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, 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 __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):
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 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, 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,
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,
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, 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, title="Expression Profile Distances"):
OWWidget.__init__(self, parent, signalManager, title)
self.inputs = [("Example Table", ExampleTable, self.set_data)]
self.outputs = [("Distances", Orange.core.SymMatrix), ("Sorted Example Table", ExampleTable)]
self.distance_measure = 0
self.auto_commit = False
self.changed_flag = False
self.loadSettings()
########
# GUI
########
self.info_box = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Input", addSpace=True), "No data on input\n"
)
box = OWGUI.widgetBox(self.controlArea, "Separate By", addSpace=True)
self.separate_view = QListView()
self.separate_view.setSelectionMode(QListView.MultiSelection)
box.layout().addWidget(self.separate_view)
box = OWGUI.widgetBox(self.controlArea, "Sort By", addSpace=True)
self.relevant_view = QListView()
self.relevant_view.setSelectionMode(QListView.MultiSelection)
box.layout().addWidget(self.relevant_view)
self.distance_view = OWGUI.comboBox(
self.controlArea,
self,
"distance_measure",
box="Distance Measure",
items=[d[0] for d in self.DISTANCE_FUNCTIONS],
)
OWGUI.rubber(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Commit")
cb = OWGUI.checkBox(
box,
self,
"auto_commit",
"Commit on any change",
tooltip="Compute and send the distances on any change.",
callback=self.commit_if,
)
b = OWGUI.button(
box,
self,
"Commit",
tooltip="Compute the distances and send the output signals.",
callback=self.commit,
default=True,
)
OWGUI.setStopper(self, b, cb, "changed_flag", callback=self.commit)
self.groups_box = OWGUI.widgetBox(self.mainArea, "Groups")
self.groups_scroll_area = QScrollArea()
self.groups_box.layout().addWidget(self.groups_scroll_area)
self.data = None
self.partitions = []
self.matrix = None
self.split_groups = []
self._disable_updates = False
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Normalize Expression Array"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Expression array", ExampleTable, self.setData)]
self.outputs = [("Normalized expression array", ExampleTable, Default), ("Filtered expression array", ExampleTable)]
self.selectedGroup = 0
self.selectedCenterMethod = 0
self.selectedMergeMethod = 0
self.zCutoff = 1.96
self.appendZScore = False
self.appendRIValues = False
self.autoCommit = False
self.loadSettings()
## GUI
self.infoBox = OWGUI.widgetLabel(OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"No data on input.")
box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True)
self.groupCombo = OWGUI.comboBox(box, self, "selectedGroup",
callback=self.onGroupSelection
)
self.centerCombo = OWGUI.comboBox(self.controlArea, self, "selectedCenterMethod",
box="Center Fold-change Using",
items=[name for name, _ in self.CENTER_METHODS],
callback=self.onCenterMethodChange,
addSpace=True
)
self.mergeCombo = OWGUI.comboBox(self.controlArea, self, "selectedMergeMethod",
box="Merge Replicates",
items=[name for name, _ in self.MERGE_METHODS],
tooltip="Select the method for replicate merging",
callback=self.onMergeMethodChange,
addSpace=True
)
box = OWGUI.doubleSpin(self.controlArea, self, "zCutoff", 0.0, 3.0, 0.01,
box="Z-Score Cutoff",
callback=[self.replotMA, self.commitIf])
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Ouput")
OWGUI.checkBox(box, self, "appendZScore", "Append Z-Scores",
tooltip="Append calculated Z-Scores to output",
callback=self.commitIf
)
OWGUI.checkBox(box, self, "appendRIValues", "Append Log Ratio and Intensity values",
tooltip="Append calculated Log Ratio and Intensity values to output data",
callback=self.commitIf
)
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on change",
tooltip="Commit data on any change",
callback=self.commitIf
)
b = OWGUI.button(box, self, "Commit", callback=self.commit)
OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit)
self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph)
OWGUI.rubber(self.controlArea)
self.graph = OWGraph(self.mainArea)
self.graph.setAxisTitle(QwtPlot.xBottom, "Intensity: log<sub>10</sub>(R*G)")
self.graph.setAxisTitle(QwtPlot.yLeft, "Log ratio: log<sub>2</sub>(R/G)")
self.graph.showFilledSymbols = True
self.mainArea.layout().addWidget(self.graph)
self.groups = []
self.split_data = None, None
self.merged_splits = None, None
self.centered = None, None
self.changedFlag = False
self.data = None
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, title="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=" 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, 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="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=" 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="KEGG Pathways"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Examples", Orange.data.Table, self.SetData),
("Reference", Orange.data.Table, self.SetRefData)]
self.outputs = [("Selected Examples", Orange.data.Table),
("Unselected Examples", Orange.data.Table)]
self.organismIndex = 0
self.geneAttrIndex = 0
self.autoCommit = False
self.autoResize = True
self.useReference = False
self.useAttrNames = 0
self.showOrthology = True
self.loadSettings()
self.organismCodes = []
self._changedFlag = False
self.controlArea.setMaximumWidth(250)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.infoLabel = OWGUI.widgetLabel(box, "No data on input\n")
