView.MultiSelection)
self.tree.setHeaderLabel("Directory/Data File")
frmListView.layout().addWidget(self.tree)
self.connect(self.tree,SIGNAL('itemSelectionChanged()'),self.selectionChanged)
# Output
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace = True)
OWGUI.checkBox(box, self, 'applyOnChange', 'Commit data on selection change')
self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.sendData, disabled=1)
self.resize(300,600)
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self,
parent,
signalManager,
"Save Data Files",
wantMainArea=0,
resizingEnabled=1)
self.inputs = [("Structured Data", DataFiles, self.structuredData,
Default)]
self.outputs = []
self.dataStructure = None
# Settings
self.recentDirs = []
self.selectedDirName = "(none)"
self.loadSettings()
# GUI
rfbox = OWGUI.widgetBox(self.controlArea,
"Directory",
orientation="horizontal",
addSpace=True)
self.dircombo = QComboBox(rfbox)
rfbox.layout().addWidget(self.dircombo)
browse = OWGUI.button(rfbox,
self,
'&...',
callback=self.browseDirectory,
disabled=0)
browse.setMaximumWidth(25)
# info
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoa = OWGUI.widgetLabel(box, 'No data on input.')
# Output
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True)
self.save = OWGUI.button(box,
self,
'&Save',
callback=self.saveData,
disabled=1)
self.adjustSize()
# initial settings
self.recentDirs = filter(os.path.exists, self.recentDirs)
self.setDirlist()
self.dircombo.setCurrentIndex(0)
self.resize(300, self.height())
def __init__(self, parent=None, signalManager=None, name="dictyExpress"):
OWWidget.__init__(self, parent, signalManager, name)
self.outputs = [("Example table", ExampleTable)]
self.serverToken = ""
self.server = obiDicty.defaddress
self.platform = None
self.selectedExperiments = []
self.buffer = obiDicty.CacheSQLite(bufferfile)
self.searchString = ""
self.excludeconstant = False
box = OWGUI.widgetBox(self.controlArea, "Cache")
OWGUI.button(box, self, "Clear cache", callback=self.clear_buffer)
OWGUI.checkBox(self.controlArea, self, "excludeconstant",
"Exclude labels with constant values")
OWGUI.button(self.controlArea, self, "&Commit", callback=self.Commit)
box = OWGUI.widgetBox(self.controlArea, "Server")
OWGUI.lineEdit(box,
self,
"serverToken",
"Token",
callback=self.Connect)
OWGUI.rubber(self.controlArea)
OWGUI.lineEdit(self.mainArea,
self,
"searchString",
"Search",
callbackOnType=True,
callback=self.SearchUpdate)
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels([
"Strain", "Treatment", "Growth condition", "Platform", "N", "Chips"
])
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
## self.experimentsWidget.setAlternatingRowColors(True)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.loadSettings()
self.dbc = None
QTimer.singleShot(0, self.UpdateExperiments)
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None,
title="Quality Control"):
OWWidget.__init__(self, parent, signalManager, title,
wantGraph=True)
self.inputs = [("Experiment Data", Orange.data.Table, self.set_data)]
## Settings
self.selected_distance_index = 0
## Attributes
self.data = None
self.distances = None
self.groups = None
self.unique_pos = None
self.base_group_index = 0
## GUI
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info_box = OWGUI.widgetLabel(box, "\n")
## Separate By box
box = OWGUI.widgetBox(self.controlArea, "Separate By")
self.split_by_model = PyListModel()
self.split_by_view = QListView()
self.split_by_view.setSelectionMode(QListView.ExtendedSelection)
self.split_by_view.setModel(self.split_by_model)
box.layout().addWidget(self.split_by_view)
self.connect(self.split_by_view.selectionModel(),
SIGNAL("selectionChanged(QItemSelection, QItemSelection)"),
self.on_split_key_changed)
## Sort By box
box = OWGUI.widgetBox(self.controlArea, "Sort By")
self.sort_by_model = PyListModel()
self.sort_by_view = QListView()
self.sort_by_view.setSelectionMode(QListView.ExtendedSelection)
self.sort_by_view.setModel(self.sort_by_model)
box.layout().addWidget(self.sort_by_view)
self.connect(self.sort_by_view.selectionModel(),
SIGNAL("selectionChanged(QItemSelection, QItemSelection)"),
self.on_sort_key_changed)
## Distance box
box = OWGUI.widgetBox(self.controlArea, "Distance Measure")
OWGUI.comboBox(box, self, "selected_distance_index",
items=[t[0] for t in self.DISTANCE_FUNCTIONS],
callback=self.on_distance_measure_changed)
self.connect(self.graphButton,
SIGNAL("clicked()"),
self.save_graph)
self.scene = QGraphicsScene()
self.scene_view = QualityGraphicsView(self.scene)
self.scene_view.setRenderHints(QPainter.Antialiasing)
self.scene_view.setAlignment(Qt.AlignLeft | Qt.AlignVCenter)
self.mainArea.layout().addWidget(self.scene_view)
self.connect(self.scene_view,
SIGNAL("view_size_changed(QSize)"),
self.on_view_resize)
self._disable_updates = False
self._cached_distances = {}
self._base_index_hints = {}
self.main_widget = None
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):
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 = Numeric.ones((3,0), Numeric.Float) # p-values: 2D Numeric.array of shape (3, numExamples)
self.selectorName = "" # for Example Selection output: (self.selectorName, [0,1,0,...])
# Settings
self.anovaType = OWHypTest.StSST
self.popMean = 0 # single sample t-test, value to compare to
self.useFactors = [0,0,0] # [use factor A, use factor B, use interaction]
self._interaction = 0 # to store last setting: 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=QFrame(self.controlArea)
gl=QGridLayout(ca,4,1,5)
# info
box = QVGroupBox("Info", ca)
gl.addWidget(box,0,0)
self.infoa = QLabel('No data on input.', box)
self.infob = QLabel('', box)
self.infoc = QLabel('', box)
# ANOVA type
self.boxAnovaType = QVButtonGroup("Statistics", ca)
gl.addWidget(self.boxAnovaType,1,0)
self.boxAnovaType.setDisabled(1)
self.boxAnovaType.setRadioButtonExclusive(1)
self.boxAnovaType.buttons = []
## for i,lbl in enumerate(OWHypTest.StNames):
## w = QRadioButton(lbl, self.boxAnovaType)
## w.setOn(self.anovaType == i)
## self.boxAnovaType.buttons.append(w)
## if i == OWHypTest.StSST:
## self.boxPopMean = QHBox(self.boxAnovaType)
## QLabel(" population mean ", self.boxPopMean)
## OWGUI.lineEdit(self.boxPopMean, self, "popMean", callback=self.onPopMeanChange)
for i,lbl in enumerate(OWHypTest.StNames):
w = QRadioButton(lbl, self.boxAnovaType)
w.setOn(self.anovaType == i)
self.boxAnovaType.buttons.append(w)
if i == OWHypTest.StSST:
self.boxPopMean = QHBox(self.boxAnovaType)
QLabel(" population mean ", self.boxPopMean)
OWGUI.lineEdit(self.boxPopMean, self, "popMean", callback=self.onPopMeanChange)
OWGUI.connectControl(self.boxAnovaType, self, "anovaType", self.onAnovaType, "clicked(int)", OWGUI.CallFront_radioButtons(self.boxAnovaType))
# selection of examples
self.boxSelection = QVGroupBox("Example Selection", ca)
gl.addWidget(self.boxSelection,2,0)
self.lblNumGenes = [] # list of labels
# selector A
self.boxSelectorA = QVBox(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 = QFrame(self.boxSelectorA)
glA = QGridLayout(frmA,1,3,5)
leA = OWGUI.lineEdit(frmA, self, "alphaA", orientation="horizontal", controlWidth=None, callback=lambda x=0: self.onAlphaChange(x))
glA.addWidget(leA,0,1) # Qt.AlignRight
glA.addWidget(QLabel(" p <= ", frmA), 0,0)
self.lblNumGenes.append(QLabel('', frmA))
glA.addWidget(self.lblNumGenes[-1],0,2) # Qt.AlignRight | 0x22
# selector B
self.boxSelectorB = QVBox(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 = QFrame(self.boxSelectorB)
glB = QGridLayout(frmB,1,3,5)
leB = OWGUI.lineEdit(frmB, self, "alphaB", orientation="horizontal", callback=lambda x=1: self.onAlphaChange(x))
glB.addWidget(leB,0,1)
glB.addWidget(QLabel(" p <= ", frmB), 0,0)
self.lblNumGenes.append(QLabel('', frmB))
glB.addWidget(self.lblNumGenes[-1],0,2)
# selector I
self.boxSelectorI = QVBox(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 = QFrame(self.boxSelectorI)
glI = QGridLayout(frmI,1,3,5)
leI = OWGUI.lineEdit(frmI, self, "alphaI", orientation="horizontal", callback=lambda x=2: self.onAlphaChange(x))
## slider could be used to replace lineEdit (but not sensitive enough)
## self.alphaIf = 0.05
## leI = OWGUI.qwtHSlider(self.boxSelectorI, self, "alphaIf", box="", label=" p < ", labelWidth=None, minValue=0.0001, maxValue=1.0, step=0.1, precision=3, callback=lambda x=2: self.onAlphaChange(x), logarithmic=1, ticks=0, maxWidth=None)
glI.addWidget(leI,0,1)
glI.addWidget(QLabel(" p <= ", frmI), 0,0)
self.lblNumGenes.append(QLabel('', frmI))
glI.addWidget(self.lblNumGenes[-1],0,2)
# output
box = QVGroupBox("Output", ca)
gl.addWidget(box,3,0)
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,
title="Gene Atlas Tissue Expression"):
OWWidget.__init__(self, parent, signalManager, title)
self.inputs = [("Example Table", Orange.data.Table, self.set_data)]
self.outputs = [("Selected Genes", Orange.data.Table)]
self.selected_organism = "H**o sapiens"
self.selected_gene_attr = 0
self.genes_in_columns = False
self.selected_ef = 0
self.selected_ef_value = 0
self.loadSettings()
#####
# GUI
#####
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
self.info_label = OWGUI.widgetLabel(box, "No data on input.\n")
box = OWGUI.widgetBox(self.controlArea, "Organism", addSpace=True)
cb = OWGUI.comboBox(box,
self,
"selected_organism",
items=self.ORGANISMS,
tooltip="Organism name",
callback=self.on_organism_change,
sendSelectedValue=True,
valueType=str)
cb.setMaximumWidth(250)
box = OWGUI.widgetBox(self.controlArea,
"Gene Attribute",
addSpace=True)
self.gene_attr_cb = OWGUI.comboBox(
box,
self,
"selected_gene_attr",
tooltip="Attribute (column) containing the gene names.",
callback=self.on_gene_attr_change,
)
self.gene_attr_cb.setMaximumWidth(250)
cb = OWGUI.checkBox(
box,
self,
"genes_in_columns",
"Use attribute names",
tooltip="Gene names in columns.",
callback=self.on_genes_change,
)
cb.disables.append((-1, self.gene_attr_cb))
cb.makeConsistent()
box = OWGUI.widgetBox(self.controlArea, "Tissues", addSpace=True)
self.categories_cb = OWGUI.comboBox(
box,
self,
"selected_ef",
box="Categories",
items=self.FACTORS,
tooltip="Experimental factor.",
callback=self.on_ef_change,
)
self.categories_cb.box.setFlat(True)
self.values_cb = OWGUI.comboBox(box,
self,
"selected_ef_value",
box="Values",
tooltip="Experimental factor value.",
callback=self.on_ef_value_change)
self.values_cb.setMaximumWidth(250)
self.values_cb.box.setFlat(True)
box = OWGUI.widgetBox(self.controlArea, "Cache", addSpace=True)
OWGUI.button(box,
self,
"Clear cache",
callback=self.on_cache_clear,
tooltip="Clear Gene Atlas cache.")