# Organism selection.
box = OWGUI.widgetBox(self.controlArea, "Organism")
self.organismComboBox = OWGUI.comboBox(
box, self, "organismIndex",
items=[],
callback=self.Update,
addSpace=True,
debuggingEnabled=0,
tooltip="Select the organism of the input genes")
# Selection of genes attribute
box = OWGUI.widgetBox(self.controlArea, "Gene attribute")
self.geneAttrCandidates = VariableListModel(parent=self)
self.geneAttrCombo = OWGUI.comboBox(
box, self, "geneAttrIndex", callback=self.Update)
self.geneAttrCombo.setModel(self.geneAttrCandidates)
OWGUI.checkBox(box, self, "useAttrNames",
"Use variable names",
disables=[(-1, self.geneAttrCombo)],
callback=self.Update)
self.geneAttrCombo.setDisabled(bool(self.useAttrNames))
OWGUI.separator(self.controlArea)
OWGUI.checkBox(self.controlArea, self, "useReference",
"From signal",
box="Reference",
callback=self.Update)
OWGUI.separator(self.controlArea)
OWGUI.checkBox(self.controlArea, self, "showOrthology",
"Show pathways in full orthology",
box="Orthology",
callback=self.UpdateListView)
OWGUI.checkBox(self.controlArea, self, "autoResize",
"Resize to fit",
box="Image",
callback=self.UpdatePathwayViewTransform)
box = OWGUI.widgetBox(self.controlArea, "Cache Control")
OWGUI.button(box, self, "Clear cache",
callback=self.ClearCache,
tooltip="Clear all locally cached KEGG data.")
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Selection")
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on update")
button = OWGUI.button(box, self, "Commit", callback=self.Commit,
default=True)
OWGUI.setStopper(self, button, cb, "_changedFlag", self.Commit)
OWGUI.rubber(self.controlArea)
spliter = QSplitter(Qt.Vertical, self.mainArea)
self.pathwayView = PathwayView(self, spliter)
self.pathwayView.scene().selectionChanged.connect(
self._onSelectionChanged
)
self.mainArea.layout().addWidget(spliter)
self.listView = QTreeWidget(spliter)
spliter.addWidget(self.listView)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(4)
self.listView.setHeaderLabels(["Pathway", "P value",
"Genes", "Reference"])
self.listView.setSelectionMode(QTreeWidget.SingleSelection)
self.listView.setSortingEnabled(True)
self.listView.setMaximumHeight(200)
self.connect(self.listView,
SIGNAL("itemSelectionChanged()"),
self.UpdatePathwayView)
self.connect(self.graphButton,
SIGNAL("clicked()"),
self.saveGraph)
select = QAction(
"Select All", self,
shortcut=QKeySequence.SelectAll
)
select.triggered.connect(self.selectAll)
self.addAction(select)
self.data = None
self.refData = None
self.resize(800, 600)
self.connect(self,
SIGNAL("widgetStateChanged(QString, int, QString)"),
self.onStateChange)
self.has_new_data = False
self.has_new_reference_set = False
self._executor = ThreadExecutor()
self.setEnabled(False)
self.setBlocking(True)
QTimer.singleShot(0, self._initialize)
self.infoLabel.setText("Fetching organism definitions\n")
def __init__(self, parent=None, signalManager=None):
# self.callbackDeposit = [] # deposit for OWGUI callback functions
OWWidget.__init__(self, parent, signalManager, 'Expression Profiles',
1)
#set default settings
self.ShowAverageProfile = 1
self.ShowSingleProfiles = 0
self.PointWidth = 2
self.CurveWidth = 1
self.AverageCurveWidth = 4
self.BoxPlotWidth = 2
self.SelectedClasses = []
self.Classes = []
self.autoSendSelected = 0
self.selectionChangedFlag = False
self.CutLow = 0
self.CutHigh = 0
self.CutEnabled = 0
self.profileLabel = None
#load settings
self.loadSettings()
# GUI
self.graph = profilesGraph(self, self.mainArea, "")
self.mainArea.layout().addWidget(self.graph)
self.graph.hide()
self.connect(self.graphButton, SIGNAL("clicked()"),
self.graph.saveToFile)
# GUI definition
self.tabs = OWGUI.tabWidget(self.space)
# GRAPH TAB
GraphTab = OWGUI.createTabPage(self.tabs, "Graph")
## display options
self.infoLabel = OWGUI.widgetLabel(OWGUI.widgetBox(GraphTab, "Info"),
"No data on input.")
displayOptBox = OWGUI.widgetBox(
GraphTab, "Display") #QVButtonGroup("Display", GraphTab)
displayOptButtons = [
'Majority Class', 'Majority Class Probability',
'Target Class Probability', 'Number of Instances'
]
OWGUI.checkBox(displayOptBox,
self,
'ShowSingleProfiles',
'Expression Profiles',
tooltip='',
callback=self.updateShowSingleProfiles)
OWGUI.checkBox(displayOptBox,
self,
'ShowAverageProfile',
'Box Plot',
tooltip='',
callback=self.updateShowAverageProfile)
## class selection (classQLB)
self.classQVGB = OWGUI.widgetBox(GraphTab,
"Classes") #QVGroupBox(GraphTab)
## self.classQVGB.setTitle("Classes")
self.classQLB = OWGUI.listBox(
self.classQVGB,
self,
"SelectedClasses",
"Classes",
selectionMode=QListWidget.MultiSelection,
callback=self.classSelectionChange) #QListBox(self.classQVGB)
## self.classQLB.setSelectionMode(QListBox.Multi)
self.unselectAllClassedQLB = OWGUI.button(
self.classQVGB, self, "Unselect all", callback=self.SUAclassQLB
) #QPushButton("(Un)Select All", self.classQVGB)