OWGUI.rubber(self.controlArea)
OWGUI.button(self.controlArea,
self,
label="Commit",
callback=self.commit,
tooltip="Send selected genes")
self.report_view = QTreeView(self.mainArea)
self.report_view.setSelectionMode(QTreeView.ExtendedSelection)
self.report_view.setSortingEnabled(True)
self.report_view.setRootIsDecorated(False)
self.report_view.setAlternatingRowColors(True)
self.report_view.setEditTriggers(QTreeView.NoEditTriggers)
self.mainArea.layout().addWidget(self.report_view)
self.report_header = ["Gene symbol", "Up", "Down"]
model = QStandardItemModel()
model.setHorizontalHeaderLabels(self.report_header)
self.report_view.setModel(model)
self.data = None
self.candidate_vars = []
self.candidate_var_names = []
self.results = {}, {}, {}
self.ensembl_info = None
self.gene_matcher = obiGene.GMDirect()
self.loaded_matcher_taxid = None
self.unknown_genes = []
self.query_genes = []
# self.set_organism(self.selected_organism, update_results=False)
self.get_atlas_summary = obiGeneAtlas.get_atlas_summary
#Cached construct_matcher
@lru_cache(maxsize=3)
def my_cached_matcher(org):
return obiGeneAtlas.default_gene_matcher(org)
self.construct_matcher = my_cached_matcher
def __init__(self, parent=None, signalManager=None, title="Gene Network"):
super(OWGeneNetwork, self).__init__(parent,
signalManager,
title,
wantMainArea=False,
resizingEnabled=False)
self.taxid = "9606"
self.gene_var_index = -1
self.use_attr_names = False
self.network_source = 1
self.include_neighborhood = True
self.autocommit = False
self.min_score = 0.9
self.loadSettings()
self.taxids = taxonomy.common_taxids()
self.current_taxid_index = self.taxids.index(self.taxid)
self.data = None
self.geneinfo = None
self.nettask = None
self._invalidated = False
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, "No data on input\n")
box = OWGUI.widgetBox(self.controlArea, "Organism")
self.organism_cb = OWGUI.comboBox(box,
self,
"current_taxid_index",
items=map(taxonomy.name,
self.taxids),
callback=self._update_organism)
box = OWGUI.widgetBox(self.controlArea, "Genes")
self.genes_cb = OWGUI.comboBox(box,
self,
"gene_var_index",
callback=self._update_query_genes)
self.varmodel = OWItemModels.VariableListModel()
self.genes_cb.setModel(self.varmodel)
OWGUI.checkBox(box,
self,
"use_attr_names",
"Use attribute names",
callback=self._update_query_genes)
box = OWGUI.widgetBox(self.controlArea, "Network")
OWGUI.comboBox(box,
self,
"network_source",
items=[s.name for s in SOURCES],
callback=self._on_source_db_changed)
OWGUI.checkBox(box,
self,
"include_neighborhood",
"Include immediate gene neighbors",
callback=self.invalidate)
self.score_spin = OWGUI.doubleSpin(box,
self,
"min_score",
0.0,
1.0,
step=0.001,
label="Minimal edge score",
callback=self.invalidate)
self.score_spin.setEnabled(SOURCES[self.network_source].score_filter)
box = OWGUI.widgetBox(self.controlArea, "Commit")
OWGUI.button(box, self, "Commit", callback=self.commit, default=True)
self.executor = ThreadExecutor()
def __init__(self, parent=None, signalManager=None, name="dictyExpress"):
OWWidget.__init__(self, parent, signalManager, name)
self.outputs = [("Example table", ExampleTable)]
self.serverToken = ""
self.server = obiDicty.defaddress
self.platform = None
self.selectedExperiments = []
self.buffer = obiDicty.CacheSQLite(bufferfile)
self.searchString = ""
self.excludeconstant = False
box = OWGUI.widgetBox(self.controlArea, "Cache")
OWGUI.button(box, self, "Clear cache", callback=self.clear_buffer)
OWGUI.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values" )
OWGUI.button(self.controlArea, self, "&Commit", callback=self.Commit)
box = OWGUI.widgetBox(self.controlArea, "Server")
OWGUI.lineEdit(box, self, "serverToken","Token", callback=self.Connect)
OWGUI.rubber(self.controlArea)
OWGUI.lineEdit(self.mainArea, self, "searchString", "Search", callbackOnType=True, callback=self.SearchUpdate)
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels(["Strain", "Treatment", "Growth condition", "Platform", "N", "Chips"])
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
## self.experimentsWidget.setAlternatingRowColors(True)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.loadSettings()
self.dbc = None
QTimer.singleShot(0, self.UpdateExperiments)
self.resize(800, 600)
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, 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 update_scores(self):
""" Compute the scores and update the histogram.
"""
self.clear_plot()
self.error(0)
label, values = self.current_target_selection
if not self.data or label is None:
return
_, score_func, _, two_sample_test = self.score_methods[
self.method_index]
if two_sample_test:
target = self.targets
score_target = set(target)
ind1, ind2 = score_func(
self.data, self.genes_in_columns).test_indices(score_target)
if not len(ind1) or not len(ind2):
self.error(
0,
"Target labels most exclude/include at least one value.")
return
else: # ANOVA should use all labels.
target = dict(self.data_labels)[label]
if self.genes_in_columns:
target = [(label, t) for t in target]
score_target = target
# indices = score_func(self.data, self.genes_in_columns).test_indices(score_target)
# TODO: Check that each label has more than one measurement, raise warning otherwise.
pb = OWGUI.ProgressBar(
self, 4 + self.permutations_count if self.compute_null else 3)
self.scores = dict(
self.compute_scores(self.data,
score_func,
self.genes_in_columns,
score_target,
advance=pb.advance))
pb.advance()
if self.compute_null:
self.null_dist = self.compute_null_distribution(
self.data,
score_func,
self.genes_in_columns,
score_target,
self.permutations_count,
advance=pb.advance)
else:
self.null_dist = []
pb.advance()
htype = self.histType[self.score_methods[self.method_index][2]]
score_type = self.score_methods[self.method_index][0]
self.histogram.type = htype
if self.scores:
self.histogram.setValues(self.scores.values())
low, high = self.thresholds.get(score_type,
(float("-inf"), float("inf")))
minx, maxx = self.histogram.minx, self.histogram.maxx
low, high = max(low, minx), min(high, maxx)
if htype == "hiTail":
low = high
if htype == "lowTail":
high = low
self.histogram.setBoundary(low, high)
if self.compute_null and self.null_dist:
nullY, nullX = numpy.histogram(self.null_dist,
bins=self.histogram.xData)
nullY = nullY / self.permutations_count
self.histogram.nullCurve = self.histogram.addCurve(
"nullCurve",
Qt.black,
Qt.black,
6,
symbol=QwtSymbol.NoSymbol,
style=QwtPlotCurve.Steps,
xData=nullX,
yData=nullY)
minx = min(min(nullX), minx)
maxx = max(max(nullX), maxx)
miny = min(min(nullY), self.histogram.miny)
maxy = max(max(nullY), self.histogram.maxy)
spanx, spany = maxx - minx, maxy - miny
self.histogram.setAxisScale(QwtPlot.xBottom,
minx - 0.05 * spanx,
maxx + 0.05 * spanx)
self.histogram.setAxisScale(QwtPlot.yLeft, miny - 0.05 * spany,
maxy + 0.05 * spany)
state = dict(hiTail=(False, True),
lowTail=(True, False),
twoTail=(True, True))
for spin, visible in zip(
(self.upperBoundarySpin, self.lowerBoundarySpin),
state[self.histogram.type]):
spin.setVisible(visible)
# If this is a two sample test add markers to the left and right
# plot indicating which target group is over-expressed in that
# part
if self.method_index in [0, 2, 6]:
if self.method_index == 0: ## fold change is centered on 1.0
x1, y1 = (self.histogram.minx + 1) / 2, self.histogram.maxy
x2, y2 = (self.histogram.maxx + 1) / 2, self.histogram.maxy
else:
x1, y1 = (self.histogram.minx) / 2, self.histogram.maxy
x2, y2 = (self.histogram.maxx) / 2, self.histogram.maxy
if self.genes_in_columns:
label = target[0][0]
target_values = [t[1] for t in target]
values = dict(self.data_labels)[label]
else:
target_values = target
values = self.data_labels[0][1]
left = ", ".join(v for v in values if v not in target_values)
right = ", ".join(v for v in values if v in target_values)
self.histogram.addMarker(left, x1, y1)
self.histogram.addMarker(right, x2, y2)
self.warning(0)
else:
self.warning(0, "No scores obtained.")
self.histogram.replot()
pb.advance()
pb.finish()
self.update_data_info_label()
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 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):
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):
self.callbackDeposit = [] # deposit for OWGUI callback functions
OWWidget.__init__(self, parent, signalManager,
'Impute & Loess Profiles')
self._data = None # exampleTable
self._dataMA = None # input 2d masked array
self._chipdata = None # [(dirname0, [et0, et1, ...]), ...]
self._chipdataMA = [] # [(dirname0, [m2d0, m2d1, ...]), ...]
self.impute = 1
self.imputeK = 20
self.smooth = 1
self.windowSize = 3
self.commitOnChange = 1
# Settings
self.loadSettings()
# GUI
self.mainArea.setFixedWidth(0)
ca = QFrame(self.controlArea)
gl = QGridLayout(ca, 4, 1, 5)
# info
box = QVGroupBox("Info", ca)
gl.addWidget(box, 0, 0)
self.infoa = QLabel("No examples on input", box)
self.infob = QLabel("", box)
QLabel("", box)
self.infoc = QLabel("No structured data on input", box)
self.infod = QLabel("", box)
# KNN impute
self.boxImpute = QVGroupBox("Impute missing values", ca)
gl.addWidget(self.boxImpute, 1, 0)
OWGUI.checkBox(
self.boxImpute,
self,
"impute",
"KNN impute",
tooltip=
"Impute missing values from values of K nearest neighbours.",
callback=self.change)
## self.sliderK = OWGUI.hSlider(self.boxImpute, self, "imputeK", box=None, minValue=1, maxValue=7744, step=1, callback=self.imputeChange, labelFormat=" K = %i", ticks=0)
## self.sliderK = OWGUI.qwtHSlider(self.boxImpute, self, "imputeK", box=None, label="K", labelWidth=12, minValue=1, maxValue=7744, step=0.02, precision=0, callback=self.imputeChange, logarithmic=1, ticks=0, maxWidth=200)
## self.sliderK = OWGUI.qwtHSlider(self.boxImpute, self, "imputeK", box=None, label="K", labelWidth=12, minValue=1, maxValue=100, step=1, precision=0, callback=self.imputeKChange, logarithmic=0, ticks=0, maxWidth=200)
self.sliderK = OWGUI.qwtHSlider(self.boxImpute,
self,
"imputeK",
box=None,
label="K",
labelWidth=15,
minValue=1,
maxValue=999,
step=1,
precision=0,
callback=self.imputeKChange,
logarithmic=0,
ticks=0,
maxWidth=None)
self.boxImpute.setDisabled(1)
# loess
self.boxLoess = QVGroupBox("Smoothing", ca)
gl.addWidget(self.boxLoess, 2, 0)
OWGUI.checkBox(self.boxLoess,
self,
"smooth",
"Loess smoothing",
tooltip="Loess profiles, impute missing columns.",
callback=self.change)
lbl = QLabel("Window size (number of points)", self.boxLoess)
lbl.setAlignment(Qt.AlignHCenter)
self.sliderW = OWGUI.qwtHSlider(self.boxLoess,
self,
"windowSize",
box=None,
label="W",
labelWidth=15,
minValue=1,
maxValue=999,
step=1,
precision=0,
callback=self.smoothWChange,
logarithmic=0,
ticks=0,
maxWidth=None)
self.boxLoess.setDisabled(1)
# output
box = QVGroupBox("Output", ca)
gl.addWidget(box, 3, 0)
OWGUI.checkBox(box, self, 'commitOnChange',
'Commit data on selection change')
self.commitBtn = OWGUI.button(box,
self,
"Commit",
callback=self.senddata,
disabled=1)
self.inputs = [("Examples", ExampleTable, self.data),
("Structured Data", DataFiles, self.chipdata)]
self.outputs = [("Examples", ExampleTable),
("Structured Data", DataFiles)]
# data dependent variables
self.numRowsMissing = 0
self.numRowsMissingChipData = 0
self.resize(100, 100)
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "&Display Motifs", 0)