## self.connect(self.unselectAllClassedQLB, SIGNAL("clicked()"), self.SUAclassQLB)
## self.connect(self.classQLB, SIGNAL("selectionChanged()"), self.classSelectionChange)
## show single/average profile
## self.showAverageQLB = QPushButton("Box Plot", self.classQVGB)
## self.showAverageQLB.setToggleButton(1)
## self.showAverageQLB.setOn(self.ShowAverageProfile)
## self.showSingleQLB = QPushButton("Single Profiles", self.classQVGB)
## self.showSingleQLB.setToggleButton(1)
## self.showSingleQLB.setOn(self.ShowSingleProfiles)
## self.connect(self.showAverageQLB, SIGNAL("toggled(bool)"), self.updateShowAverageProfile)
## self.connect(self.showSingleQLB, SIGNAL("toggled(bool)"), self.updateShowSingleProfiles)
## self.tabs.insertTab(GraphTab, "Graph")
# SETTINGS TAB
SettingsTab = OWGUI.createTabPage(self.tabs,
"Settings") #QVGroupBox(self)
self.profileLabelComboBox = OWGUI.comboBox(SettingsTab,
self,
'profileLabel',
'Profile Labels',
sendSelectedValue=True,
valueType=str)
OWGUI.hSlider(SettingsTab,
self,
'PointWidth',
box='Point Width',
minValue=0,
maxValue=9,
step=1,
callback=self.updatePointWidth,
ticks=1)
OWGUI.hSlider(SettingsTab,
self,
'CurveWidth',
box='Profile Width',
minValue=1,
maxValue=9,
step=1,
callback=self.updateCurveWidth,
ticks=1)
OWGUI.hSlider(SettingsTab,
self,
'AverageCurveWidth',
box='Average Profile Width',
minValue=1,
maxValue=9,
step=1,
callback=self.updateAverageCurveWidth,
ticks=1)
OWGUI.hSlider(SettingsTab,
self,
'BoxPlotWidth',
box='Box Plot Width',
minValue=0,
maxValue=9,
step=1,
callback=self.updateBoxPlotWidth,
ticks=1)
OWGUI.checkBox(SettingsTab,
self,
'graph.renderAntialiased',
"Render antialiased",
callback=self.graph.setCurveRenderHints)
## graph y scale
box = OWGUI.widgetBox(
SettingsTab, "Threshold/ Values"
) #QVButtonGroup("Threshol/ Values", SettingsTab)
OWGUI.checkBox(box,
self,
'CutEnabled',
"Enabled",
callback=self.setCutEnabled)
self.sliderCutLow = OWGUI.qwtHSlider(box,
self,
'CutLow',
label='Low:',
labelWidth=33,
minValue=-20,
maxValue=0,
step=0.1,
precision=1,
ticks=0,
maxWidth=80,
callback=self.updateYaxis)
self.sliderCutHigh = OWGUI.qwtHSlider(box,
self,
'CutHigh',
label='High:',
labelWidth=33,
minValue=0,
maxValue=20,
step=0.1,
precision=1,
ticks=0,
maxWidth=80,
callback=self.updateYaxis)
if not self.CutEnabled:
self.sliderCutLow.box.setDisabled(1)
self.sliderCutHigh.box.setDisabled(1)
## self.tabs.insertTab(SettingsTab, "Settings")
self.toolbarSelection = ZoomSelectToolbar(
self,
self.controlArea,
self.graph,
self.autoSendSelected,
buttons=(ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan,
ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconSpace,
ZoomSelectToolbar.IconRemoveLast,
ZoomSelectToolbar.IconRemoveAll,
ZoomSelectToolbar.IconSendSelection))
cb = OWGUI.checkBox(self.controlArea, self, "autoSendSelected",
"Auto send on selection change")
OWGUI.setStopper(self, self.toolbarSelection.buttonSendSelections, cb,
"selectionChangedFlag", self.commit)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.data,
Default + Multiple)]
self.outputs = [("Examples", ExampleTable, Default)]
# temp variables
self.MAdata = []
self.classColor = None
self.classBrighterColor = None
self.numberOfClasses = 0
self.classValues = []
self.ctrlPressed = False
self.attrIcons = self.createAttributeIconDict()
self.graph.canvas().setMouseTracking(1)
# self.zoomStack = []
## self.connect(self.graph,
## SIGNAL('plotMousePressed(const QMouseEvent&)'),
## self.onMousePressed)
## self.connect(self.graph,
## SIGNAL('plotMouseReleased(const QMouseEvent&)'),
## self.onMouseReleased)
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None,
title="Venn Diagram"):
super(OWVennDiagram, self).__init__(parent, signalManager, title,
wantGraph=True)
self.autocommit = False
# Selected disjoint subset indices
self.selection = []
# Stored input set hints
# {(index, inputname, attributes): (selectedattrname, itemsettitle)}
# The 'selectedattrname' can be None
self.inputhints = {}
# Use identifier columns for instance matching
self.useidentifiers = 1
self.loadSettings()
# Output changed flag
self._changed = False
# Diagram update is in progress
self._updating = False
# Input update is in progress
self._inputUpdate = False
# All input tables have the same domain.
self.samedomain = True
# Input datasets in the order they were 'connected'.
self.data = OrderedDict()
# Extracted input item sets in the order they were 'connected'
self.itemsets = OrderedDict()
# GUI
box = OWGUI.widgetBox(self.controlArea, "Info")
self.info = OWGUI.widgetLabel(box, "No data on input\n")
self.identifiersBox = OWGUI.radioButtonsInBox(
self.controlArea, self, "useidentifiers", [],
box="Data Instance Identifiers",
callback=self._on_useidentifiersChanged
)
self.useequalityButton = OWGUI.appendRadioButton(
self.identifiersBox, self, "useidentifiers",
"Use instance equality"
)
rb = OWGUI.appendRadioButton(
self.identifiersBox, self, "useidentifiers",
"Use identifiers"
)
self.inputsBox = OWGUI.indentedBox(
self.identifiersBox, sep=OWGUI.checkButtonOffsetHint(rb)
)
self.inputsBox.setEnabled(self.useidentifiers == 1)
for i in range(5):
box = OWGUI.widgetBox(self.inputsBox, "Data set #%i" % (i + 1),
flat=True)
model = OWItemModels.VariableListModel(parent=self)
cb = QComboBox()
cb.setModel(model)
cb.activated[int].connect(self._on_inputAttrActivated)
box.setEnabled(False)