# set default settings
self.colorBy = None
self.pvalThresholdIndex = None
self.pvalThreshold = None
#load settings
self.loadSettings()
# GUI
self.graph = OWGraph(self.mainArea)
self.graph.setYRlabels(None)
self.graph.enableGridXB(0)
self.graph.enableGridYL(1)
self.graph.setAxisMaxMinor(QwtPlot.xBottom, 10)
self.graph.setAxisMaxMajor(QwtPlot.xBottom, 10)
self.graph.setAxisAutoScale(QwtPlot.xBottom)
self.graph.setAxisScale(QwtPlot.xBottom, -1020, 0, 0)
self.mainArea.layout().addWidget(self.graph)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.cdata, Default),
("Genes", list, self.newGeneList, Default),
("Motifs", list, self.newMotifList, Default)]
self.data = None
self.motifLines = []
self.visibleValues = []
self.valueToCurve = {}
self.allGenes = [] ## genes displayed always in same order
self.geneList = [] ## selected genes
self.motifList = [] ## selected motifs
self.valuesPresentInData = []
self.clusterPostProbThreshold = 0
# GUI
self.selValues = OWGUI.widgetBox(self.controlArea, "Values")
self.selcolorBy = OWGUI.widgetBox(self.controlArea, "Color By")
self.colorByCombo = OWGUI.comboBox(self.selcolorBy,
self,
"colorBy",
items=[],
callback=self.colorByChanged)
self.pvalThresholdCombo = OWGUI.comboBox(
self.selValues,
self,
"pvalThresholdIndex",
items=[],
callback=self.pvalThresholdChanged)
self.valuesQLB = QListWidget(self.selValues)
self.valuesQLB.setSelectionMode(QListWidget.MultiSelection)
self.connect(self.valuesQLB, SIGNAL("itemSelectionChanged()"),
self.valuesSelectionChange)
self.selValues.layout().addWidget(self.valuesQLB)
self.unselectAllQLB = OWGUI.button(self.selValues,
self,
"Unselect all",
callback=self.unselAll)
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 createSquarePixmap(color = Qt.black):
return OWGUI.createAttributePixmap("", color)
def __init__(self, parent=None, signalManager = None, loaddata=1):
OWWidget.__init__(self, parent, signalManager, 'Data Files', wantMainArea = 0, resizingEnabled = 1)
self.callbackDeposit = []
self.inputs = []
self.outputs = [("Examples", ExampleTable), ("Structured Data", DataFiles)]
self.dataStructure = []
self.datasets = None
self.lastSentIds = []
# Settings
self.recentDirs=[]
self.selectedDirName = "None"
self.applyOnChange = 0
self.loadSettings()
# CONTROLS
box = OWGUI.widgetBox(self.controlArea, "Directory", addSpace = True, orientation=0)
self.dircombo=QComboBox(box)
box.layout().addWidget(self.dircombo)
button = OWGUI.button(box, self, '...', callback = self.browseDirectory, disabled=0)
button.setMaximumWidth(25)
# connecting GUI to code
self.connect(self.dircombo,SIGNAL('activated(int)'),self.selectDir)
# info
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace = True)
self.infoa = OWGUI.widgetLabel(box, 'No data loaded.')
self.infob = OWGUI.widgetLabel(box, '')
self.infoc = OWGUI.widgetLabel(box, '')
# LIST VIEW
frmListView = OWGUI.widgetBox(self.controlArea, None, addSpace = True)
self.tree = QTreeWidget(frmListView)
self.tree.setSelectionMode(QAbstractItemView.MultiSelection)
self.tree.setHeaderLabel("Directory/Data File")
frmListView.layout().addWidget(self.tree)
self.connect(self.tree,SIGNAL('itemSelectionChanged()'),self.selectionChanged)
# Output
box = OWGUI.widgetBox(self.controlArea, "Output", addSpace = True)
OWGUI.checkBox(box, self, 'applyOnChange', 'Commit data on selection change')
self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.sendData, disabled=1)
self.resize(300,600)
# initial settings
self.recentDirs=filter(os.path.exists,self.recentDirs)
self.setDirlist()
self.dircombo.setCurrentIndex(0)
if self.recentDirs!=[] and loaddata:
self.loadData(self.recentDirs[0])
def compute(self, res=None, dm=None):
collectionNames = [ self.geneSel[a] for a in self.gridSel ]
organism = self.organismTaxids[self.organismIndex]
if self.gsgo:
collectionNames.append((("GO",),organism))
if self.gskegg:
collectionNames.append((("KEGG",),organism))
self.geneSets = obiGeneSets.collections(*collectionNames)
self.resultsOut(None)
qApp.processEvents()
self.res = res
self.dm = dm
clearListView(self.listView)
self.addComment("Computing...")
qApp.processEvents()
self.phenVar = self.phenCands[self.selectedPhenVar][0]
self.geneVar = self.geneCands[self.selectedGeneVar]
if self.res == None and self.data:
self.setSelMode(False)
pb = OWGUI.ProgressBar(self, iterations=self.perms+2)
if hasattr(self, "btnApply"):
self.btnApply.setFocus()
kwargs = {}
dkwargs = {}
dkwargs["phenVar"] = self.phenVar
dkwargs["geneVar"] = self.geneVar
if not obiGsea.already_have_correlations(self.data):
selectedClasses = self.psel.getSelection()
fc = "Phenotype group empty. Stopped."
if len(selectedClasses[0]) == 0:
self.addComment(fc)
return
elif len(selectedClasses[1]) == 0:
self.addComment(fc)
return
dkwargs["classValues"] = selectedClasses
dkwargs["atLeast"] = self.atLeast
permtype = self.permutationTypes[self.ptype][1]
kwargs["permutation"] = "class" if permtype == "p" else "genes"
def ifr(case, t, f):
if case: return t
else: return f
kwargs["minSize"] = \
ifr(self.minSubsetSizeC, self.minSubsetSize, 1)
kwargs["maxSize"] = \
ifr(self.maxSubsetSizeC, self.maxSubsetSize, 1000000)
kwargs["minPart"] = \
ifr(self.minSubsetPartC, self.minSubsetPart/100.0, 0.0)
#create gene matcher
genematcher = obiGene.matcher([[obiGene.GMKEGG(organism)] + ([obiGene.GMDicty()] if organism == "352472" else [])])
#dkwargs["caseSensitive"] = self.csgm
gso = obiGsea.GSEA(self.data, matcher=genematcher, **dkwargs)
for gs in self.geneSets:
gso.addGenesets([gs])
qApp.processEvents()
self.res = gso.compute(n=self.perms, callback=pb.advance, **kwargs)
pb.finish()
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, 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, 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,
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, "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, 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,
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='Approximate Profiles'):
self.callbackDeposit = [] # deposit for OWGUI callback functions
OWWidget.__init__(self, parent, signalManager, name)
self._data = None # exampleTable
self._dataN = None # 2d numeric array
self._chipdata = None # [(dirname0, [et0, et1, ...]), ...]