# Store the combo in the box for later use.
box.combo_box = cb
box.layout().addWidget(cb)
OWGUI.rubber(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Output")
cb = OWGUI.checkBox(box, self, "autocommit", "Commit on any change")
b = OWGUI.button(box, self, "Commit", callback=self.commit,
default=True)
OWGUI.setStopper(self, b, cb, "_changed", callback=self.commit)
# Main area view
self.scene = QGraphicsScene()
self.view = QGraphicsView(self.scene)
self.view.setRenderHint(QPainter.Antialiasing)
self.view.setBackgroundRole(QPalette.Window)
self.view.setFrameStyle(QGraphicsView.StyledPanel)
self.mainArea.layout().addWidget(self.view)
self.vennwidget = VennDiagram()
self.vennwidget.resize(400, 400)
self.vennwidget.itemTextEdited.connect(self._on_itemTextEdited)
self.scene.selectionChanged.connect(self._on_selectionChanged)
self.scene.addItem(self.vennwidget)
self.resize(self.controlArea.sizeHint().width() + 550,
max(self.controlArea.sizeHint().height(), 550))
self._queue = []
self.graphButton.clicked.connect(self.saveImage)
def __init__(self, parallelWidget, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager,
"Parallel Optimization Dialog", False)
self.setCaption("Parallel Optimization Dialog")
self.parallelWidget = parallelWidget
self.optimizationMeasure = 0
self.attributeCount = 5
self.numberOfAttributes = 6
self.fileName = ""
self.lastSaveDirName = os.getcwd() + "/"
self.fileBuffer = []
self.projections = []
self.allResults = []
self.canOptimize = 0
self.orderAllAttributes = 1 # do we wish to order all attributes or find just an interesting subset
self.worstVal = -1 # used in heuristics to stop the search in uninteresting parts of the graph
self.loadSettings()
self.measureBox = OWGUI.radioButtonsInBox(
self.controlArea,
self,
"optimizationMeasure", ["Correlation", "VizRank"],
box="Select optimization measure",
callback=self.updateGUI)
self.vizrankSettingsBox = OWGUI.widgetBox(self.controlArea,
"VizRank settings")
self.optimizeBox = OWGUI.widgetBox(self.controlArea, "Optimize")
self.manageBox = OWGUI.widgetBox(self.controlArea, "Manage results")
self.resultsBox = OWGUI.widgetBox(self.mainArea, "Results")
self.resultList = OWGUI.listBox(self.resultsBox, self)
self.resultList.setMinimumSize(200, 200)
self.connect(self.resultList, SIGNAL("itemSelectionChanged()"),
self.showSelectedAttributes)
# remove non-existing files
names = []
for i in range(len(self.fileBuffer) - 1, -1, -1):
(short, longName) = self.fileBuffer[i]
if not os.path.exists(longName):
self.fileBuffer.remove((short, longName))
else:
names.append(short)
names.append("(None)")
self.fileName = "(None)"
self.hbox1 = OWGUI.widgetBox(self.vizrankSettingsBox,
"VizRank projections file",
orientation="horizontal")
self.vizrankFileCombo = OWGUI.comboBox(
self.hbox1,
self,
"fileName",
items=names,
tooltip=
"File that contains information about interestingness of scatterplots\n"
"generated by VizRank method in scatterplot widget",
callback=self.changeProjectionFile,
sendSelectedValue=1,
valueType=str)
self.browseButton = OWGUI.button(self.hbox1,
self,
"...",
callback=self.loadProjections)
self.browseButton.setMaximumWidth(20)
self.resultsInfoBox = OWGUI.widgetBox(self.vizrankSettingsBox,
"VizRank parameters")
self.kNeighborsLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Number of neighbors (k):")
self.percentDataUsedLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Percent of data used:")
self.testingMethodLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Testing method used:")
self.qualityMeasureLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Quality measure used:")
self.allAttributesRadio = QRadioButton("Order all attributes",
self.optimizeBox)
self.optimizeBox.layout().addWidget(self.allAttributesRadio)
self.connect(self.allAttributesRadio, SIGNAL("clicked()"),
self.setAllAttributeRadio)
box = OWGUI.widgetBox(self.optimizeBox, orientation="horizontal")
self.subsetAttributeRadio = QRadioButton("Find subsets of", box)
box.layout().addWidget(self.subsetAttributeRadio)
self.connect(self.subsetAttributeRadio, SIGNAL("clicked()"),
self.setSubsetAttributeRadio)
self.subsetAttributeEdit = OWGUI.lineEdit(box,
self,
"numberOfAttributes",
valueType=int)
self.subsetAttributeEdit.setMaximumWidth(30)
OWGUI.widgetLabel(box, "attributes")
self.startOptimizationButton = OWGUI.button(
self.optimizeBox,
self,
"Start Optimization",
callback=self.startOptimization)
f = self.startOptimizationButton.font()
f.setBold(1)
self.startOptimizationButton.setFont(f)
self.stopOptimizationButton = OWGUI.button(
self.optimizeBox,
self,
"Stop Evaluation",
callback=self.stopOptimizationClick)
self.stopOptimizationButton.setFont(f)
self.stopOptimizationButton.hide()
self.connect(self.stopOptimizationButton, SIGNAL("clicked()"),
self.stopOptimizationClick)
self.clearButton = OWGUI.button(self.manageBox, self, "Clear Results",
self.clearResults)
self.loadButton = OWGUI.button(self.manageBox, self, "Load",
self.loadResults)
self.saveButton = OWGUI.button(self.manageBox, self, "Save",
self.saveResults)
self.closeButton = OWGUI.button(self.manageBox, self, "Close Dialog",
self.hide)
self.changeProjectionFile()
self.updateGUI()
if self.orderAllAttributes:
self.setAllAttributeRadio()
else:
self.setSubsetAttributeRadio()
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="Normalize Expression Array"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Expression array", ExampleTable, self.setData)]
self.outputs = [("Normalized expression array", ExampleTable, Default),
("Filtered expression array", ExampleTable)]
self.selectedGroup = 0
self.selectedCenterMethod = 0
self.selectedMergeMethod = 0
self.zCutoff = 1.96
self.appendZScore = False
self.appendRIValues = False
self.autoCommit = False
self.loadSettings()
## GUI
self.infoBox = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"No data on input.")
box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True)
self.groupCombo = OWGUI.comboBox(box,
self,
"selectedGroup",
callback=self.onGroupSelection)
self.centerCombo = OWGUI.comboBox(
self.controlArea,
self,
"selectedCenterMethod",
box="Center Fold-change Using",
items=[name for name, _ in self.CENTER_METHODS],
callback=self.onCenterMethodChange,
addSpace=True)
self.mergeCombo = OWGUI.comboBox(
self.controlArea,
self,
"selectedMergeMethod",
box="Merge Replicates",
items=[name for name, _ in self.MERGE_METHODS],
tooltip="Select the method for replicate merging",
callback=self.onMergeMethodChange,
addSpace=True)
box = OWGUI.doubleSpin(self.controlArea,
self,
"zCutoff",
0.0,
3.0,
0.01,
box="Z-Score Cutoff",
callback=[self.replotMA, self.commitIf])
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Ouput")
OWGUI.checkBox(box,
self,
"appendZScore",
"Append Z-Scores",
tooltip="Append calculated Z-Scores to output",
callback=self.commitIf)
OWGUI.checkBox(
box,
self,
"appendRIValues",
"Append Log Ratio and Intensity values",
tooltip=
"Append calculated Log Ratio and Intensity values to output data",
callback=self.commitIf)
cb = OWGUI.checkBox(box,
self,
"autoCommit",
"Commit on change",
tooltip="Commit data on any change",
callback=self.commitIf)
b = OWGUI.button(box, self, "Commit", callback=self.commit)
OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit)
self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph)
OWGUI.rubber(self.controlArea)
self.graph = OWGraph(self.mainArea)
self.graph.setAxisTitle(QwtPlot.xBottom,
"Intensity: log<sub>10</sub>(R*G)")
self.graph.setAxisTitle(QwtPlot.yLeft,
"Log ratio: log<sub>2</sub>(R/G)")
self.graph.showFilledSymbols = True
self.mainArea.layout().addWidget(self.graph)
self.groups = []
self.split_data = None, None
self.merged_splits = None, None
self.centered = None, None
self.changedFlag = False
self.data = None
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None, name="Gene Info"):
OWWidget.__init__(self, parent, signalManager, name)
self.inputs = [("Examples", Orange.data.Table, self.setData)]
self.outputs = [("Selected Examples", Orange.data.Table)]
self.organismIndex = 0
self.taxid = None
self.geneAttr = 0
self.useAttr = False
self.autoCommit = False
self.searchString = ""
self.selectionChangedFlag = False
self.useAltSource = 0
self.loadSettings()
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.infoLabel = OWGUI.widgetLabel(
OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n"
)
self.organisms = None
self.organismBox = OWGUI.widgetBox(
self.controlArea, "Organism", addSpace=True)
self.organismComboBox = OWGUI.comboBox(
self.organismBox, self, "organismIndex",
callback=self._onSelectedOrganismChanged,
debuggingEnabled=0)
# For now only support one alt source, with a checkbox
# In the future this can be extended to multiple selections
self.altSourceCheck = OWGUI.checkBox(self.organismBox, self,
"useAltSource", "Show information from dictyBase",
callback=self.onAltSourceChange,
# debuggingEnabled=0,
)
self.altSourceCheck.hide()
box = OWGUI.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = OWGUI.comboBox(
box, self, "geneAttr",
"Gene atttibute", callback=self.updateInfoItems
)
OWGUI.checkBox(box, self, "useAttr", "Use attribute names",
callback=self.updateInfoItems,
disables=[(-1, self.geneAttrComboBox)])
self.geneAttrComboBox.setDisabled(bool(self.useAttr))
box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True)
b = OWGUI.button(box, self, "Commit", callback=self.commit)
c = OWGUI.checkBox(box, self, "autoCommit", "Commit on change")
OWGUI.setStopper(self, b, c, "selectionChangedFlag",
callback=self.commit)
# A label for dictyExpress link
self.dictyExpressBox = OWGUI.widgetBox(
self.controlArea, "Dicty Express")
self.linkLabel = OWGUI.widgetLabel(self.dictyExpressBox, "")
self.linkLabel.setOpenExternalLinks(False)
self.connect(self.linkLabel, SIGNAL("linkActivated(QString)"),
self.onDictyExpressLink)
self.dictyExpressBox.hide()
OWGUI.rubber(self.controlArea)
OWGUI.lineEdit(self.mainArea, self, "searchString", "Filter",
callbackOnType=True, callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSelectionMode(
QAbstractItemView.ExtendedSelection)
self.treeWidget.setItemDelegate(
LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.viewport().setMouseTracking(True)
self.treeWidget.setSortingEnabled(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = OWGUI.widgetBox(self.mainArea, "",
orientation="horizontal")
OWGUI.button(box, self, "Select Filtered",
callback=self.selectFiltered)
OWGUI.button(box, self, "Clear Selection",
callback=self.treeWidget.clearSelection)
self.resize(1000, 700)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
self.selectionUpdateInProgress = False
self.setBlocking(True)