self._chipdataN = None # 3d numeric array
self.kernel = 0
self.kernels = ["Orthogonal polynomials", "Trigonometric functions"]
self.kernelSize = None
self.kernelSizes = [ ["Const"] + map(lambda x: "degree <= %i"%x, range(1,99)),
["Const", "cos x", "sin x"] + reduce(lambda x,y: x+[y[0],y[1]], map(lambda i: ("cos %ix"%i, "sin %ix"%i), range(2,99)), [])
]
self.useSignificance = 0
self.alpha = 3
self.alphas = [0.0001, 0.001, 0.01, 0.05, 0.1, 0.2, 0.5]
self.commitOnChange = 1
# Settings
self.loadSettings()
# GUI: info, comboKernelSize, cbUseSignificance, vboxSignificance, commitBtn
# info
box = QVGroupBox("Info", self.controlArea)
self.infoa = QLabel("No examples on input", box)
OWGUI.separator(box,250)
self.infob = QLabel("No structured data on input", box)
OWGUI.separator(self.controlArea)
# kernel selection
box = QVGroupBox("Kernel functions", self.controlArea)
OWGUI.comboBox(box, self, "kernel", items=self.kernels, callback=self.kernelChange)
OWGUI.separator(self.controlArea)
# kernel settings
box = QVGroupBox("Kernel settings", self.controlArea)
self.comboKernelSize = OWGUI.comboBox(box, self, "kernelSize", callback=self.kernelSizeChange, label="Number of kernel functions", labelWidth=135, orientation="horizontal", valueType=int)
self.comboKernelSize.setDisabled(1)
self.cbUseSignificance = OWGUI.checkBox(box, self, "useSignificance", "Significance of coefficients (F-statistics)", callback=self.useSignificanceChange, tooltip="Use kernels with coefficients significantly different from 0.")
self.vboxSignificance = QVBox(box)
OWGUI.comboBox(self.vboxSignificance, self, "alpha", items = self.alphas, callback=self.alphaChange, label="p <", labelWidth=20, orientation="horizontal")
OWGUI.separator(self.controlArea)
# output
box = QVGroupBox("Output", self.controlArea)
OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change')
self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.senddata, disabled=1)
self.inputs = [("Examples", ExampleTable, self.data), ("Structured Data", DataFiles, self.chipdata)]
self.outputs = [("Approximated Examples", ExampleTable, Default), ("Approximation Coefficients", ExampleTable), ("Approximated Structured Data", DataFiles, Default), ("Structured Approximation Coefficients", DataFiles)]
self.resize(200,100)
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="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='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, title="Gene Atlas Tissue Expression"):
OWWidget.__init__(self, parent, signalManager, title)
self.inputs = [("Example Table", Orange.data.Table, self.set_data)]
self.outputs = [("Selected Genes", Orange.data.Table)]
self.selected_organism = "H**o sapiens"
self.selected_gene_attr = 0
self.genes_in_columns = False
self.selected_ef = 0
self.selected_ef_value = 0
self.loadSettings()
#####
# GUI
#####
box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
self.info_label = OWGUI.widgetLabel(box, "No data on input.\n")
box = OWGUI.widgetBox(self.controlArea, "Organism", addSpace=True)
cb = OWGUI.comboBox(box, self, "selected_organism",
items=self.ORGANISMS,
tooltip="Organism name",
callback=self.on_organism_change,
sendSelectedValue=True,
valueType=str
)
cb.setMaximumWidth(250)
box = OWGUI.widgetBox(self.controlArea, "Gene Attribute", addSpace=True)
self.gene_attr_cb = OWGUI.comboBox(box, self, "selected_gene_attr",
tooltip="Attribute (column) containing the gene names.",
callback=self.on_gene_attr_change,
)
self.gene_attr_cb.setMaximumWidth(250)
cb = OWGUI.checkBox(box, self, "genes_in_columns", "Use attribute names",
tooltip="Gene names in columns.",
callback=self.on_genes_change,)
cb.disables.append((-1, self.gene_attr_cb))
cb.makeConsistent()
box = OWGUI.widgetBox(self.controlArea, "Tissues", addSpace=True)
self.categories_cb = OWGUI.comboBox(box, self, "selected_ef",
box="Categories",
items=self.FACTORS,
tooltip="Experimental factor.",
callback=self.on_ef_change,
)
self.categories_cb.box.setFlat(True)
self.values_cb = OWGUI.comboBox(box, self, "selected_ef_value",
box="Values",
tooltip="Experimental factor value.",
callback=self.on_ef_value_change
)
self.values_cb.setMaximumWidth(250)
self.values_cb.box.setFlat(True)
box = OWGUI.widgetBox(self.controlArea, "Cache", addSpace=True)
OWGUI.button(box, self, "Clear cache",
callback=self.on_cache_clear,
tooltip="Clear Gene Atlas cache.")
OWGUI.rubber(self.controlArea)
OWGUI.button(self.controlArea, self, label="Commit",
callback=self.commit,
tooltip="Send selected genes")
self.report_view = QTreeView(self.mainArea)
self.report_view.setSelectionMode(QTreeView.ExtendedSelection)
self.report_view.setSortingEnabled(True)
self.report_view.setRootIsDecorated(False)
self.report_view.setAlternatingRowColors(True)
self.report_view.setEditTriggers(QTreeView.NoEditTriggers)
self.mainArea.layout().addWidget(self.report_view)
self.report_header = ["Gene symbol", "Up", "Down"]
model = QStandardItemModel()
model.setHorizontalHeaderLabels(self.report_header)
self.report_view.setModel(model)
self.data = None
self.candidate_vars = []
self.candidate_var_names = []
self.results = {}, {}, {}
self.ensembl_info = None
self.gene_matcher = obiGene.GMDirect()
self.loaded_matcher_taxid = None
self.unknown_genes = []
self.query_genes = []
# self.set_organism(self.selected_organism, update_results=False)
self.get_atlas_summary = obiGeneAtlas.get_atlas_summary
#Cached construct_matcher
@lru_cache(maxsize=3)
def my_cached_matcher(org):
return obiGeneAtlas.default_gene_matcher(org)
self.construct_matcher = my_cached_matcher
def __init__(self, parent=None, signalManager=None,
name="Databases update", domains=None):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
self.accessCode = ""
self.domains = domains or DOMAINS
self.serverFiles = serverfiles.ServerFiles()
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
self.retryButton = gui.button(
box, self, "Reconnect", callback=self.RetrieveFilesList
)
self.retryButton.hide()
gui.rubber(box)
gui.lineEdit(box, self, "accessCode", "Access Code",
orientation="horizontal",
callback=self.RetrieveFilesList)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
def __init__(self, parent=None, signalManager=None, title="Gene Network"):
super(OWGeneNetwork, self).__init__(
parent, signalManager, title, wantMainArea=False,
resizingEnabled=False
)
self.taxid = "9606"
self.gene_var_index = -1
self.use_attr_names = False
self.network_source = 1
self.include_neighborhood = True
self.autocommit = False
self.min_score = 0.9
self.loadSettings()
self.taxids = taxonomy.common_taxids()
self.current_taxid_index = self.taxids.index(self.taxid)
self.data = None
self.geneinfo = None
self.nettask = None
self._invalidated = False
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, "No data on input\n")
box = OWGUI.widgetBox(self.controlArea, "Organism")
self.organism_cb = OWGUI.comboBox(
box, self, "current_taxid_index",
items=map(taxonomy.name, self.taxids),
callback=self._update_organism
)
box = OWGUI.widgetBox(self.controlArea, "Genes")
self.genes_cb = OWGUI.comboBox(
box, self, "gene_var_index", callback=self._update_query_genes
)
self.varmodel = OWItemModels.VariableListModel()
self.genes_cb.setModel(self.varmodel)
OWGUI.checkBox(
box, self, "use_attr_names",
"Use attribute names",
callback=self._update_query_genes
)
box = OWGUI.widgetBox(self.controlArea, "Network")
OWGUI.comboBox(
box, self, "network_source",
items=[s.name for s in SOURCES],
callback=self._on_source_db_changed
)
OWGUI.checkBox(
box, self, "include_neighborhood",
"Include immediate gene neighbors",
callback=self.invalidate
)
self.score_spin = OWGUI.doubleSpin(
box, self, "min_score", 0.0, 1.0, step=0.001,
label="Minimal edge score",
callback=self.invalidate
)
self.score_spin.setEnabled(SOURCES[self.network_source].score_filter)
box = OWGUI.widgetBox(self.controlArea, "Commit")
OWGUI.button(box, self, "Commit", callback=self.commit, default=True)
self.executor = ThreadExecutor()
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, 'Epistasis Analysis')
self.inputs = [("Examples", ExampleTable, self.dataset, Multiple),
("Structured Data", DataFiles, self.chipdata, 1)]
self.outputs = [("Gene Selection", ExampleSelection),
("Examples A->B", ExampleTable),
("Examples B->A", ExampleTable),
("Examples A||B", ExampleTable)]
self.data = []
self.selectedFile = None
self.A, self.B, self.AB = (None, None, None)
self.epiA, self.epiB, self.para = (0, 0, 0)
self.distype = 0
#set default settings
self.loadSettings()
# Selection of data files
box = OWGUI.widgetBox(self.controlArea, "Data files", addSpace=True)
# box = QVButtonGroup("Data Files", self.controlArea)
# self.fileLB = OWGUI.listBox(box, self, "selectedFile", "files",
# tooltip="Select example table",
## callback=self.fileSelectionChanged,
# selectionMode=QListWidget.SingleSelection,
# )
# self.connect(self.fileLB, SIGNAL("currentRowChanged(int)"), self.fileSelectionChanged)
self.fileLB = QListWidget()
# self.fileLB.setMaximumWidth(10)
self.connect(self.fileLB, SIGNAL("highlighted(int)"),
self.fileSelectionChanged)
# self.connect(self.fileLB, SIGNAL("selected(int)"), self.setFileReferenceBySelection)
box.layout().addWidget(self.fileLB)
hbox = OWGUI.widgetBox(box, "", orientation="horizontal")
# hbox = QHBox(box)
self.markBtns = []
for (i, lbl) in enumerate(["A", "B", "D"]):
btn = OWGUI.button(hbox,
self,
lbl,
callback=lambda i=i: self.setMark(i),
disabled=1)
# btn.setMaximumWidth(45)
# btn.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed)
self.markBtns.append(btn)
# Relations, checkbox for gene selection
self.sbox = OWGUI.widgetBox(self.controlArea,
"Relations (Gene Selection)")
# self.sbox = QVButtonGroup("Relations (Gene Selection)", self.controlArea)
self.selChkbox = []
self.cbinfo = (("epiA", "A -> B", "Gene B is epistatic to gene A"),
("epiB", "B -> A", "Gene A is epistatic to gene B"),
("para", "A || B",
"Genes A and B are on parallel pathways"))
for (i, cb) in enumerate(self.cbinfo):
cb = OWGUI.checkBox(self.sbox,
self,
cb[0],
cb[1],
tooltip=cb[2],
callback=self.filterSelectionChanged)
self.selChkbox.append(cb)
self.infochi = OWGUI.widgetLabel(self.sbox, "") #QLabel(self.sbox, '')
self.sbox.setDisabled(1)
OWGUI.radioButtonsInBox(self.controlArea,
self,
"distype",
["Average By Gene", "Average By Measurement"],
box="Distance",
tooltips=None,
callback=self.analysis)
# scene
self.scene = QGraphicsScene()
self.sceneView = QGraphicsView()