self.executor = ThreadExecutor(self)
self.progressBarInit()
task = Task(
function=partial(
taxonomy.ensure_downloaded,
callback=methodinvoke(self, "advance", ())
)
)
task.resultReady.connect(self.initialize)
task.exceptionReady.connect(self._onInitializeError)
self.initfuture = self.executor.submit(task)
def __init__(self, parent=None, signalManager=None, name="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='GSEA'):
OWWidget.__init__(self, parent, signalManager, name)
self.inputs = [("Examples", ExampleTable, self.setData)]
self.outputs = [("Examples with selected genes only", ExampleTable), ("Results", ExampleTable), ("Distance Matrix", orange.SymMatrix) ]
self.res = None
self.dm = None
self.name = 'GSEA'
self.minSubsetSize = 3
self.minSubsetSizeC = True
self.maxSubsetSize = 1000
self.maxSubsetSizeC = True
self.minSubsetPart = 10
self.minSubsetPartC = True
self.perms = 100
self.csgm = False
self.gsgo = False
self.gskegg = False
self.buildDistances = False
self.selectedPhenVar = 0
self.organismIndex = 0
self.atLeast = 3
self.permutationTypes = [("Phenotype", "p"),("Gene", "g") ]
self.ptype = 0
self.correlationTypes = [ ("Signal2Noise", "s2n") ]
self.ctype = 0
self.data = None
self.geneSets = {}
self.tabs = OWGUI.tabWidget(self.controlArea)
ca = OWGUI.createTabPage(self.tabs, "Basic")
box = OWGUI.widgetBox(ca, 'Organism')
#FROM KEGG WIDGET - organism selection
self.organismTaxids = []
self.organismComboBox = cb = OWGUI.comboBox(box, self, "organismIndex", items=[], debuggingEnabled=0) #changed
cb.setMaximumWidth(200)
#OWGUI.checkBox(box, self, "csgm", "Case sensitive gene matching")
box2 = OWGUI.widgetBox(ca, "Descriptors")
self.phenCombo = OWGUI.comboBox(box2, self, "selectedPhenVar", items=[], callback=self.phenComboChange, label="Phenotype:")
self.geneCombo = OWGUI.comboBox(box2, self, "selectedGeneVar", items=[], label = "Gene:")
self.allowComboChangeCallback = False
ma = self.mainArea
self.listView = QTreeWidget(ma)
ma.layout().addWidget(self.listView)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(9)
self.listView.setHeaderLabels(["Collection", "Geneset", "NES", "ES", "P-value", "FDR", "Size", "Matched Size", "Genes"])
self.listView.header().setStretchLastSection(True)
self.listView.header().setClickable(True)
self.listView.header().setSortIndicatorShown(True)
self.listView.setSortingEnabled(True)
#self.listView.header().setResizeMode(0, QHeaderView.Stretch)
self.listView.setSelectionMode(QAbstractItemView.NoSelection)
self.connect(self.listView, SIGNAL("itemSelectionChanged()"), self.newPathwaySelected)
OWGUI.separator(ca)
OWGUI.widgetLabel(ca, "Phenotype selection:")
self.psel = PhenotypesSelection(ca)
self.resize(600,50)
OWGUI.separator(ca)
OWGUI.checkBox(ca, self, "buildDistances", "Compute geneset distances")
self.btnApply = OWGUI.button(ca, self, "&Compute", callback = self.compute, disabled=0)
fileBox = OWGUI.widgetBox(ca, orientation='horizontal')
OWGUI.button(fileBox, self, "Load", callback = self.loadData, disabled=0, debuggingEnabled=0)
OWGUI.button(fileBox, self, "Save", callback = self.saveData, disabled=0, debuggingEnabled=0)
#ca.layout().addStretch(1)
ca = OWGUI.createTabPage(self.tabs, "Gene sets")
box = OWGUI.widgetBox(ca)
self.gridSel = []
self.geneSel = [] #FIXME temporary disabled - use the same as in new "David" widget
self.lbgs = OWGUI.listBox(box, self, "gridSel", "geneSel", selectionMode = QListWidget.MultiSelection)
OWGUI.button(box, self, "From &File", callback = self.addCollection, disabled=0, debuggingEnabled=0)
box = OWGUI.widgetBox(box, "Additional sources:")
OWGUI.checkBox(box, self, "gskegg", "KEGG pathways")
OWGUI.checkBox(box, self, "gsgo", "GO terms")
#ca.layout().addStretch(1)
ca = OWGUI.createTabPage(self.tabs, "Settings")
box = OWGUI.widgetBox(ca, 'Properties')
self.permTypeF = OWGUI.comboBoxWithCaption(box, self, "ptype", items=nth(self.permutationTypes, 0), \
tooltip="Permutation type.", label="Permute")
_ = OWGUI.spin(box, self, "perms", 50, 1000, orientation="horizontal", label="Times")
self.corTypeF = OWGUI.comboBoxWithCaption(box, self, "ctype", items=nth(self.correlationTypes, 0), \
tooltip="Correlation type.", label="Correlation")
box = OWGUI.widgetBox(ca, 'Subset Filtering')
_,_ = OWGUI.checkWithSpin(box, self, "Min. Subset Size", 1, 10000, "minSubsetSizeC", "minSubsetSize", "") #TODO check sizes
_,_ = OWGUI.checkWithSpin(box, self, "Max. Subset Size", 1, 10000, "maxSubsetSizeC", "maxSubsetSize", "")
_,_ = OWGUI.checkWithSpin(box, self, "Min. Subset Part (%)", 1, 100, "minSubsetPartC", "minSubsetPart", "")
box = OWGUI.widgetBox(ca, 'Gene Filtering')
_ = OWGUI.spin(box, self, "atLeast", 2, 10, label="Min. Values in Group")
ca.layout().addStretch(1)
self.addComment("Computation was not started.")