self.sceneView.setScene(self.scene)
self.scene.setSceneRect(QRectF(0, 0, canvasW, canvasW))
self.mainArea.layout().addWidget(self.sceneView)
# canvas
# self.canvas = QCanvas()
# self.layout = QVBoxLayout(self.mainArea)
# self.canvasView = QCanvasView(self.canvas, self.mainArea)
# self.canvas.resize(canvasW, canvasW)
# self.layout.add(self.canvasView)
self.resize(420, 350)
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="Databases update"):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
self.retryButton = gui.button(
box, self, "Reconnect", callback=self.RetrieveFilesList
)
self.retryButton.hide()
gui.rubber(box)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
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):
OWWidget.__init__(self, parent, signalManager, 'Epistasis Analysis')
self.inputs = [("Examples", ExampleTable, self.dataset, Multiple), ("Structured Data", DataFiles, self.chipdata, 1)]
self.outputs = [("Gene Selection", ExampleSelection), ("Examples A->B", ExampleTable), ("Examples B->A", ExampleTable), ("Examples A||B", ExampleTable)]
self.data = []
self.selectedFile = None
self.A, self.B, self.AB = (None, None, None)
self.epiA, self.epiB, self.para = (0, 0, 0)
self.distype = 0
#set default settings
self.loadSettings()
# Selection of data files
box = OWGUI.widgetBox(self.controlArea, "Data files", addSpace=True)
# box = QVButtonGroup("Data Files", self.controlArea)
# self.fileLB = OWGUI.listBox(box, self, "selectedFile", "files",
# tooltip="Select example table",
## callback=self.fileSelectionChanged,
# selectionMode=QListWidget.SingleSelection,
# )
# self.connect(self.fileLB, SIGNAL("currentRowChanged(int)"), self.fileSelectionChanged)
self.fileLB = QListWidget()
# self.fileLB.setMaximumWidth(10)
self.connect(self.fileLB, SIGNAL("highlighted(int)"), self.fileSelectionChanged)
# self.connect(self.fileLB, SIGNAL("selected(int)"), self.setFileReferenceBySelection)
box.layout().addWidget(self.fileLB)
hbox = OWGUI.widgetBox(box, "", orientation="horizontal")
# hbox = QHBox(box)
self.markBtns = []
for (i, lbl) in enumerate(["A","B","D"]):
btn = OWGUI.button(hbox, self, lbl,
callback=lambda i=i: self.setMark(i),
disabled=1)
# btn.setMaximumWidth(45)
# btn.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed)
self.markBtns.append(btn)
# Relations, checkbox for gene selection
self.sbox = OWGUI.widgetBox(self.controlArea, "Relations (Gene Selection)")
# self.sbox = QVButtonGroup("Relations (Gene Selection)", self.controlArea)
self.selChkbox = []
self.cbinfo = (("epiA", "A -> B", "Gene B is epistatic to gene A"),
("epiB", "B -> A", "Gene A is epistatic to gene B"),
("para", "A || B", "Genes A and B are on parallel pathways"))
for (i, cb) in enumerate(self.cbinfo):
cb = OWGUI.checkBox(self.sbox, self, cb[0], cb[1],
tooltip=cb[2],
callback=self.filterSelectionChanged)
self.selChkbox.append(cb)
self.infochi = OWGUI.widgetLabel(self.sbox, "") #QLabel(self.sbox, '')
self.sbox.setDisabled(1)
OWGUI.radioButtonsInBox(self.controlArea, self, "distype", ["Average By Gene", "Average By Measurement"],
box="Distance", tooltips=None, callback=self.analysis)
# scene
self.scene = QGraphicsScene()
self.sceneView = QGraphicsView()
self.sceneView.setScene(self.scene)
self.scene.setSceneRect(QRectF(0, 0, canvasW, canvasW))
self.mainArea.layout().addWidget(self.sceneView)
# canvas
# self.canvas = QCanvas()
# self.layout = QVBoxLayout(self.mainArea)
# self.canvasView = QCanvasView(self.canvas, self.mainArea)
# self.canvas.resize(canvasW, canvasW)
# self.layout.add(self.canvasView)
self.resize(420,350)
def __init__(self, parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, 'Process Chip Data')
self.callbackDeposit = []
self.inputs = [("Structured Data", DataFiles, self.chipdata)]
self.outputs = [("Structured Data", DataFiles)]
self.chipdata = None; self.datasets = None
self.std = [("No preprocessing", None),
("Array-based standardization", chipstat.standardize_arrays),
("Gene-based standardization", chipstat.standardize_genes),
("First array-, then gene-based standardization", lambda e,r: chipstat.standardize_genes(chipstat.standardize_arrays(e,r),r)),
("First gene-, then array-based standardization", lambda e,r: chipstat.standardize_arrays(chipstat.standardize_genes(e,r),r))]
# Settings
self.data = None
self.preStdMethod = 0; self.preStdRob = 1
self.postStdMethod = 0; self.postStdRob = 1
self.mergeType = 0
self.commitOnChange = 0
self.loadSettings()
# GUI
# info
box = QVGroupBox("Info", self.controlArea)
self.infoa = QLabel('No data on input.', box)
self.infob = QLabel('', box)
# preprocessing
OWGUI.separator(self.controlArea)
box = QVGroupBox("Preprocessing", self.controlArea)
labels = [x[0] for x in self.std]
OWGUI.comboBox(box, self, 'preStdMethod', label=None, labelWidth=None, orientation='vertical', items=labels, callback=self.selectionChange)
self.preRobBtn = OWGUI.checkBox(box, self, "preStdRob", "Robust standardization", callback=self.selectionChange)
# merge
OWGUI.separator(self.controlArea)
self.mergeTypes = [(0, "No merging"), ('mean', 'Mean'), ('median', 'Median'), ('min', 'Minimum expression'), ('max', 'Maximum expression')]
labels = [x[1] for x in self.mergeTypes]
OWGUI.radioButtonsInBox(self.controlArea, self, 'mergeType', labels, box='Merge Replicas', tooltips=None, callback=self.selectionChange)
# postprocessing
OWGUI.separator(self.controlArea)
self.boxPostproc = QVGroupBox("Postprocessing", self.controlArea)
labels = [x[0] for x in self.std]
OWGUI.comboBox(self.boxPostproc, self, 'postStdMethod', label=None, labelWidth=None, orientation='vertical', items=labels, callback=self.selectionChange)
self.postRobBtn = OWGUI.checkBox(self.boxPostproc, self, "postStdRob", "Robust standardization", callback=self.selectionChange)
# output
OWGUI.separator(self.controlArea)
box = QVGroupBox("Output", self.controlArea)
OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change')
self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.selectionChange, disabled=1)
self.setBtnsState()
self.resize(100,100)