if sys.platform == "darwin":
self.loadFileName = os.path.expanduser("~/")
else:
self.loadFileName = "."
self.gridSels = []
self.loadSettings()
self.setBlocking(True)
QTimer.singleShot(0, self.UpdateOrganismComboBox)
def cleanInvalid(maxn):
"""
Removes invalid gene set selection
"""
notAllOk = True
while notAllOk:
self.gridSels = getattr(self, "gridSels")
notAllOk = False
for i,a in enumerate(self.gridSels):
if a >= maxn:
self.gridSels.pop(i)
notAllOk = True
break
cleanInvalid(len(self.geneSel))
self.gridSel = self.gridSels
self.gridSels = self.gridSel
def __init__(self, parent=None, signalManager=None, name="Gene selection"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True, showSaveGraph=True)
self.inputs = [("Examples", ExampleTable, self.set_data)]
self.outputs = [("Example table with selected genes", ExampleTable), ("Example table with remaining genes", ExampleTable), ("Selected genes", ExampleTable)]
self.method_index = 0
self.genes_in_columns = False
self.compute_null = False
self.permutations_count = 10
self.auto_commit = False
self.selectNBest = 20
self.selectPValue = 0.01
self.data_changed_flag = False
self.add_scores_to_output = True
self.thresholds = {
"fold change": (0.5, 2.),
"log2 fold change": (-1, 1),
"t-test": (-2, 2),
"t-test p-value": (0.01, 0.01),
}
self.oneTailTestHi = oneTailTestHi = lambda array, low, hi: array >= hi
self.oneTailTestLow = oneTailTestLow = lambda array, low, hi: array <= low
self.twoTailTest = twoTailTest = lambda array, low, hi: (array >= hi) | (array <= low)
self.middleTest = middleTest = lambda array, low, hi: (array <= hi) | (array >= low)
self.histType = {oneTailTestHi:"hiTail", oneTailTestLow:"lowTail", twoTailTest:"twoTail", middleTest:"middle"}
# [(name, func, tail test, two sample test), ...]
self.score_methods = [("fold change", ExpressionSignificance_FoldChange, twoTailTest, True),
("log2 fold change", ExpressionSignificance_Log2FoldChange, twoTailTest, True),
("t-test", ExpressionSignificance_TTest_T, twoTailTest, True),
("t-test p-value", ExpressionSignificance_TTest_PValue, oneTailTestLow, True),
("anova", ExpressionSignificance_ANOVA_F, oneTailTestHi, False),
("anova p-value", ExpressionSignificance_ANOVA_PValue, oneTailTestLow, False),
("signal to noise ratio", ExpressionSignificance_SignalToNoise, twoTailTest, True),
("info gain", ExpressionSignificance_Info, oneTailTestHi, True),
("chi-square", ExpressionSignificance_ChiSquare, oneTailTestHi, True),
("mann-whitney", ExpressionSignigicance_MannWhitneyu_U, oneTailTestLow, True)]
boxHistogram = OWGUI.widgetBox(self.mainArea)
self.histogram = ScoreHist(self, boxHistogram)
boxHistogram.layout().addWidget(self.histogram)
self.histogram.show()
box = OWGUI.widgetBox(self.controlArea, "Info")
self.dataInfoLabel = OWGUI.widgetLabel(box, "\n\n")
self.dataInfoLabel.setWordWrap(True)
self.selectedInfoLabel = OWGUI.widgetLabel(box, "")
box1 = OWGUI.widgetBox(self.controlArea, "Scoring Method")
self.testRadioBox = OWGUI.comboBox(box1, self, "method_index",
items=[sm[0] for sm in self.score_methods],
callback=[self.on_scoring_method_changed, self.update_scores])
box = OWGUI.widgetBox(self.controlArea, "Target Labels")
self.label_selection_widget = LabelSelectionWidget(self)
self.label_selection_widget.setMaximumHeight(150)
box.layout().addWidget(self.label_selection_widget)
self.connect(self.label_selection_widget,
SIGNAL("selection_changed()"),
self.on_target_changed)
self.connect(self.label_selection_widget,
SIGNAL("label_activated(int)"),
self.on_label_activated)
self.genes_in_columns_check = OWGUI.checkBox(box, self, "genes_in_columns",
"Genes in columns",
callback=self.on_genes_in_columns_change)
box = OWGUI.widgetBox(self.controlArea, "Selection")
box.layout().setSpacing(0)
self.upperBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.upperBoundary",
min=-1e6, max=1e6, step= 1e-6,
label="Upper threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
self.lowerBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.lowerBoundary",
min=-1e6, max=1e6, step= 1e-6,
label="Lower threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
check = OWGUI.checkBox(box, self, "compute_null", "Compute null distribution",
callback=self.update_scores)
check.disables.append(OWGUI.spin(box, self, "permutations_count", min=1, max=10,
label="Permutations:", callback=self.update_scores,
callbackOnReturn=True))
box1 = OWGUI.widgetBox(box, orientation='horizontal')
check.disables.append(OWGUI.doubleSpin(box1, self, "selectPValue",
min=2e-7, max=1.0, step=1e-7,
label="P-value:"))
check.disables.append(OWGUI.button(box1, self, "Select", callback=self.select_p_best))
check.makeConsistent()
box1 = OWGUI.widgetBox(box, orientation='horizontal')
OWGUI.spin(box1, self, "selectNBest", 0, 10000, step=1, label="Best Ranked:")
OWGUI.button(box1, self, "Select", callback=self.select_n_best)
box = OWGUI.widgetBox(self.controlArea, "Output")
b = OWGUI.button(box, self, "&Commit", callback=self.commit)
cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change")
OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit)
OWGUI.checkBox(box, self, "add_scores_to_output", "Add gene scores to output",
callback=self.commit_if)
OWGUI.rubber(self.controlArea)
self.connect(self.graphButton, SIGNAL("clicked()"), self.histogram.saveToFile)
self.loadSettings()
self.data = None
self.discData = None
self.scoreCache = {}
self.nullDistCache = {}
self.cuts = {}
self.null_dist = []
self.targets = []
self.scores = {}
self.genes_in_columns = True
self.target_selections = None
self.on_scoring_method_changed()
self.resize(800, 600)
def __init__(self, parent=None, signalManager=None):
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):
# 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):
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, parallelWidget, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "Parallel Optimization Dialog", False)
self.setCaption("Parallel Optimization Dialog")
self.parallelWidget = parallelWidget
self.optimizationMeasure = 0
self.attributeCount = 5
self.numberOfAttributes = 6
self.fileName = ""
self.lastSaveDirName = os.getcwd() + "/"
self.fileBuffer = []
self.projections = []
self.allResults = []
self.canOptimize = 0
self.orderAllAttributes = 1 # do we wish to order all attributes or find just an interesting subset
self.worstVal = -1 # used in heuristics to stop the search in uninteresting parts of the graph
self.loadSettings()
self.measureBox = OWGUI.radioButtonsInBox(self.controlArea, self, "optimizationMeasure",
["Correlation", "VizRank"], box="Select optimization measure",
callback=self.updateGUI)
self.vizrankSettingsBox = OWGUI.widgetBox(self.controlArea, "VizRank settings")
self.optimizeBox = OWGUI.widgetBox(self.controlArea, "Optimize")
self.manageBox = OWGUI.widgetBox(self.controlArea, "Manage results")
self.resultsBox = OWGUI.widgetBox(self.mainArea, "Results")
self.resultList = OWGUI.listBox(self.resultsBox, self)
self.resultList.setMinimumSize(200, 200)
self.connect(self.resultList, SIGNAL("itemSelectionChanged()"), self.showSelectedAttributes)
# remove non-existing files
names = []
for i in range(len(self.fileBuffer) - 1, -1, -1):
(short, longName) = self.fileBuffer[i]
if not os.path.exists(longName):
self.fileBuffer.remove((short, longName))
else:
names.append(short)
names.append("(None)")
self.fileName = "(None)"
self.hbox1 = OWGUI.widgetBox(self.vizrankSettingsBox, "VizRank projections file", orientation="horizontal")
self.vizrankFileCombo = OWGUI.comboBox(self.hbox1, self, "fileName", items=names,
tooltip="File that contains information about interestingness of scatterplots\n"
"generated by VizRank method in scatterplot widget",
callback=self.changeProjectionFile, sendSelectedValue=1, valueType=str)
self.browseButton = OWGUI.button(self.hbox1, self, "...", callback=self.loadProjections)
self.browseButton.setMaximumWidth(20)
self.resultsInfoBox = OWGUI.widgetBox(self.vizrankSettingsBox, "VizRank parameters")
self.kNeighborsLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Number of neighbors (k):")
self.percentDataUsedLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Percent of data used:")
self.testingMethodLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Testing method used:")
self.qualityMeasureLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Quality measure used:")
self.allAttributesRadio = QRadioButton("Order all attributes", self.optimizeBox)
self.optimizeBox.layout().addWidget(self.allAttributesRadio)
self.connect(self.allAttributesRadio, SIGNAL("clicked()"), self.setAllAttributeRadio)
box = OWGUI.widgetBox(self.optimizeBox, orientation="horizontal")
self.subsetAttributeRadio = QRadioButton("Find subsets of", box)
box.layout().addWidget(self.subsetAttributeRadio)
self.connect(self.subsetAttributeRadio, SIGNAL("clicked()"), self.setSubsetAttributeRadio)
self.subsetAttributeEdit = OWGUI.lineEdit(box, self, "numberOfAttributes", valueType=int)
self.subsetAttributeEdit.setMaximumWidth(30)
OWGUI.widgetLabel(box, "attributes")
self.startOptimizationButton = OWGUI.button(self.optimizeBox, self, "Start Optimization",
callback=self.startOptimization)
f = self.startOptimizationButton.font()
f.setBold(1)
self.startOptimizationButton.setFont(f)
self.stopOptimizationButton = OWGUI.button(self.optimizeBox, self, "Stop Evaluation",
callback=self.stopOptimizationClick)
self.stopOptimizationButton.setFont(f)
self.stopOptimizationButton.hide()
self.connect(self.stopOptimizationButton, SIGNAL("clicked()"), self.stopOptimizationClick)
self.clearButton = OWGUI.button(self.manageBox, self, "Clear Results", self.clearResults)
self.loadButton = OWGUI.button(self.manageBox, self, "Load", self.loadResults)
self.saveButton = OWGUI.button(self.manageBox, self, "Save", self.saveResults)
self.closeButton = OWGUI.button(self.manageBox, self, "Close Dialog", self.hide)
self.changeProjectionFile()
self.updateGUI()
if self.orderAllAttributes:
self.setAllAttributeRadio()
else:
self.setSubsetAttributeRadio()
